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Article ; Online: Multi-level interaction between HIF and AHR transcriptional pathways in kidney carcinoma.

Lafleur, Véronique N / Halim, Silvia / Choudhry, Hani / Ratcliffe, Peter J / Mole, David R

Life science alliance

2023 Volume 6, Issue 4

Abstract: Hypoxia-inducible factor (HIF) and aryl hydrocarbon receptor (AHR) are members of the bHLH-PAS family of transcription factors that underpin cellular responses to oxygen and to endogenous and exogenous ligands, respectively, and have central roles in the ...

Abstract	Hypoxia-inducible factor (HIF) and aryl hydrocarbon receptor (AHR) are members of the bHLH-PAS family of transcription factors that underpin cellular responses to oxygen and to endogenous and exogenous ligands, respectively, and have central roles in the pathogenesis of renal cancer. Composed of heterodimers, they share a common HIF-1β/ARNT subunit and similar DNA-binding motifs, raising the possibility of crosstalk between the two transcriptional pathways. Here, we identify both general and locus-specific mechanisms of interaction between HIF and AHR that act both antagonistically and cooperatively. Specifically, we observe competition for the common HIF-1β/ARNT subunit, in cis synergy for chromatin binding, and overlap in their transcriptional targets. Recently, both HIF and AHR inhibitors have been developed for the treatment of solid tumours. However, inhibition of one pathway may promote the oncogenic effects of the other. Therefore, our work raises important questions as to whether combination therapy targeting both of these pro-tumourigenic pathways might show greater efficacy than targeting each system independently.
MeSH term(s)	Humans ; Receptors, Aryl Hydrocarbon/genetics ; Receptors, Aryl Hydrocarbon/metabolism ; Cell Hypoxia/physiology ; Carcinoma, Renal Cell/genetics ; Kidney Neoplasms/genetics ; Kidney/metabolism
Chemical Substances	Receptors, Aryl Hydrocarbon
Language	English
Publishing date	2023-02-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202201756
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Article ; Online: Pan-cancer analysis of tissue and single-cell HIF-pathway activation using a conserved gene signature.

Lombardi, Olivia / Li, Ran / Halim, Silvia / Choudhry, Hani / Ratcliffe, Peter J / Mole, David R

Cell reports

2022 Volume 41, Issue 7, Page(s) 111652

Abstract: Activation of cellular hypoxia pathways, orchestrated by HIF (hypoxia-inducible factor) transcription factors, is a common feature of multiple tumor types, resulting from microenvironment factors and oncogenic mutation. Although they help drive many of ... ...

Abstract	Activation of cellular hypoxia pathways, orchestrated by HIF (hypoxia-inducible factor) transcription factors, is a common feature of multiple tumor types, resulting from microenvironment factors and oncogenic mutation. Although they help drive many of the "hallmarks" of cancer and are associated with poor outcome and resistance to therapy, the transcriptional targets of HIF vary considerably depending on the cell type. By integrating 72 genome-wide assays of HIF binding and transcriptional regulation from multiple cancer types, we define a consensus set of 48 HIF target genes that is highly conserved across cancer types and cell lineages. These genes provide an effective marker of HIF activation in bulk and single-cell transcriptomic analyses across a wide range of cancer types and in malignant and stromal cell types. This allows the tissue-orchestrated responses to the hypoxic tumor microenvironment and to oncogenic HIF activation to be deconvoluted at the tumor and single-cell level.
MeSH term(s)	Humans ; Neoplasms/genetics ; Transcription Factors/metabolism ; Tumor Microenvironment/genetics ; Cell Hypoxia/genetics ; Hypoxia/metabolism
Chemical Substances	Transcription Factors
Language	English
Publishing date	2022-11-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.111652
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Article ; Online: Analysis of cell proliferation and tissue remodelling uncovers a KLF4 activity score associated with poor prognosis in colorectal cancer.

