- Email: [email protected]
37 Causes and Consequences of microRNA Dysregulation in Cancer
S8
european journal of cancer 48, suppl. 5 (2012) S5–S12
Sunday 8 July 2012
32 Mechanisms of Ageing and Longevity A. Brunet1 . 1 Stanford Center on Longevity, Medicine Genetics, Stanford (CA), USA Aging, long thought to be solely the byproduct of wear and tear, is actually a highly controlled process, regulated by a combination of genetic and environmental factors. Our overarching goals are: (1) to understand the molecular mechanisms by which known ‘longevity genes’ regulate aging in mammals; and (2) to discover novel genes and processes that control lifespan using two genetic models for aging: the nematode C. elegans and the extremely short-lived African fish N. furzeri. We are particularly interested in the aging of the nervous system. My presentation will be focused on the importance of stem cells in the brain during aging in mammals. In the nervous system, neural stem cells (NSCs) are thought to be important for learning, memory, and mood regulation. During aging, both the pool of NSCs and their ability to give rise to new neurons decline, raising the possibility that NSC depletion may underlie part of the cognitive dysfunctions during aging. However, the molecular mechanisms that regulate the maintenance of the NSC pool throughout lifespan are largely unknown. We have found that FoxO3, a member of a transcription factor family known to extend lifespan in invertebrates, maintains the NSC pool in adult mice. Analysis of the program of genes regulated by FoxO3 in NSCs suggests that FoxO3 maintains the adult NSC pool by inducing a program of genes that preserves cellular quiescence and regulates oxygen metabolism. Because NSCs are thought to be important for cognitive function and mood regulation, the ability of FoxO3 to maintain the NSC pool in adult organisms might have important implications for counteracting brain aging in long-lived species, including humans. 33 Proffered Paper: Age-associated Cytokine Signaling Impairs Epidermal Stem Cell Function W.M. Keyes1 , M.A. Storer1 , L. Cozzuto1 , G. Roma1 , J. Doles1 . 1 CRG, Barcelona, Spain Introduction: Two processes that are intrinsically linked to tumor initiation are the age of the tissue where the tumor develops, and the deregulation of tissue-specific stem cell proliferation. However, how aging specifically alters stem cell function in such a way that may facilitate tumor development is not clear. This highlights the necessity to understand how stem cells respond to, and are altered by the normal aging process in order to better understand tumor initiation and progression. Materials and Methods: We phenotypically and molecularly characterized epidermal stem cell aging in mice at different stages throughout the normal lifespan. We FACS sorted a highly purified population of aging stem cells and performed high-throughput RNA-sequencing analysis on these cells to uncover novel age-associated changes, which we then functionally validated using in vitro and in vivo stem cell assays. Results and Discussion: Surprisingly, we discovered that during the aging process, the Keratin-15 positive population of epidermal stem cells displays previously unseen age-associated changes, including increasing significantly in number, while decreasing in functional capacity, both normally and in response to damage. Using high-throughput RNA-sequencing of purified aging stem cells, coupled with cytokine arrays on aging tissues, we identified aberrant cytokine signaling derived from the epidermis as a major alteration that occurs during the normal aging process. Furthermore, we demonstrate that these inflammatory signals can impact epidermal stem cell function and likely contribute to the age-mediated decline seen in the tissue. Importantly, we found that chemical inhibition of Jak/Stat signaling, a critical mediator of cytokine signaling, reverses the age-mediated decline in stem cell function and restores aged stem cell capacity both in vitro and in vivo in the adult skin. Conclusion: Enhanced tumor suppression is suggested as playing a causative role in the aging process. Our data uncovers chronic cytokine signaling during aging as an inhibitor of normal stem cell function, possibly as part of a broader tumor suppressive response. However, a consequence of this is the accumulation of a population of altered stem cells that are frequently targeted during tumor initiation that may prime aged tissue for tumor development. Ultimately however, the net effect is the inhibition of stem cell function, which likely contributes significantly to the aging process. 34 Ageing and Cancer: the Somatotropic Link No abstract received.
