- Email: [email protected]
11: Functional heterogeneity of tumour-initiating cells in gastrointestinal cancers
S4
EACR-23 Oral Presentations, Sunday 6 July 2014 / European Journal of Cancer 50, Suppl. 5 (2014) S3–S11
breast cancer patients (OR = 4.05–4.46), independently of single mutations in BRCA1 or BRCA2. Strikingly, increased error-prone homologous DSB repair was also found in BALB/c-Trp53 +/− mice. siRNA screening identified a cluster of 25 genes causing DSB repair differences in the predisposed strain. Interactome analysis revealed clustering of replication-related and Fanconi anemia (FA)/breast cancer susceptibility (BRCA) genes. Dissection of the functional and molecular changes in BALB/c-Trp53 +/− uncovered differences in crosslink- and replication stress-associated repair and a FA pathway defect downstream of FancD2 associated with reduced levels of BRCA2. Conclusion: In conclusion, detection of error-prone homologous DSB repair activities in patient cells could be a method to estimate breast cancer susceptibility beyond the limitations of genotyping and to predict responsiveness to therapeutics targeting DSB repair-dysfunctional tumors. Consistent with polygenic models for breast cancer susceptibility, mammary carcinogenesis in BALB/c-Trp53 +/− mice may be promoted by a modifier allele in the FA pathway, again resulting in error-prone homologous DSB repair. No conflict of interest. 9 The ATM-mediated DNA damage response: Implications for cancer development and treatment Y. Shiloh1 . 1 Tel Aviv University, Department of Human Molecular Genetics and Biochemistry, Tel Aviv, Israel Genome stability is essential for the prevention of undue cellular death and neoplasia. A central axis in maintaining genome stability is the DNA damage response (DDR) − a complex signaling network that is vigorously activated by DNA double strand breaks (DSBs). The primary transducer of the DSB response is the serine-threonine kinase ATM, which mobilizes the DSB response network by phosphorylating key players in its various branches. ATM is missing or inactivated in patients with the genomic instability syndrome ataxia–telangiectasia (A-T). A-T is characterized by neurodegeneration, immunodeficiency, striking cancer predisposition and radiosensitivity. The lymphoreticular malignancies in A-T patients reflect genomic aberrations caused by defective rearrangement of the antigen receptor genes, a physiological process which involves breakage and reunion of DNA. We are exploring the DSB response network at both the transcriptional and posttranscriptional levels using systems biology tools, alongside proteomic and genetic high-throughput screens. Subsequently, in-depth analysis of novel pathways is carried out. Understanding this network is important not only for understanding the early events in cancer formation but also for refining radiation therapy and chemotherapy for cancer, since the cytotoxicity of these agents results primarily from the damage they cause to the DNA molecule. Importantly, loss of the ATM protein, as observed in A-T cells, confers the highest degree of sensitivity to ionizing radiation and radiomimetic chemicals known in humans. ATM is thus a preferred target for radio-sensitization of cancer cells. Indeed, powerful inhibitors of ATM have recently been developed, which can rapidly abolish ATM activity in a reversible manner. Targeting these small molecules to cancer cells has the potential to radiosensitize these cells differentially, allowing for the efficient treatment of patients with very low doses of radiation or radiomimetic chemicals. No conflict of interest.