Halim, Silvia / Markert, Elke K / Vazquez, Alexei

British journal of cancer

2018 Volume 119, Issue 7, Page(s) 855–863

Abstract: Background: Human cancers can be classified based on gene signatures quantifying the degree of cell proliferation and tissue remodelling (PR). However, the specific factors that drive the increased tissue remodelling in tumours are not fully understood. ...

Abstract	Background: Human cancers can be classified based on gene signatures quantifying the degree of cell proliferation and tissue remodelling (PR). However, the specific factors that drive the increased tissue remodelling in tumours are not fully understood. Here we address this question using colorectal cancer as a case study. Methods: We reanalysed a reported cohort of colorectal cancer patients. The patients were stratified based on gene signatures of cell proliferation and tissue remodelling. Putative transcription factors activity was inferred using gene expression profiles and annotations of transcription factor targets as input. Results: We demonstrate that the PR classification performs better than the currently adopted consensus molecular subtyping (CMS). Although CMS classification differentiates patients with a mesenchymal signature, it cannot distinguish the remaining patients based on survival. We demonstrate that the missing factor is cell proliferation, which is indicative of good prognosis. We also uncover a KLF4 transcription factor activity score associated with the tissue remodelling gene signature. We further show that the KLF4 activity score is significantly higher in colorectal tumours with predicted infiltration of cells from the myeloid lineage. Conclusion: The KLF4 activity score is associated with tissue remodelling, myeloid cell infiltration and poor prognosis in colorectal cancer.
MeSH term(s)	Cell Line, Tumor ; Cell Proliferation ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/pathology ; Epithelial-Mesenchymal Transition ; Female ; Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic ; Humans ; Kruppel-Like Factor 4 ; Kruppel-Like Transcription Factors/genetics ; Male ; Myeloid Cells/chemistry ; Prognosis ; Survival Analysis ; Up-Regulation
Chemical Substances	KLF4 protein, human ; Kruppel-Like Factor 4 ; Kruppel-Like Transcription Factors
Language	English
Publishing date	2018-10-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80075-2
ISSN	1532-1827 ; 0007-0920
ISSN (online)	1532-1827
ISSN	0007-0920
DOI	10.1038/s41416-018-0253-0
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Article ; Online: FGFR2 risk SNPs confer breast cancer risk by augmenting oestrogen responsiveness.

Campbell, Thomas M / Castro, Mauro A A / de Santiago, Ines / Fletcher, Michael N C / Halim, Silvia / Prathalingam, Radhika / Ponder, Bruce A J / Meyer, Kerstin B

Carcinogenesis

2016 Volume 37, Issue 8, Page(s) 741–750

Abstract: The fibroblast growth factor receptor 2 (FGFR2) locus is consistently the top hit in genome-wide association studies for oestrogen receptor-positive (ER(+)) breast cancer. Yet, its mode of action continues to be controversial. Here, we employ a systems ... ...