Sunday 8 July 2012
12:15−13:00
EMBO Lecture: Cancer Genomics 35 The Genomics of Drug Sensitivity in Cancer M. Stratton1 , M. Garnett1 , E.J. Edelman2 , S. Heidorn1 , P.A. Futreal1 , D. Haber2 , S. Ramaswamy2 , U. McDermott1 , C. Benes2 . 1 Wellcome Trust Sanger Institute, Cancer Genome Project, Cambridge, United Kingdom, 2 Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, USA Clinical responses to anticancer therapies are often restricted to a subset of patients. In some cases, for example the presence of the BCR-ABL translocation or point mutations in BRAF, mutated cancer genes are potent biomarkers of response to targeted agents. To uncover new biomarkers of sensitivity and resistance to cancer therapeutics, we are systematically screening a panel of several hundred cancer cell lines, which represent much of the tissue-type and genetic diversity of human cancers, with hundreds of drugs in clinical use or under preclinical investigation. We have found that mutated cancer genes are associated with cellular response to most currently available cancer drugs. Classic oncogene addiction paradigms are modified by tissue-specific or expression biomarkers, and some frequently mutated genes are associated with sensitivity to a broad range of therapeutic agents. Unexpected relationships have been revealed, including the marked sensitivity of Ewing’s sarcoma cells harboring the EWS-FLI1 gene translocation to PARP inhibitors. By linking drug activity to the functional complexity of cancer genomes, systematic pharmacogenomic profiling in cancer cell lines provides a powerful biomarker discovery platform which can guide rational cancer therapeutic strategies and trial design in the future.
Sunday 8 July 2012
14:30−15:15
OECI Lecture: Cancer Systems Biology 36 Network and Systems Biology in Cancer Y. Yarden1 . 1 Weizmann Institute, Biological Regulation, Rehovot, Israel Biological systems integrate metabolic, energy and signaling networks, by maintaining dense webs of control circuits and multiple adaptors common to two or more interfacing networks. My lecture will concentrate on systemic defects in signaling networks involved in malignant cell proliferation and migration. As a starting point, I will argue that primordial signaling pathways have been replaced in the course of metazoan evolution by layered signaling networks. The driving process behind this transformation has been whole genome duplications, which established modularity, an essential feature of biological robustness. Other features of robustness include redundancy and systems control, primarily feedback and feed-forward loops that maintain homeostasis and determine the outcome of network activation. Unlike linear pathways, networks can be trained to overcome perturbations, and their control wirings are much more sophisticated. These transitions are relevant to pharmacological attempts to intercept signaling networks, as well as to the excessive reliance of oncogenic networks on 1−2 essential hubs (’oncogene addiction’). Using the epidermal growth factor receptor (EGFR) and its kin, a kinase called HER2/ERBB2, I will exemplify defects in system control and feedback regulation, and highlight some of the currently approved drugs that target the EGFR-HER2 axis. Along with illuminating the rationale of combination therapies, the lecture will focus on acquired (secondary) resistance to molecular targeted therapies, as an exemple of the remarkable adaptation capacity of signaling networks.
Sunday 8 July 2012
15:15−16:00
Award Lecture: Anthony Dipple Carcinogenesis Award 37 Causes and Consequences of microRNA Dysregulation in Cancer C.M. Croce1 . 1 The Ohio State University Medical Center, Department of Molecular Virology, Immunology and Medical Genetics Since the discovery of miR-15a and miR-16−1 deletions in CLL15, many laboratories around the world have shown miRNA dysregulation in all tumours studied, including the most common, such as lung, breast, prostate and gastrointestinal cancers. Such dysregulation, like the dysregulation of oncogenes and tumour suppressor genes, can be caused by multiple mechanisms, such as deletion, amplification, mutation, transcriptional dysregulation and epigenetic changes.