Sunday 6 July 2014
08:30−10:15
Symposium
Tumour Heterogeneity 10 Intra-tumour heterogeneity in early-stage lung cancer inferred by multi-region sequencing E. De Bruin1 , N. McGranahan2 , M. Salm3 , D. Wedge4 , R. Mitter3 , L. Yates4 , N. Matthews5 , A. Stewart3 , P. Campbell4 , C. Swanton1,2 . 1 University College London Cancer Institute, Translational Cancer Therapeutics Lab, London, United Kingdom, 2 Cancer Research UK London Research Institute, Translational Cancer Therapeutics Lab, London, United Kingdom, 3 Cancer Research UK London Research Institute, Bioinformatics, London, United Kingdom, 4 Wellcome Trust Sanger Institute, Cancer Genetics and Genomics, Cambridge, United Kingdom, 5 Cancer Research UK London Research Institute, Advanced Sequencing Facility, London, United Kingdom Introduction: Lung cancer is the most common cancer worldwide, and the 5-years overall survival remains poor. Understanding the genetic evolution of the most common type of lung cancer, non-small lung cancer (NSCLC), may improve therapeutic interventions. Material and Methods: We performed multi-region exome and/or genome sequencing to analyse a total of 25 tumour regions from seven early-stage NSCLC samples. Results and Discussion: All samples revealed branched tumour evolution with potential driver mutations occurring both on the trunk and on the branches of the phylogenetic trees. While most driver mutations and large-scale genomic
events such as genome doubling occurred predominantly early in the life history of these tumours, on-going chromosomal instability enhanced the intra-tumour heterogeneity at later stages of tumour development. Temporal analyses of mutational patterns revealed regional differences in processes that might drive further intra-tumour heterogeneity. Conclusion: Our multi-region sequencing approach enables both spatial and temporal dissection of mutations and of processes that drive these mutations, revealing the persistent nature of genomic instability that occur in early-stage NSCLCs. No conflict of interest. 11 Functional heterogeneity of tumour-initiating cells in gastrointestinal cancers No abstract received. No conflict of interest information specified. 12 Proffered Paper: The life history of lethal metastatic prostate cancer (The UK prostate cancer working group of the International Cancer Genome Consortium) D.C. Wedge1 , G. Gundem1 , P. Van Loo1 , D. Brewer2 , K. Leinonen3 , R. Eeles4 , C. Cooper2 , T. Visakorpi3 , U. McDermott1 , G.S. Bova3 . 1 The Wellcome Trust Sanger Institute, Cancer Genome Project, Cambridgeshire, United Kingdom, 2 University of East Anglia, Cancer Genetics School of Biological Sciences, Norwich, United Kingdom, 3 University of Tampere, Institute of Biomedical Technology, Tampere, Finland, 4 Institute of Cancer Research, Division of Genetics and Epidemiology, Sutton, United Kingdom Introduction: Tumour metastasis is the cause of 90% of cancer-related deaths. Despite its clinical importance, little is known about the principles governing the dissemination of cancer cells to distant organs. The analysis of the cancer genomes of multiple metastases from a single patient yields a wealth of information: allowing the separation of these processes across time and space; revealing the effects of treatment and host tissue in driving selection; and vastly increasing the power to identify competing subclones within the tumour cell diaspora. Materials and Methods: Fifty-two samples from the metastases and primary prostate tumours of 10 men were whole genome sequenced to an average 60-fold coverage. Bioinformatic algorithms were developed to disaggregate the population of tumour cells into competing subclones and identify the mutational processes that have been operative on each subpopulation, using an integrated analysis of point mutations, small insertions/deletions, copy number changes and structural rearrangements. Results: The phylogenetic trees for 10 tumours reveal a variety of mutational processes operative at different timepoints. Loss of tumour suppressor genes was commonly an early event, resulting from complex structural rearrangement. In 2 patients, amplification of the AR locus resulted from separate copy number events in different metastases, indicating the occurrence of convergent evolution. The mutational processes operative in different tumours could, in many cases, be linked to specific causes, such as a tandem duplicator phenotype observed in 2 tumours with mutations in genes associated with DNA repair. Mutational processes were ongoing within all samples and indicated a temporal ordering of the appearance of the founding cells of each metastasis. Metastases within the same tissue type were more closely related than those in different tissue types. Integrated analyses of subclonal architecture across the metastases of each patient produced convincing evidence for the seeding of metastases from multiple cells derived from different subclonal populations in up to 4 patients. Conclusions: The application of bioinformatic analyses to whole genome sequences of multiple metastases reveals the competing subclones within the tumour population and the complexity of the mutational processes and selection pressures acting thereon. These subclones are found to be spread across time and space while maintaining their clonal integrity. No conflict of interest. 