Abstract	The fibroblast growth factor receptor 2 (FGFR2) locus is consistently the top hit in genome-wide association studies for oestrogen receptor-positive (ER(+)) breast cancer. Yet, its mode of action continues to be controversial. Here, we employ a systems biology approach to demonstrate that signalling via FGFR2 counteracts cell activation by oestrogen. In the presence of oestrogen, the oestrogen receptor (ESR1) regulon (set of ESR1 target genes) is in an active state. However, signalling by FGFR2 is able to reverse the activity of the ESR1 regulon. This effect is seen in multiple distinct FGFR2 signalling model systems, across multiple cells lines and is dependent on the presence of FGFR2. Increased oestrogen exposure has long been associated with an increased risk of breast cancer. We therefore hypothesized that risk variants should reduce FGFR2 expression and subsequent signalling. Indeed, transient transfection experiments assaying the three independent variants of the FGFR2 risk locus (rs2981578, rs35054928 and rs45631563) in their normal chromosomal context show that these single-nucleotide polymorphisms (SNPs) map to transcriptional silencer elements and that, compared with wild type, the risk alleles augment silencer activity. The presence of risk variants results in lower FGFR2 expression and increased oestrogen responsiveness. We thus propose a molecular mechanism by which FGFR2 can confer increased breast cancer risk that is consistent with oestrogen exposure as a major driver of breast cancer risk. Our findings may have implications for the clinical use of FGFR2 inhibitors.
MeSH term(s)	Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; Estrogen Receptor alpha/genetics ; Estrogen Receptor alpha/metabolism ; Estrogens/genetics ; Estrogens/metabolism ; Female ; Gene Expression Regulation, Neoplastic ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Genotype ; Haplotypes ; Humans ; MCF-7 Cells ; Receptor, Fibroblast Growth Factor, Type 2/biosynthesis ; Receptor, Fibroblast Growth Factor, Type 2/genetics ; Signal Transduction ; Systems Biology
Chemical Substances	ESR1 protein, human ; Estrogen Receptor alpha ; Estrogens ; FGFR2 protein, human (EC 2.7.10.1) ; Receptor, Fibroblast Growth Factor, Type 2 (EC 2.7.10.1)
Language	English
Publishing date	2016-05-28
Publishing country	England
Document type	Journal Article
ZDB-ID	603134-1
ISSN	1460-2180 ; 0143-3334
ISSN (online)	1460-2180
ISSN	0143-3334
DOI	10.1093/carcin/bgw065
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Article: 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer

Genome biology. 2015 Dec., v. 16, no. 1

2015

Abstract: BACKGROUND: The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferating ... ...

Abstract	BACKGROUND: The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferating cells such as colon tumours and the gut crypt progenitors, from which tumours can arise. RESULTS: Here, we show that colorectal tumours and cancer cells express Ten-Eleven-Translocation (TET) transcripts at levels similar to normal tissues. Genome-wide analyses show that promoters marked by 5hmC in normal tissue, and those identified as TET2 targets in colorectal cancer cells, are resistant to methylation gain in cancer. In vitro studies of TET2 in cancer cells confirm that these promoters are resistant to methylation gain independently of sustained TET2 expression. We also find that a considerable number of the methylation gain-resistant promoters marked by 5hmC in normal colon overlap with those that are marked with poised bivalent histone modifications in embryonic stem cells. CONCLUSIONS: Together our results indicate that promoters that acquire 5hmC upon normal colon differentiation are innately resistant to neoplastic hypermethylation by mechanisms that do not require high levels of 5hmC in tumours. Our study highlights the potential of cytosine modifications as biomarkers of cancerous cell proliferation.
Keywords	DNA ; DNA methylation ; biomarkers ; cell proliferation ; colon ; colorectal neoplasms ; cytosine ; embryonic stem cells ; histones ; in vitro studies ; neoplasm cells ; promoter regions
Language	English
Dates of publication	2015-12
Size	p. 69.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6906
ISSN (online)	1474-760X
ISSN	1465-6906
DOI	10.1186/s13059-015-0605-5
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Article ; Online: Gene regulatory mechanisms underpinning prostate cancer susceptibility.

Whitington, Thomas / Gao, Ping / Song, Wei / Ross-Adams, Helen / Lamb, Alastair D / Yang, Yuehong / Svezia, Ilaria / Klevebring, Daniel / Mills, Ian G / Karlsson, Robert / Halim, Silvia / Dunning, Mark J / Egevad, Lars / Warren, Anne Y / Neal, David E / Grönberg, Henrik / Lindberg, Johan / Wei, Gong-Hong / Wiklund, Fredrik

Nature genetics

2016 Volume 48, Issue 4, Page(s) 387–397

Abstract: Molecular characterization of genome-wide association study (GWAS) loci can uncover key genes and biological mechanisms underpinning complex traits and diseases. Here we present deep, high-throughput characterization of gene regulatory mechanisms ... ...