Komen for the Cure Supported Symposium
european journal of cancer 48, suppl. 5 (2012) S5–S12
As miRNAs have multiple targets, their function in tumorigenesis could be due to their regulation of a few specific targets, possibly even one, or many targets. A future challenge will be to identify all of the targets of the miRNAs involved in cancer and establish their contribution to malignant transformation. An additional challenge will be the identification of all of the miRNAs that are dysregulated by pathways that are consistently dysregulated in various types of human cancers. This point is of particular importance, as instead of focusing on specific alterations in protein-coding oncogenes or tumour suppressor genes − which may be difficult to treat − we could focus on their downstream miRNA targets. If these miRNA targets are crucial for the expression of the malignant phenotype and the cancer cells depend on their dysregulation for proliferation and survival, we can expect that the use of miRNAs or anti-miRNAs will result in tumour regression. Genomic analyses for alteration in miRNA genes or for copy number alterations in various human tumours by deep sequencing is in progress but has not been completed. These studies could provide additional information concerning the involvements of miRNAs in cancer and in many other diseases. Over the past few years, we have observed a shift from conventional chemotherapy to targeted therapies, and miRNAs and anti-miRNAs will contribute extensively to the latter.
Sunday 8 July 2012
17:30−19:15
Susan G Komen® for the Cure Supported Symposium
Susceptibility Genes 38 The COGS (Collaborative Oncological Gene-environment Study): Progress and Results D.F. Easton1 , on behalf of the COGS collaboration and Breast Cancer Association Consortium. 1 Strangeways Research Laboratory, Cancer Research Campaign Genetic Epidemiology Unit, Cambridge, United Kingdom Susceptibility to common cancers is largely polygenic, resulting from the combined effects of many genetic loci. Improvements in genotyping technology have enabled many common variants underlying susceptibility to cancer to be identified, but these still explain a minority of the heritability. COGS is a collaborative EU funded project to characterise susceptibility in three hormone related cancers: breast, ovary and prostate. A major component of this project is a large scale genotyping effort involving more the 200,000 samples, genotyped for more than 200,000 genetic variants using a custom array (iCOGS). For breast cancer, more than 30 novel susceptibility variants have been identified through this project, so that more than 60 susceptibility loci have now been found. These loci together explain approximately 16% of the familial risk of breast cancer. While the risks conferred by any individual locus are small, these common susceptibility loci combine together multiplicatively, and can be used to define a genetic risk profile. Under this model, the top 10% of the population have a risk that is 2.2 fold higher than the population average, while the top 1% have a risk that is 3.6 fold. Many of the loci confer risks that are specific to the tumour pathology: in particular many loci confer risks of predominantly ER-positive or ER-negative disease. These results can be utilised (in combination with other risk factors such as reproductive history and breast density) to stratify women for targeted screening (for example, varying the age of mammographic screening, or utilising MRI), or for chemoprevention. 39 The Search for Rare Variants That Contribute to Cancer Susceptibility F. Lesueur1 , C. Bertolotto2 , D.J. Park3 , F. Demenais4 , R. Ballotti2 , B. Bressac-de Paillerets5 , M.C. Southey3 , D.E. Goldgar6 , S.V. Tavtitgian7 . 1 International Agency for Research on Cancer, Genetic Cancer Susceptibility, Lyon, France, 2 INSERM U895, University of Nice Sophia-Antipolis, Nice, France, 3 Genetic Epidemiology Laboratory, University of Melbourne, Melbourne, Australia, 4 INSERM U946, Centre d’Etude du Polymorphisme ´ Gustave Humain, Paris, France, 5 INSERM U946, Institut de Cancerologie Roussy, Villejuif, France, 6 Department of Dermatology, University of Utah School of Medicine, Salt Lake City, USA, 7 Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, USA Introduction: Most cancers are known to cluster in families and to be influenced by several genetic and environmental factors. Known loci explain only relatively small fractions of the total genetic variance and additional strategies beyond that of traditional linkage and genome-wide association studies (GWAS) are required to identify novel cancer genes that confer substantial increased disease risk (>2-fold). As with high penetrance mutations in genes like BRCA1/2, the MMR genes and CDKN2A, a subset of coding variants conferring disease risks are probably ‘functionally deleterious’ (e.g. nonsense, splice site, frameshift variants). The very nature of such alterations suggests that genes are likely to contain several, very rare (or private)