13 Tumor heterogeneity and cell-of-origin of mouse small cell and non-small cell lung cancer A. Berns1 , K. Sutherland1 , M. Kwon1 , J.Y. Song2 , I. Huijbers1 . 1 The Netherlands Cancer Institute, Division of Molecular Genetics, Amsterdam, Netherlands, 2 The Netherlands Cancer Institute, Department of Pathology, Amsterdam, Netherlands Small cell lung cancer (SCLC) is one of the most lethal human malignancies, due to its high metastatic potential and chemo-resistance upon relapse. Using the Rbf/f;p53f/f mouse model for SCLC, we found that the tumors are often composed of phenotypically different cells, characterized by mesenchymal and neuroendocrine markers. These cells often share a common origin. Crosstalk between these cells can endow the neuroendocrine component with metastatic capacity, illustrating the potential relevance of tumor cell heterogeneity in dictating functional tumor properties. Also specific genetic lesions appear to
EACR-23 Oral Presentations, Sunday 6 July 2014 / European Journal of Cancer 50, Suppl. 5 (2014) S3–S11
breast cancer patients (OR = 4.05–4.46), independently of single mutations in BRCA1 or BRCA2. Strikingly, increased error-prone homologous DSB repair was also found in BALB/c-Trp53 +/− mice. siRNA screening identified a cluster of 25 genes causing DSB repair differences in the predisposed strain. Interactome analysis revealed clustering of replication-related and Fanconi anemia (FA)/breast cancer susceptibility (BRCA) genes. Dissection of the functional and molecular changes in BALB/c-Trp53 +/− uncovered differences in crosslink- and replication stress-associated repair and a FA pathway defect downstream of FancD2 associated with reduced levels of BRCA2. Conclusion: In conclusion, detection of error-prone homologous DSB repair activities in patient cells could be a method to estimate breast cancer susceptibility beyond the limitations of genotyping and to predict responsiveness to therapeutics targeting DSB repair-dysfunctional tumors. Consistent with polygenic models for breast cancer susceptibility, mammary carcinogenesis in BALB/c-Trp53 +/− mice may be promoted by a modifier allele in the FA pathway, again resulting in error-prone homologous DSB repair. No conflict of interest. 9 The ATM-mediated DNA damage response: Implications for cancer development and treatment Y. Shiloh1 . 1 Tel Aviv University, Department of Human Molecular Genetics and Biochemistry, Tel Aviv, Israel Genome stability is essential for the prevention of undue cellular death and neoplasia. A central axis in maintaining genome stability is the DNA damage response (DDR) − a complex signaling network that is vigorously activated by DNA double strand breaks (DSBs). The primary transducer of the DSB response is the serine-threonine kinase ATM, which mobilizes the DSB response network by phosphorylating key players in its various branches. ATM is missing or inactivated in patients with the genomic instability syndrome ataxia–telangiectasia (A-T). A-T is characterized by neurodegeneration, immunodeficiency, striking cancer predisposition and radiosensitivity. The lymphoreticular malignancies in A-T patients reflect genomic aberrations caused by defective rearrangement of the antigen receptor genes, a physiological process which involves breakage and reunion of DNA. We are exploring the DSB response network at both the transcriptional and posttranscriptional levels using systems biology tools, alongside proteomic and genetic high-throughput screens. Subsequently, in-depth analysis of novel pathways is carried out. Understanding this network is important not only for understanding the early events in cancer formation but also for refining radiation therapy and chemotherapy for cancer, since the cytotoxicity of these agents results primarily from the damage they cause to the DNA molecule. Importantly, loss of the ATM protein, as observed in A-T cells, confers the highest degree of sensitivity to ionizing radiation and radiomimetic chemicals known in humans. ATM is thus a preferred target for radio-sensitization of cancer cells. Indeed, powerful inhibitors of ATM have recently been developed, which can rapidly abolish ATM activity in a reversible manner. Targeting these small molecules to cancer cells has the potential to radiosensitize these cells differentially, allowing for the efficient treatment of patients with very low doses of radiation or radiomimetic chemicals. No conflict of interest.