Abstract	Molecular characterization of genome-wide association study (GWAS) loci can uncover key genes and biological mechanisms underpinning complex traits and diseases. Here we present deep, high-throughput characterization of gene regulatory mechanisms underlying prostate cancer risk loci. Our methodology integrates data from 295 prostate cancer chromatin immunoprecipitation and sequencing experiments with genotype and gene expression data from 602 prostate tumor samples. The analysis identifies new gene regulatory mechanisms affected by risk locus SNPs, including widespread disruption of ternary androgen receptor (AR)-FOXA1 and AR-HOXB13 complexes and competitive binding mechanisms. We identify 57 expression quantitative trait loci at 35 risk loci, which we validate through analysis of allele-specific expression. We further validate predicted regulatory SNPs and target genes in prostate cancer cell line models. Finally, our integrated analysis can be accessed through an interactive visualization tool. This analysis elucidates how genome sequence variation affects disease predisposition via gene regulatory mechanisms and identifies relevant genes for downstream biomarker and drug development.
MeSH term(s)	Base Sequence ; Binding Sites ; CCCTC-Binding Factor ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Male ; Polymorphism, Single Nucleotide ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/metabolism ; Protein Binding ; Quantitative Trait Loci ; Repressor Proteins/metabolism ; Risk Factors ; Sequence Analysis, DNA
Chemical Substances	CCCTC-Binding Factor ; CTCF protein, human ; Repressor Proteins
Language	English
Publishing date	2016-03-07
Publishing country	United States
Document type	Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/ng.3523
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Article ; Online: 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer.

Genome biology

2015 Volume 16, Page(s) 69

Abstract: Background: The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferating ... ...

Abstract	Background: The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferating cells such as colon tumours and the gut crypt progenitors, from which tumours can arise. Results: Here, we show that colorectal tumours and cancer cells express Ten-Eleven-Translocation (TET) transcripts at levels similar to normal tissues. Genome-wide analyses show that promoters marked by 5hmC in normal tissue, and those identified as TET2 targets in colorectal cancer cells, are resistant to methylation gain in cancer. In vitro studies of TET2 in cancer cells confirm that these promoters are resistant to methylation gain independently of sustained TET2 expression. We also find that a considerable number of the methylation gain-resistant promoters marked by 5hmC in normal colon overlap with those that are marked with poised bivalent histone modifications in embryonic stem cells. Conclusions: Together our results indicate that promoters that acquire 5hmC upon normal colon differentiation are innately resistant to neoplastic hypermethylation by mechanisms that do not require high levels of 5hmC in tumours. Our study highlights the potential of cytosine modifications as biomarkers of cancerous cell proliferation.
MeSH term(s)	5-Methylcytosine/analogs & derivatives ; Cell Proliferation/genetics ; Colonic Neoplasms/genetics ; Colonic Neoplasms/pathology ; Cytosine/analogs & derivatives ; Cytosine/metabolism ; DNA Methylation/genetics ; DNA-Binding Proteins/biosynthesis ; DNA-Binding Proteins/genetics ; Dioxygenases ; Gene Expression Regulation, Neoplastic ; HCT116 Cells ; Humans ; Proto-Oncogene Proteins/biosynthesis ; Proto-Oncogene Proteins/genetics
Chemical Substances	DNA-Binding Proteins ; Proto-Oncogene Proteins ; 5-hydroxymethylcytosine (1123-95-1) ; 5-Methylcytosine (6R795CQT4H) ; Cytosine (8J337D1HZY) ; Dioxygenases (EC 1.13.11.-) ; TET2 protein, human (EC 1.13.11.-)
Language	English
Publishing date	2015-04-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-015-0605-5
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Article ; Online: HNF1B variants associate with promoter methylation and regulate gene networks activated in prostate and ovarian cancer.