S9
mutations, as shown from limited candidate gene studies (e.g. ATM, CHEK2, PALB2 in breast cancer studies). Material and Method: Rare, moderate-risk susceptibility alleles are identifiable through sequencing of candidate genes selected on the basis of biological plausibility, or through exome sequencing in large sample sizes with cases enriched for genetic factors (family history, age, multiple primary cancers). Results and Discussion: Through target sequencing we identified a rare missense substitution in MITF that was significantly more frequent in high-risk patients diagnosed with melanoma, renal cell carcinoma or both cancers, than in the general population. This mutation severely impairs SUMOylation of the transcription factor, leading to a gain-of-function role in tumorigenesis. In the context of breast cancer, exome sequencing first suggested a role for the DNA repair gene XRCC2 with a protein-truncating in one, and a likely deleterious missense variant in another multiple-case family. Additional evolutionarily unlikely variants were further identified in 10 high-risk families. We performed a population-based case-control mutation screening study and confirmed that rare XRCC2 variants confer increased risk of breast cancer. Hence, our findings increase the proportion of breast cancers that are associated with homologous recombination DNA repair dysfunction and Fanconi Anemia. Conclusion: Due to the rarity and to the incomplete penetrance of MITF and XRCC2 mutations, the two genes were likely to be missed by linkage or GWAS. However, the significant disease risks associated with such cancer susceptibility genes, combined with the development of new sequencing technologies that are being developed, suggest that their identification could rapidly be translated into meaningful clinical benefit, through population driven risk prediction and disease prevention strategies. 40 Proffered Paper: Dissecting the Genetic Components of Breast Cancer Transcriptomes S. Nord1 , O.C. Lingjærde2 , D. Nebdal1 , W. Sun3 , G.I.G. Alnæs1 , P. Van Loo4 , B. Naume5 , A.L. Børresen-Dale1,6 , V.N. Kristensen1,7 . 1 Genetics Department, Institute for Cancer Research, OUS, 2 Department of Informatics, UiO, Oslo, Norway, 3 Department of Biostatistics, UNC, NC, USA, 4 Wellcome Trust Sanger Institute, Cambridge, United Kingdom, 5 Oncology, OUS, Oslo, Norway, 6 Institute for Clinical Medicine, Faculty of Medicine, UiO, 7 Department of Clinical Molecular Biology and Lab Science, Division of Medicine, Akershus University Hospital and UiO, Norway Introduction: Breast Cancer is a complex disease, where gene expression has been proposed as a basis for tumor classification and related to clinical outcome. Our previous results suggests that SNPs in the recently discovered susceptibility genes may exert their effect through the expression of their genes in tumors, giving rise to the various subtypes. Material and Methods: We dissected the influence of germline and somatic variation on mRNA levels in 92 breast carcinomas using genome wide Illumina SNP arrays genotyped on both blood and tumor DNA, and Agilent expression of tumors. Total copy number and allele specific aberrations were called using the ASCAT algorithm, adjusting for both tumor percentage and ploidy. Results and Discussion: We detected 4,364 unique genes whose expression associated in cis with genetic variation, either germline and/or somatic. SNPs correlated with the expression of 8.8% of these 4,364 genes, and somatic copy number explained 92.9% of the expression variation. A novel finding was that 5.6% of the variation in expression was allele specific with respect to copy number. The existence of selective amplification of the germline allelic variant associated with elevated expression in breast carcinomas prompted us to investigate the tumor genome for novel, potential oncogenes, and to strengthen the candidacy of others. While eQTLs target by germline and somatic variation showed limited overlap, our interrogation of the tumor genome revealed allele specific amplification in the major, focal amplicons of the variant allele associated with elevated expression. This pattern of natural selection confirmed well-known oncogenes such as ErbB2 and MDM2, and strengthening the candidacy of others including BAG4, BRIP1, TAOK1 and IGF1R. Conclusion: Taken together these results suggest that the germline background plays a significant role in the expression phenotype of tumors, and interrogating the genome for all three types of variants may be an effective way to elucidate the underlying genetic factors of susceptibility of complex phenotypes such as breast cancer. 41 Clinical Applications of Genome-wide Association Study Data − Lessons from Breast and Prostate Cancer B. Ponder1 , P. Pharoah2 , N. Pashayan3 . 1 Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom, 2 University of Cambridge, Depts Oncology and Public Health & Primary Care, Cambridge, United Kingdom, 3 University College London, Epidemiology and Public Health, London, United Kingdom Polygenic inheritance of cancer susceptibility implies a distribution of risk across the population. Using the observed familial clustering of breast cancer
