complex with biochemical relapse in prostate cancer patients. ... 1 Princess Margaret Cancer Centre, University Health Network 2 National Cancer Centre ...
Prognostic value of copy-number alterations of the Cohesin complex in intermediate-risk prostate cancer recurrence Jonathan So1, Melvin Chua2, Emilie Lalonde3, Osman Mahamud4, Alejandro Berlin1, Alan Dal Pra5, Michele Orain6, Helene Hovington7, Alain Bergeron7, Yves Fradet7, Bernard Tetu6, Alice Meng1, Junyan Zhang1, Gaetano Zafarana1, Julie Livingstone3, Melania Pintilie1, Theodorus van der Kwast8, Michael Fraser1, Paul Boutros3, Robert G. Bristow1 Princess Margaret Cancer Centre, University Health Network 2 National Cancer Centre Singapore 3 Ontario Institute for Cancer Research 4 Department of Medical Biophysics, University of Toronto 5 Department of Radiation Oncology, University of Bern Department of Pathology and Research Center, CHUQ 7 Universite Laval 8 Department of Laboratory Medicine and Pathology, University Health Network ●
Background: The Cohesin complex plays a critical role in mitotic progression and post-replicative DNA damage repair. It serves to bring together sister chromatids both in metaphase and in homologous recombination repair following ionizing radiation. The expression of various proteins in the complex are dysregulated in many cancers: breast, prostate, etc. Interestingly, in breast cancer cell lines, Cohesin is required for MYC activation in response to estrogen. Our study sought to correlate copy number alterations in this pivotal complex with biochemical relapse in prostate cancer patients.
SMC1B – CNA and mutation frequency
Prostate cancer
RESEARCH POSTER PRESENTATION DESIGN © 2011
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Sister chromatid cohesion in mitosis
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Homologous recombination repair of DSBs
(N = 100)
(N = 133)
192
82
110
T2b/c
41
18
23
6
36
19
17
7
191
76
115
PSA
median (range)
7.7 (0.9-19.9)
8.1 (0.9-19.9)
6.9 (1.7-19.5)
PGA
median (range)
5.4 (0-39.2)
7.5 (0-39.2)
4.8 (0.1-31.9)
IGRT
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We investigated whether copy number alterations of Cohesin subunit genes as well as others involved in DDR [Mahamud et al., F11, Chua et al., E12] are prognostic determinants of biochemical relapses in localized prostate cancer
RADP All patients
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250 patients with pathologically confirmed NCCN-defined lowand intermediate-risk prostate cancers: N = 116, Image-guided radiotherapy (Toronto) and N = 134, Radical prostatectomy (Toronto and Quebec) For radiotherapy cohort, a single ultrasound-guided needle biopsy was obtained prior to the start of therapy, as previously described [Lalonde, 2014]. Fresh-frozen prostatectomy specimens were obtained from the University Health Network Pathology BioBank or from the Genito-Urinary BioBank of the Centre Hospitalier Universitaire de Québec (CHUQ). DNA was extracted from macrodissected tumors with >70% cellularity. For CNA profiling, SNP microarrays were performed using 200 ng of DNA by Affymetrix OncoScan FFPE Express 3.0. Analysis of Affymetrix OncoScan FFPE Express 3.0 SNP probe assays was performed using .OSCHP files generated by OncoScan Console 1.1 using a custom reference (prostate and thyroid cancers, and hapmap cell lines). BioDiscovery’s Nexus ExpressTM for OncoScan 3 Software was used to call copy number aberrations using the SNP-FASST2 algorithm with default parameters. Gene level copy number aberrations for each patient were identified by overlapping CN segments with RefGene annotation using BEDTools (v2.17.0). Percentage of genome altered (PGA) was calculated for each sample by dividing the number of base-pairs that are involved in a copy number change by the total length of the genome. We focused on genes RAD21 and SMC1B in the Cohesin complex
● This study was the first to demonstrate the prognostic significance of Cohesin complex genes in prostate cancer
RAD21 amplification
HR = 7.4 p-value (Bonferroni) < 10-2
● Of note, amplifications in RAD21 but deletions in SMC1B were prognostic. This may point to the importance of the right gene dose or perhaps the genes differently affect the diverse pathways of Cohesin
HR = 7.7 p-value (Bonferroni) < 10-2
HR = 8.3 p-value (Bonferroni) < 10-2
SMC1B CNA and biochemical recurrence (Cox-PH model): Whole cohort
Methods
● Copy number alterations in Cohesin complex genes (RAD21 and SMC1B) are prognostic for biochemical recurrence in a cohort of intermediate-risk prostate CA treated with IGRT or RadP ● RAD21 amplifications also conferred a risk for distant metastases ● SMC1B remained significant even when controlling for known, strong prognostic factors such as Percent genome altered (PGA)
Discussion
RAD21 CNA and biochemical recurrence (Cox-PH model):
Time (years)
RAD21
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(N = 233)
T1/2a
Whole cohort
SMC3 SMC1
The Cohesin complex
Prostatectomy
T-category
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MRN Complex
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Radiotherapy
Median (range)
IGRT
RADP All patients
● Further study is warranted to determine whether the CNAs seen are also recapitulated at the RNA and protein level
SMC1B deletion
HR = 13.2 p-value (Bonferroni) < 10-3
HR = 5.5 p-value (Bonferroni) < 10-2
HR = 11.1 p-value (Bonferroni) < 10-5
● This study hints at the potential utility of targeting the Cohesin complex, a novel pathway in prostate cancer, involved in the cell-cycle and DNA damage repair
Time (years)
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RAD21 amplification and distant metastases (RadP cohort):
References
All patients
Bakhoum SF, Compton DA. “Chromosomal instability and cancer: a complex relationship with therapeutic potential.” J Clin Invest 2012, 122:1138-1143.