Ross-Adams, Helen / Ball, Stephen / Lawrenson, Kate / Halim, Silvia / Russell, Roslin / Wells, Claire / Strand, Siri H / Ørntoft, Torben F / Larson, Melissa / Armasu, Sebastian / Massie, Charles E / Asim, Mohammad / Mortensen, Martin M / Borre, Michael / Woodfine, Kathryn / Warren, Anne Y / Lamb, Alastair D / Kay, Jonathan / Whitaker, Hayley /

Ramos-Montoya, Antonio / Murrell, Adele / Sørensen, Karina D / Fridley, Brooke L / Goode, Ellen L / Gayther, Simon A / Masters, John / Neal, David E / Mills, Ian G

Oncotarget

2016 Volume 7, Issue 46, Page(s) 74734–74746

Abstract: Two independent regions within HNF1B are consistently identified in prostate and ovarian cancer genome-wide association studies (GWAS); their functional roles are unclear. We link prostate cancer (PC) risk SNPs rs11649743 and rs3760511 with elevated ... ...

Abstract	Two independent regions within HNF1B are consistently identified in prostate and ovarian cancer genome-wide association studies (GWAS); their functional roles are unclear. We link prostate cancer (PC) risk SNPs rs11649743 and rs3760511 with elevated HNF1B gene expression and allele-specific epigenetic silencing, and outline a mechanism by which common risk variants could effect functional changes that increase disease risk: functional assays suggest that HNF1B is a pro-differentiation factor that suppresses epithelial-to-mesenchymal transition (EMT) in unmethylated, healthy tissues. This tumor-suppressor activity is lost when HNF1B is silenced by promoter methylation in the progression to PC. Epigenetic inactivation of HNF1B in ovarian cancer also associates with known risk SNPs, with a similar impact on EMT. This represents one of the first comprehensive studies into the pleiotropic role of a GWAS-associated transcription factor across distinct cancer types, and is the first to describe a conserved role for a multi-cancer genetic risk factor.
MeSH term(s)	Alleles ; Cell Line, Tumor ; Cell Movement ; Cell Proliferation ; DNA Methylation ; Epithelial-Mesenchymal Transition ; Female ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Genetic Predisposition to Disease ; Genetic Variation ; Genome-Wide Association Study ; Genotype ; Hepatocyte Nuclear Factor 1-beta/genetics ; Humans ; Linkage Disequilibrium ; Male ; Ovarian Neoplasms/genetics ; Ovarian Neoplasms/pathology ; Polymorphism, Single Nucleotide ; Promoter Regions, Genetic ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/pathology ; Risk
Chemical Substances	HNF1B protein, human ; Hepatocyte Nuclear Factor 1-beta (138674-15-4)
Language	English
Publishing date	2016-05-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.12543
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Article ; Online: Translating a Prognostic DNA Genomic Classifier into the Clinic: Retrospective Validation in 563 Localized Prostate Tumors.

Lalonde, Emilie / Alkallas, Rached / Chua, Melvin Lee Kiang / Fraser, Michael / Haider, Syed / Meng, Alice / Zheng, Junyan / Yao, Cindy Q / Picard, Valerie / Orain, Michele / Hovington, Helène / Murgic, Jure / Berlin, Alejandro / Lacombe, Louis / Bergeron, Alain / Fradet, Yves / Têtu, Bernard / Lindberg, Johan / Egevad, Lars /

Grönberg, Henrik / Ross-Adams, Helen / Lamb, Alastair D / Halim, Silvia / Dunning, Mark J / Neal, David E / Pintilie, Melania / van der Kwast, Theodorus / Bristow, Robert G / Boutros, Paul C

European urology

2016 Volume 72, Issue 1, Page(s) 22–31

Abstract: Background: Localized prostate cancer is clinically heterogeneous, despite clinical risk groups that represent relative prostate cancer-specific mortality. We previously developed a 100-locus DNA classifier capable of substratifying patients at risk of ... ...