european journal of cancer 48, suppl. 5 (2012) S5–S12
Sunday 8 July 2012
32 Mechanisms of Ageing and Longevity A. Brunet1 . 1 Stanford Center on Longevity, Medicine Genetics, Stanford (CA), USA Aging, long thought to be solely the byproduct of wear and tear, is actually a highly controlled process, regulated by a combination of genetic and environmental factors. Our overarching goals are: (1) to understand the molecular mechanisms by which known ‘longevity genes’ regulate aging in mammals; and (2) to discover novel genes and processes that control lifespan using two genetic models for aging: the nematode C. elegans and the extremely short-lived African fish N. furzeri. We are particularly interested in the aging of the nervous system. My presentation will be focused on the importance of stem cells in the brain during aging in mammals. In the nervous system, neural stem cells (NSCs) are thought to be important for learning, memory, and mood regulation. During aging, both the pool of NSCs and their ability to give rise to new neurons decline, raising the possibility that NSC depletion may underlie part of the cognitive dysfunctions during aging. However, the molecular mechanisms that regulate the maintenance of the NSC pool throughout lifespan are largely unknown. We have found that FoxO3, a member of a transcription factor family known to extend lifespan in invertebrates, maintains the NSC pool in adult mice. Analysis of the program of genes regulated by FoxO3 in NSCs suggests that FoxO3 maintains the adult NSC pool by inducing a program of genes that preserves cellular quiescence and regulates oxygen metabolism. Because NSCs are thought to be important for cognitive function and mood regulation, the ability of FoxO3 to maintain the NSC pool in adult organisms might have important implications for counteracting brain aging in long-lived species, including humans. 33 Proffered Paper: Age-associated Cytokine Signaling Impairs Epidermal Stem Cell Function W.M. Keyes1 , M.A. Storer1 , L. Cozzuto1 , G. Roma1 , J. Doles1 . 1 CRG, Barcelona, Spain Introduction: Two processes that are intrinsically linked to tumor initiation are the age of the tissue where the tumor develops, and the deregulation of tissue-specific stem cell proliferation. However, how aging specifically alters stem cell function in such a way that may facilitate tumor development is not clear. This highlights the necessity to understand how stem cells respond to, and are altered by the normal aging process in order to better understand tumor initiation and progression. Materials and Methods: We phenotypically and molecularly characterized epidermal stem cell aging in mice at different stages throughout the normal lifespan. We FACS sorted a highly purified population of aging stem cells and performed high-throughput RNA-sequencing analysis on these cells to uncover novel age-associated changes, which we then functionally validated using in vitro and in vivo stem cell assays. Results and Discussion: Surprisingly, we discovered that during the aging process, the Keratin-15 positive population of epidermal stem cells displays previously unseen age-associated changes, including increasing significantly in number, while decreasing in functional capacity, both normally and in response to damage. Using high-throughput RNA-sequencing of purified aging stem cells, coupled with cytokine arrays on aging tissues, we identified aberrant cytokine signaling derived from the epidermis as a major alteration that occurs during the normal aging process. Furthermore, we demonstrate that these inflammatory signals can impact epidermal stem cell function and likely contribute to the age-mediated decline seen in the tissue. Importantly, we found that chemical inhibition of Jak/Stat signaling, a critical mediator of cytokine signaling, reverses the age-mediated decline in stem cell function and restores aged stem cell capacity both in vitro and in vivo in the adult skin. Conclusion: Enhanced tumor suppression is suggested as playing a causative role in the aging process. Our data uncovers chronic cytokine signaling during aging as an inhibitor of normal stem cell function, possibly as part of a broader tumor suppressive response. However, a consequence of this is the accumulation of a population of altered stem cells that are frequently targeted during tumor initiation that may prime aged tissue for tumor development. Ultimately however, the net effect is the inhibition of stem cell function, which likely contributes significantly to the aging process. 34 Ageing and Cancer: the Somatotropic Link No abstract received.