Distant metastases-free survival
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Whole cohort
Age (years)
Gleason’s score
Introduction
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Summary statistics
Prostate cancer
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The Cohesin complex has been implicated in sister chromatid cohesion in mitosis and homologous recombination repair of double-strand DNA breaks (DSBs) [Losada et al, 2014; Potts et al, 2006] Expression of Cohesin subunits are associated with poor prognosis in breast cancer [Xu et al, 2011] and colorectal cancer [Deb et al, 2014] DNA damage response and genes involved in genome integrity has been linked to chromosome instability and prostate cancer aggressiveness [Lalonde et al, 2014]
Patient cohort:
Clinical factors
Conclusions: We identified a novel association of copy-number alterations in members of the Cohesin complex with biochemical recurrence following radical prostatectomy or image-guided radiotherapy. This points to the central role of Cohesin in cell-cycle and DNA damage pathways promoting prostate cancer progression.
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6
Conclusion
RAD21 – CNA and mutation frequency
Methods: Our cohort consists of 250 patients with D’ Amico-classified intermediate-risk prostate cancer, treated with image-guided radiotherapy (IGRT, N=116) or radical prostatectomy (RadP, N=134). Pre-treatment biopsies were analyzed using the Affymetrix Oncoscan array. The Phoenix and AUA criteria was used to define biochemical relapse for RadP and IGRT patients respectively. Results: Copy number alterations of RAD21 and SMC1B were observed in 18% (n = 52) and 6.3% (n = 18) of the cohort respectively. They were predominantly losses in SMC1B, but gains in RAD21. Both genes in the Cohesin complex were associated with increased risk of biochemical relapse: RAD21 on chromosome and SMC1B on chromosome. However, when controlled for percent genome alteration and pre-treatment serum PSA levels, only copy number loss of SMC1B was a significant predictor of biochemical relapse.
Results
From cBioPortal, RAD21 amplification and SMC1B deletions and mutations are seen in a variety of cancers [Gao et al, 2013; Cerami et al, 2012]
Biochemical recurrence – free survival
Abstract
Biochemical recurrence – free survival
1
RAD21 amplification
HR = 8.2 p-value < 10-2
Deb et al. “RAD21 cohesin overexpression is a prognostic and predictive marker exacerbating poor prognosis in KRAS mutant colorectal carcinomas.” Br J Cancer. 2014 Mar 18;110(6):1606-13
Time (years)
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Only SMC1B CNA remained significant in a multivariate analysis of variance of biochemical RFR along with PSA and Percent Genome Altered (PGA)
Chi-square
p-value
T-stage
8.5
0.12
PSA
6.5
0.01 *
Gleason-score
0.8
0.6
13.0
0.0003 *
SMC1B CNA
7.7
0.005 *
RAD21 CNA
2.6
0.27
MANOVA
Percent Genome Altered (PGA)
Lalonde et al. “Genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: A retrospective cohort study.” Lancet Oncol. 2014, 15:15211532. Losada, A. “Cohesin in cancer: chromosome segregation and beyond.” Nat Rev Cancer. 2014 Jun;14(6):389-93 Potts et al. “Human SMC5/6 complex promotes sister chromatid homologous recombination by recruiting the SMC1/3 cohesin complex to double-strand breaks.” EMBO J. 2006 Jul 26;25(14):3377-88