Abstract	Background: Localized prostate cancer is clinically heterogeneous, despite clinical risk groups that represent relative prostate cancer-specific mortality. We previously developed a 100-locus DNA classifier capable of substratifying patients at risk of biochemical relapse within clinical risk groups. Objective: The 100-locus genomic classifier was refined to 31 functional loci and tested with standard clinical variables for the ability to predict biochemical recurrence (BCR) and metastasis. Design, setting, and participants: Four retrospective cohorts of radical prostatectomy specimens from patients with localized disease were pooled, and an additional 102-patient cohort used to measure the 31-locus genomic classifier with the NanoString platform. Outcome measurements and statistical analysis: The genomic classifier scores were tested for their ability to predict BCR (n=563) and metastasis (n=154), and compared with clinical risk stratification schemes. Results and limitations: The 31-locus genomic classifier performs similarly to the 100-locus classifier. It identifies patients with elevated BCR rates (hazard ratio=2.73, p<0.001) and patients that eventually develop metastasis (hazard ratio=7.79, p<0.001). Combining the genomic classifier with standard clinical variables outperforms clinical models. Finally, the 31-locus genomic classifier was implemented using a NanoString assay. The study is limited to retrospective cohorts. Conclusions: The 100-locus and 31-locus genomic classifiers reliably identify a cohort of men with localized disease who have an elevated risk of failure. The NanoString assay will be useful for selecting patients for treatment deescalation or escalation in prospective clinical trials based on clinico-genomic scores from pretreatment biopsies. Patient summary: It is challenging to determine whether tumors confined to the prostate are aggressive, leading to significant undertreatment and overtreatment. We validated a test based on prostate tumor DNA that improves estimations of relapse risk, and that can help guide treatment planning.
MeSH term(s)	Biomarkers, Tumor/genetics ; Clinical Decision-Making ; DNA Copy Number Variations ; Decision Support Techniques ; Disease Progression ; Gene Dosage ; Gene Expression Profiling/methods ; Humans ; Male ; Neoplasm Grading ; Neoplasm Metastasis ; Neoplasm Recurrence, Local ; Neoplasm Staging ; Predictive Value of Tests ; Prostatectomy ; Prostatic Neoplasms/classification ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/pathology ; Prostatic Neoplasms/surgery ; Reproducibility of Results ; Retrospective Studies ; Risk Assessment ; Risk Factors ; Time Factors ; Transcriptome ; Treatment Outcome
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2016-11-01
Publishing country	Switzerland
Document type	Comparative Study ; Journal Article ; Validation Study
ZDB-ID	193790-x
ISSN	1873-7560 ; 1421-993X ; 0302-2838
ISSN (online)	1873-7560 ; 1421-993X
ISSN	0302-2838
DOI	10.1016/j.eururo.2016.10.013
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Article ; Online: Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study.

Lalonde, Emilie / Ishkanian, Adrian S / Sykes, Jenna / Fraser, Michael / Ross-Adams, Helen / Erho, Nicholas / Dunning, Mark J / Halim, Silvia / Lamb, Alastair D / Moon, Nathalie C / Zafarana, Gaetano / Warren, Anne Y / Meng, Xianyue / Thoms, John / Grzadkowski, Michal R / Berlin, Alejandro / Have, Cherry L / Ramnarine, Varune R / Yao, Cindy Q /

The Lancet. Oncology

2014 Volume 15, Issue 13, Page(s) 1521–1532

Abstract: Background: Clinical prognostic groupings for localised prostate cancers are imprecise, with 30-50% of patients recurring after image-guided radiotherapy or radical prostatectomy. We aimed to test combined genomic and microenvironmental indices in ... ...