Sunday 8 July 2012
12:15−13:00
EMBO Lecture: Cancer Genomics 35 The Genomics of Drug Sensitivity in Cancer M. Stratton1 , M. Garnett1 , E.J. Edelman2 , S. Heidorn1 , P.A. Futreal1 , D. Haber2 , S. Ramaswamy2 , U. McDermott1 , C. Benes2 . 1 Wellcome Trust Sanger Institute, Cancer Genome Project, Cambridge, United Kingdom, 2 Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, USA Clinical responses to anticancer therapies are often restricted to a subset of patients. In some cases, for example the presence of the BCR-ABL translocation or point mutations in BRAF, mutated cancer genes are potent biomarkers of response to targeted agents. To uncover new biomarkers of sensitivity and resistance to cancer therapeutics, we are systematically screening a panel of several hundred cancer cell lines, which represent much of the tissue-type and genetic diversity of human cancers, with hundreds of drugs in clinical use or under preclinical investigation. We have found that mutated cancer genes are associated with cellular response to most currently available cancer drugs. Classic oncogene addiction paradigms are modified by tissue-specific or expression biomarkers, and some frequently mutated genes are associated with sensitivity to a broad range of therapeutic agents. Unexpected relationships have been revealed, including the marked sensitivity of Ewing’s sarcoma cells harboring the EWS-FLI1 gene translocation to PARP inhibitors. By linking drug activity to the functional complexity of cancer genomes, systematic pharmacogenomic profiling in cancer cell lines provides a powerful biomarker discovery platform which can guide rational cancer therapeutic strategies and trial design in the future.
Sunday 8 July 2012
14:30−15:15
OECI Lecture: Cancer Systems Biology 36 Network and Systems Biology in Cancer Y. Yarden1 . 1 Weizmann Institute, Biological Regulation, Rehovot, Israel Biological systems integrate metabolic, energy and signaling networks, by maintaining dense webs of control circuits and multiple adaptors common to two or more interfacing networks. My lecture will concentrate on systemic defects in signaling networks involved in malignant cell proliferation and migration. As a starting point, I will argue that primordial signaling pathways have been replaced in the course of metazoan evolution by layered signaling networks. The driving process behind this transformation has been whole genome duplications, which established modularity, an essential feature of biological robustness. Other features of robustness include redundancy and systems control, primarily feedback and feed-forward loops that maintain homeostasis and determine the outcome of network activation. Unlike linear pathways, networks can be trained to overcome perturbations, and their control wirings are much more sophisticated. These transitions are relevant to pharmacological attempts to intercept signaling networks, as well as to the excessive reliance of oncogenic networks on 1−2 essential hubs (’oncogene addiction’). Using the epidermal growth factor receptor (EGFR) and its kin, a kinase called HER2/ERBB2, I will exemplify defects in system control and feedback regulation, and highlight some of the currently approved drugs that target the EGFR-HER2 axis. Along with illuminating the rationale of combination therapies, the lecture will focus on acquired (secondary) resistance to molecular targeted therapies, as an exemple of the remarkable adaptation capacity of signaling networks.
Sunday 8 July 2012
15:15−16:00
Award Lecture: Anthony Dipple Carcinogenesis Award 37 Causes and Consequences of microRNA Dysregulation in Cancer C.M. Croce1 . 1 The Ohio State University Medical Center, Department of Molecular Virology, Immunology and Medical Genetics Since the discovery of miR-15a and miR-16−1 deletions in CLL15, many laboratories around the world have shown miRNA dysregulation in all tumours studied, including the most common, such as lung, breast, prostate and gastrointestinal cancers. Such dysregulation, like the dysregulation of oncogenes and tumour suppressor genes, can be caused by multiple mechanisms, such as deletion, amplification, mutation, transcriptional dysregulation and epigenetic changes.
