Prof. Dr. med. Lukas Bubendorf Faculty of Medicine Profiles & Affiliations OverviewResearch Publications Projects & Collaborations Projects & Collaborations OverviewResearch Publications Projects & Collaborations Profiles & Affiliations Projects & Collaborations 15 foundShow per page10 10 20 50 Exploring the genomic, epigenomic and transcriptomic landscapes of adenosquamous and pleomorphic lung cancer Research Project | 2 Project MembersLung cancer remains the leading cause of cancer related death worldwide with approximately 1.8 million new cases and 1.6 million deaths per year. Fortunately, there have been significant improvements in the last decade. Better treatment options guided by the discovery of targetable genomic alterations have been identified and improved patient's survival. However, personalized medicine with targeted therapeutics is suitable for less than 20-30% of Western patients. Landmark studies investigating the genomics of non-small cell lung cancer (NSCLC) have focused mainly on the most frequent types of NSCLC, namely lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). In contrast, rare but clinically relevant subtypes of NSCLCs, such as adenosquamous carcinoma (ASC) and pleomorphic carcinoma (PMC), have not yet been thoroughly investigated, despite affecting large patient numbers globally. The here proposed study draws upon the experiences and developments made in the previous SNF studies with LUAD (310030_138513) and LUSC (320030_162781), especially for the potential of whole-exome sequencing (WES) for the analysis of tumor evolution. Over the course of said studies, we have improved our bioinformatic pipeline and approaches from genomic analysis of targeted panel sequencing (310030_138513) to WES (320030_162781). Always in the context with our refined technology of multiparameter ploidy profiling (MPP), which allows separation of tumor population with high purity enabling the genomic analysis of complex tumor samples and tumors with low tumor cell content. The main aim of this study is to explore the molecular and genetic background of tumor heterogeneity and evolution in ASC and PMC in a comprehensive manner. For this purpose, we will analyze the morphological distinct tumor components of the two rare NSCLC subtypes ASC and PMC, which are defined by their distinct morphological heterogeneity and aggressive clinical behavior. We selected 20 patients with ASC and 20 patients with PMC from our pathology archive. In both cohorts, tumor regions will be separated by histology (adenosquamous carcinoma and squamous cell carcinoma components in ASC; adenocarcinoma or squamous cell carcinoma and spindle and/or giant cell components in PMC) using macrodissection or the above-mentioned MPP approach in tumor specimens with low tumor cell proportion. DNA of all separated tumor regions will be tested for the presence of mutations, insertions- and deletions, copy number aberrations and mirrored allelic imbalances using WES. Further, epigenomic and transcriptomic profiles will be assessed using DNA methylation arrays and genome-wide gene expression arrays, respectively. This will allow us to elucidate the genomic, epigenomic and transcriptomic background of morphologically different histologies in the two rare NSCLC subtypes, ASC and PMC that are defined by the striking intratumoral heterogeneity of their morphology. Importantly, we will be able to define to which extent each of the three 'Omic' profiles contribute to the morphological heterogeneity and to decipher the evolution of these tumors. This may not only provide new fundamental insights into the molecular mechanisms of morphological tumor heterogeneity in general but also pinpoint new therapeutic avenues in these NSCLC subtypes, which are known for their aggressive clinical behavior. We anticipate that the here proposed study will lead to a better understanding of the evolution and the underlying clonal composition of rare NSCLC subtypes and thus contribute to the further development of personalized cancer medicine in patients with ASC and PMC. Defining the driver population in prostate cancer Research Project | 1 Project MembersTumor heterogeneity is a hallmark of cancer. It occurs due to genetic instability fostering random mutations eventually developing into genetically and phenotypically different clones of a tumor. The inherent potential to kill patients is restricted to a small cancer population that maintains a balance of a well-selected set of mutations and defense mechanisms to withstand therapeutic pressure. We call these cell populations driver cell populations in order to distinguish them from the bulk tumor mass. We postulate that the driver cancer cell population in prostate cancer consists of androgen independent stem cell like cells. At the time of surgery for localized disease these