Sunday 6 July 2014
08:30−10:15
Symposium
Tumour Heterogeneity 10 Intra-tumour heterogeneity in early-stage lung cancer inferred by multi-region sequencing E. De Bruin1 , N. McGranahan2 , M. Salm3 , D. Wedge4 , R. Mitter3 , L. Yates4 , N. Matthews5 , A. Stewart3 , P. Campbell4 , C. Swanton1,2 . 1 University College London Cancer Institute, Translational Cancer Therapeutics Lab, London, United Kingdom, 2 Cancer Research UK London Research Institute, Translational Cancer Therapeutics Lab, London, United Kingdom, 3 Cancer Research UK London Research Institute, Bioinformatics, London, United Kingdom, 4 Wellcome Trust Sanger Institute, Cancer Genetics and Genomics, Cambridge, United Kingdom, 5 Cancer Research UK London Research Institute, Advanced Sequencing Facility, London, United Kingdom Introduction: Lung cancer is the most common cancer worldwide, and the 5-years overall survival remains poor. Understanding the genetic evolution of the most common type of lung cancer, non-small lung cancer (NSCLC), may improve therapeutic interventions. Material and Methods: We performed multi-region exome and/or genome sequencing to analyse a total of 25 tumour regions from seven early-stage NSCLC samples. Results and Discussion: All samples revealed branched tumour evolution with potential driver mutations occurring both on the trunk and on the branches of the phylogenetic trees. While most driver mutations and large-scale genomic
events such as genome doubling occurred predominantly early in the life history of these tumours, on-going chromosomal instability enhanced the intra-tumour heterogeneity at later stages of tumour development. Temporal analyses of mutational patterns revealed regional differences in processes that might drive further intra-tumour heterogeneity. Conclusion: Our multi-region sequencing approach enables both spatial and temporal dissection of mutations and of processes that drive these mutations, revealing the persistent nature of genomic instability that occur in early-stage NSCLCs. No conflict of interest. 11 Functional heterogeneity of tumour-initiating cells in gastrointestinal cancers No abstract received. No conflict of interest information specified. 12 Proffered Paper: The life history of lethal metastatic prostate cancer (The UK prostate cancer working group of the International Cancer Genome Consortium) D.C. Wedge1 , G. Gundem1 , P. Van Loo1 , D. Brewer2 , K. Leinonen3 , R. Eeles4 , C. Cooper2 , T. Visakorpi3 , U. McDermott1 , G.S. Bova3 . 1 The Wellcome Trust Sanger Institute, Cancer Genome Project, Cambridgeshire, United Kingdom, 2 University of East Anglia, Cancer Genetics School of Biological Sciences, Norwich, United Kingdom, 3 University of Tampere, Institute of Biomedical Technology, Tampere, Finland, 4 Institute of Cancer Research, Division of Genetics and Epidemiology, Sutton, United Kingdom Introduction: Tumour metastasis is the cause of 90% of cancer-related deaths. Despite its clinical importance, little is known about the principles governing the dissemination of cancer cells to distant organs. The analysis of the cancer genomes of multiple metastases from a single patient yields a wealth of information: allowing the separation of these processes across time and space; revealing the effects of treatment and host tissue in driving selection; and vastly increasing the power to identify competing subclones within the tumour cell diaspora. Materials and Methods: Fifty-two samples from the metastases and primary prostate tumours of 10 men were whole genome sequenced to an average 60-fold coverage. Bioinformatic algorithms were developed to disaggregate the population of tumour cells into competing subclones and identify the mutational processes that have been operative on each subpopulation, using an integrated analysis of point mutations, small insertions/deletions, copy number changes and structural rearrangements. Results: The phylogenetic trees for 10 tumours reveal a variety of mutational processes operative at different timepoints. Loss of tumour suppressor genes was commonly an early event, resulting from complex structural rearrangement. In 2 patients, amplification of the AR locus resulted from separate copy number events in different metastases, indicating the occurrence of convergent evolution. The mutational processes operative in different tumours could, in many cases, be linked to specific causes, such as a tandem duplicator phenotype observed in 2 tumours with mutations in genes associated with DNA repair. Mutational processes were ongoing within all samples and indicated a temporal ordering of the appearance of the founding cells of each metastasis. Metastases within the same tissue type were more closely related than those in different tissue types. Integrated analyses of subclonal architecture across the metastases of each patient produced convincing evidence for the seeding of metastases from multiple cells derived from different subclonal populations in up to 4 patients. Conclusions: The application of bioinformatic analyses to whole genome sequences of multiple metastases reveals the competing subclones within the tumour population and the complexity of the mutational processes and selection pressures acting thereon. These subclones are found to be spread across time and space while maintaining their clonal integrity. No conflict of interest. 13 Tumor heterogeneity and cell-of-origin of mouse small cell and non-small cell lung cancer A. Berns1 , K. Sutherland1 , M. Kwon1 , J.Y. Song2 , I. Huijbers1 . 1 The Netherlands Cancer Institute, Division of Molecular Genetics, Amsterdam, Netherlands, 2 The Netherlands Cancer Institute, Department of Pathology, Amsterdam, Netherlands Small cell lung cancer (SCLC) is one of the most lethal human malignancies, due to its high metastatic potential and chemo-resistance upon relapse. Using the Rbf/f;p53f/f mouse model for SCLC, we found that the tumors are often composed of phenotypically different cells, characterized by mesenchymal and neuroendocrine markers. These cells often share a common origin. Crosstalk between these cells can endow the neuroendocrine component with metastatic capacity, illustrating the potential relevance of tumor cell heterogeneity in dictating functional tumor properties. Also specific genetic lesions appear to