Komen for the Cure Supported Symposium
european journal of cancer 48, suppl. 5 (2012) S5–S12
As miRNAs have multiple targets, their function in tumorigenesis could be due to their regulation of a few specific targets, possibly even one, or many targets. A future challenge will be to identify all of the targets of the miRNAs involved in cancer and establish their contribution to malignant transformation. An additional challenge will be the identification of all of the miRNAs that are dysregulated by pathways that are consistently dysregulated in various types of human cancers. This point is of particular importance, as instead of focusing on specific alterations in protein-coding oncogenes or tumour suppressor genes − which may be difficult to treat − we could focus on their downstream miRNA targets. If these miRNA targets are crucial for the expression of the malignant phenotype and the cancer cells depend on their dysregulation for proliferation and survival, we can expect that the use of miRNAs or anti-miRNAs will result in tumour regression. Genomic analyses for alteration in miRNA genes or for copy number alterations in various human tumours by deep sequencing is in progress but has not been completed. These studies could provide additional information concerning the involvements of miRNAs in cancer and in many other diseases. Over the past few years, we have observed a shift from conventional chemotherapy to targeted therapies, and miRNAs and anti-miRNAs will contribute extensively to the latter.
Sunday 8 July 2012
17:30−19:15
Susan G Komen® for the Cure Supported Symposium
Susceptibility Genes 38 The COGS (Collaborative Oncological Gene-environment Study): Progress and Results D.F. Easton1 , on behalf of the COGS collaboration and Breast Cancer Association Consortium. 1 Strangeways Research Laboratory, Cancer Research Campaign Genetic Epidemiology Unit, Cambridge, United Kingdom Susceptibility to common cancers is largely polygenic, resulting from the combined effects of many genetic loci. Improvements in genotyping technology have enabled many common variants underlying susceptibility to cancer to be identified, but these still explain a minority of the heritability. COGS is a collaborative EU funded project to characterise susceptibility in three hormone related cancers: breast, ovary and prostate. A major component of this project is a large scale genotyping effort involving more the 200,000 samples, genotyped for more than 200,000 genetic variants using a custom array (iCOGS). For breast cancer, more than 30 novel susceptibility variants have been identified through this project, so that more than 60 susceptibility loci have now been found. These loci together explain approximately 16% of the familial risk of breast cancer. While the risks conferred by any individual locus are small, these common susceptibility loci combine together multiplicatively, and can be used to define a genetic risk profile. Under this model, the top 10% of the population have a risk that is 2.2 fold higher than the population average, while the top 1% have a risk that is 3.6 fold. Many of the loci confer risks that are specific to the tumour pathology: in particular many loci confer risks of predominantly ER-positive or ER-negative disease. These results can be utilised (in combination with other risk factors such as reproductive history and breast density) to stratify women for targeted screening (for example, varying the age of mammographic screening, or utilising MRI), or for chemoprevention. 39 The Search for Rare Variants That Contribute to Cancer Susceptibility F. Lesueur1 , C. Bertolotto2 , D.J. Park3 , F. Demenais4 , R. Ballotti2 , B. Bressac-de Paillerets5 , M.C. Southey3 , D.E. Goldgar6 , S.V. Tavtitgian7 . 1 International Agency for Research on Cancer, Genetic Cancer Susceptibility, Lyon, France, 2 INSERM U895, University of Nice Sophia-Antipolis, Nice, France, 3 Genetic Epidemiology Laboratory, University of Melbourne, Melbourne, Australia, 4 INSERM U946, Centre d’Etude du Polymorphisme ´ Gustave Humain, Paris, France, 5 INSERM U946, Institut de Cancerologie Roussy, Villejuif, France, 6 Department of Dermatology, University of Utah School of Medicine, Salt Lake City, USA, 7 Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, USA Introduction: Most cancers are known to cluster in families and to be influenced by several genetic and environmental factors. Known loci explain only relatively small fractions of the total genetic variance and additional strategies beyond that of traditional linkage and genome-wide association studies (GWAS) are required to identify novel cancer genes that confer substantial increased disease risk (>2-fold). As with high penetrance mutations in genes like BRCA1/2, the MMR genes and CDKN2A, a subset of coding variants conferring disease risks are probably ‘functionally deleterious’ (e.g. nonsense, splice site, frameshift variants). The very nature of such alterations suggests that genes are likely to contain several, very rare (or private)
S9