Abstract	Background: Clinical prognostic groupings for localised prostate cancers are imprecise, with 30-50% of patients recurring after image-guided radiotherapy or radical prostatectomy. We aimed to test combined genomic and microenvironmental indices in prostate cancer to improve risk stratification and complement clinical prognostic factors. Methods: We used DNA-based indices alone or in combination with intra-prostatic hypoxia measurements to develop four prognostic indices in 126 low-risk to intermediate-risk patients (Toronto cohort) who will receive image-guided radiotherapy. We validated these indices in two independent cohorts of 154 (Memorial Sloan Kettering Cancer Center cohort [MSKCC] cohort) and 117 (Cambridge cohort) radical prostatectomy specimens from low-risk to high-risk patients. We applied unsupervised and supervised machine learning techniques to the copy-number profiles of 126 pre-image-guided radiotherapy diagnostic biopsies to develop prognostic signatures. Our primary endpoint was the development of a set of prognostic measures capable of stratifying patients for risk of biochemical relapse 5 years after primary treatment. Findings: Biochemical relapse was associated with indices of tumour hypoxia, genomic instability, and genomic subtypes based on multivariate analyses. We identified four genomic subtypes for prostate cancer, which had different 5-year biochemical relapse-free survival. Genomic instability is prognostic for relapse in both image-guided radiotherapy (multivariate analysis hazard ratio [HR] 4·5 [95% CI 2·1-9·8]; p=0·00013; area under the receiver operator curve [AUC] 0·70 [95% CI 0·65-0·76]) and radical prostatectomy (4·0 [1·6-9·7]; p=0·0024; AUC 0·57 [0·52-0·61]) patients with prostate cancer, and its effect is magnified by intratumoral hypoxia (3·8 [1·2-12]; p=0·019; AUC 0·67 [0·61-0·73]). A novel 100-loci DNA signature accurately classified treatment outcome in the MSKCC low-risk to intermediate-risk cohort (multivariate analysis HR 6·1 [95% CI 2·0-19]; p=0·0015; AUC 0·74 [95% CI 0·65-0·83]). In the independent MSKCC and Cambridge cohorts, this signature identified low-risk to high-risk patients who were most likely to fail treatment within 18 months (combined cohorts multivariate analysis HR 2·9 [95% CI 1·4-6·0]; p=0·0039; AUC 0·68 [95% CI 0·63-0·73]), and was better at predicting biochemical relapse than 23 previously published RNA signatures. Interpretation: This is the first study of cancer outcome to integrate DNA-based and microenvironment-based failure indices to predict patient outcome. Patients exhibiting these aggressive features after biopsy should be entered into treatment intensification trials. Funding: Movember Foundation, Prostate Cancer Canada, Ontario Institute for Cancer Research, Canadian Institute for Health Research, NIHR Cambridge Biomedical Research Centre, The University of Cambridge, Cancer Research UK, Cambridge Cancer Charity, Prostate Cancer UK, Hutchison Whampoa Limited, Terry Fox Research Institute, Princess Margaret Cancer Centre Foundation, PMH-Radiation Medicine Program Academic Enrichment Fund, Motorcycle Ride for Dad (Durham), Canadian Cancer Society.
MeSH term(s)	Biomarkers, Tumor/genetics ; DNA, Neoplasm/genetics ; Follow-Up Studies ; Gene Expression Profiling ; Genomics ; Humans ; Male ; Neoplasm Recurrence, Local/diagnosis ; Neoplasm Recurrence, Local/genetics ; Oligonucleotide Array Sequence Analysis ; Prognosis ; Prostatic Neoplasms/genetics ; Retrospective Studies ; Time Factors ; Tumor Microenvironment/genetics
Chemical Substances	Biomarkers, Tumor ; DNA, Neoplasm
Language	English
Publishing date	2014-11-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2049730-1
ISSN	1474-5488 ; 1470-2045
ISSN (online)	1474-5488
ISSN	1470-2045
DOI	10.1016/S1470-2045(14)71021-6
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In stock of ZB MED Cologne/Königswinter

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Full text online

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In stock of ZB MED Cologne/Königswinter

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