mutations, as shown from limited candidate gene studies (e.g. ATM, CHEK2, PALB2 in breast cancer studies). Material and Method: Rare, moderate-risk susceptibility alleles are identifiable through sequencing of candidate genes selected on the basis of biological plausibility, or through exome sequencing in large sample sizes with cases enriched for genetic factors (family history, age, multiple primary cancers). Results and Discussion: Through target sequencing we identified a rare missense substitution in MITF that was significantly more frequent in high-risk patients diagnosed with melanoma, renal cell carcinoma or both cancers, than in the general population. This mutation severely impairs SUMOylation of the transcription factor, leading to a gain-of-function role in tumorigenesis. In the context of breast cancer, exome sequencing first suggested a role for the DNA repair gene XRCC2 with a protein-truncating in one, and a likely deleterious missense variant in another multiple-case family. Additional evolutionarily unlikely variants were further identified in 10 high-risk families. We performed a population-based case-control mutation screening study and confirmed that rare XRCC2 variants confer increased risk of breast cancer. Hence, our findings increase the proportion of breast cancers that are associated with homologous recombination DNA repair dysfunction and Fanconi Anemia. Conclusion: Due to the rarity and to the incomplete penetrance of MITF and XRCC2 mutations, the two genes were likely to be missed by linkage or GWAS. However, the significant disease risks associated with such cancer susceptibility genes, combined with the development of new sequencing technologies that are being developed, suggest that their identification could rapidly be translated into meaningful clinical benefit, through population driven risk prediction and disease prevention strategies. 40 Proffered Paper: Dissecting the Genetic Components of Breast Cancer Transcriptomes S. Nord1 , O.C. Lingjærde2 , D. Nebdal1 , W. Sun3 , G.I.G. Alnæs1 , P. Van Loo4 , B. Naume5 , A.L. Børresen-Dale1,6 , V.N. Kristensen1,7 . 1 Genetics Department, Institute for Cancer Research, OUS, 2 Department of Informatics, UiO, Oslo, Norway, 3 Department of Biostatistics, UNC, NC, USA, 4 Wellcome Trust Sanger Institute, Cambridge, United Kingdom, 5 Oncology, OUS, Oslo, Norway, 6 Institute for Clinical Medicine, Faculty of Medicine, UiO, 7 Department of Clinical Molecular Biology and Lab Science, Division of Medicine, Akershus University Hospital and UiO, Norway Introduction: Breast Cancer is a complex disease, where gene expression has been proposed as a basis for tumor classification and related to clinical outcome. Our previous results suggests that SNPs in the recently discovered susceptibility genes may exert their effect through the expression of their genes in tumors, giving rise to the various subtypes. Material and Methods: We dissected the influence of germline and somatic variation on mRNA levels in 92 breast carcinomas using genome wide Illumina SNP arrays genotyped on both blood and tumor DNA, and Agilent expression of tumors. Total copy number and allele specific aberrations were called using the ASCAT algorithm, adjusting for both tumor percentage and ploidy. Results and Discussion: We detected 4,364 unique genes whose expression associated in cis with genetic variation, either germline and/or somatic. SNPs correlated with the expression of 8.8% of these 4,364 genes, and somatic copy number explained 92.9% of the expression variation. A novel finding was that 5.6% of the variation in expression was allele specific with respect to copy number. The existence of selective amplification of the germline allelic variant associated with elevated expression in breast carcinomas prompted us to investigate the tumor genome for novel, potential oncogenes, and to strengthen the candidacy of others. While eQTLs target by germline and somatic variation showed limited overlap, our interrogation of the tumor genome revealed allele specific amplification in the major, focal amplicons of the variant allele associated with elevated expression. This pattern of natural selection confirmed well-known oncogenes such as ErbB2 and MDM2, and strengthening the candidacy of others including BAG4, BRIP1, TAOK1 and IGF1R. Conclusion: Taken together these results suggest that the germline background plays a significant role in the expression phenotype of tumors, and interrogating the genome for all three types of variants may be an effective way to elucidate the underlying genetic factors of susceptibility of complex phenotypes such as breast cancer. 41 Clinical Applications of Genome-wide Association Study Data − Lessons from Breast and Prostate Cancer B. Ponder1 , P. Pharoah2 , N. Pashayan3 . 1 Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom, 2 University of Cambridge, Depts Oncology and Public Health & Primary Care, Cambridge, United Kingdom, 3 University College London, Epidemiology and Public Health, London, United Kingdom Polygenic inheritance of cancer susceptibility implies a distribution of risk across the population. Using the observed familial clustering of breast cancer