cells are either dormant and need to acquire the ability to proliferate, or already hold the ability to proliferate without androgen stimulus ? or both. Here, we propose to analyze these potential driver populations in a xenograft model of human prostate cancer. Tumors will be processed by DNA content based sorting of cancer cells, and the sorted populations will be subjected to genomic analysis before xenografting, before and after castration, and after in vivo passaging. Consequently, this will allow us to characterize the heterogeneity of a single tumor in a so far unmatched resolution and to identify a castration resistant cell population within the tumor at the time of surgery. Assuming that the castration resistant cell population represents a potential driver population in prostate cancer, the identification of the specific mutations within this population may contribute to the basic understanding of meaningful genetic changes associated with prostate cancer. This should have critical impact on the future design of new therapies. The genomic analysis clonal tumor populations in NSCLC: Evolution over time and during metastasis in non-small cell lung cancers (NSCLC) Research Project | 1 Project MembersBei der Entstehung des Bronchialkarzinoms ereignen sich sogenannte genomische Aberrationen, wie Genvermehrungen (Amplifikationen), Genverluste (Deletionen), Translokationen (Ortsveränderung von Genen) oder Mutationen (Änderung der DNA-Sequenz). Da diese Aberrationen spezifisch für den Tumor sind und das Tumorwachstum antreiben, sind die Proteinprodukte dieser Aberrationen vielversprechende Angriffsziele von zielgerichteten Krebsmedikamenten. Ein Beispiel hierfür ist die EML4-ALK Translokation. Patienten, deren Bronchialkarzinom diese Aberration aufweist, können mit dem Medikament Crizotinib behandelt werden, da es spezifisch die Aktivität des aus dieser Aberration resultierenden Proteins hemmt. Es ist demnach von grossem Interesse, neue genomische Aberrationen zu entdecken, welche die Prognose oder das Ansprechen auf zielgerichtete Medikamente vorhersagen können. Die meisten Tumoren sind heterogen, d.h. sie bestehen aus verschiedenen klonalen Tumorpopulationen, die zum Teil eigenständige morphologische Charakteristiken und genomische Aberrationen aufweisen. Unter Berücksichtigung dieser Eigenschaft haben wir einen technologischen Ansatz entwickelt, um die verschiedenen Populationen innerhalb eines Tumors voneinander zu trennen und separat genomisch zu untersuchen. Dies erlaubt uns populationsspezifische genomische Aberrationen zu bestimmen. In diesem Forschungsprojekt werden wir diese neue Methode auf Tumorgewebe von Patienten mit nicht-kleinzelligem Bronchialkarzinom anwenden. Wir werden uns dabei auf Patienten konzentrieren, von welchen wir mehrere Tumorproben analysieren können: entweder Primärtumor und Rezidiv, oder Primärtumor und Metastase. Damit möchten wir die Charakteristiken der verschiedenen klonalen Tumorpopulationen untersuchen und bestimmen, wie sich die einzelnen Populationen über Zeit und Ort entwickelt haben und welche genomische Aberrationen sie erwerben mussten, um der Therapie zu widerstehen. Durch die Kultivierung und genomische Analyse von malignen Pleuraergüssen von Patienten mit Bronchialkarzinom möchten wir neue potentielle Zielgene auch funktionell in vitro untersuchen. Diese Studie wird dazu beitragen, die genomischen Aberrationen in vivo und in vitro zu bestimmen, welche für ein Therapieversagen bei gewissen Patienten mit nicht-kleinzelligem Bronchialkarzinom verantwortlich sind. Genomic analysis of flow-sorted clonal tumor populations from breast cancer patients: Assessment of the clinically relevant genomic heterogeneity and clonal evolution Research Project | 1 Project MembersBreast carcinomas are composed of different clonal populations with distinct population-specific genomic aberrations. This so-called genomic heterogeneity impacts the response to therapeutic regimens. The development of therapy resistance and metastases in breast cancer are clonal processes that are driven by genomic aberrations. It is generally accepted that cancer is caused and driven by a sequential accumulation of genomic aberrations (so-called mutations) in cancer-relevant genes. These mutations might affect only one or a few nucleotides (small scale mutations) or larger segments with an effect on the structure of a chromosome, as it is the case for deletions, amplifications and translocations. Although hundreds of these mutations have been reported in cancer and in breast cancer in particular, the impact of these mutations on cancer development has not been completely elucidated yet. Nevertheless, the detection of a genomic aberration can impact the cancer treatment decision and predict therapeutic response. Trastuzumab against HER2 amplified breast cancer and erlotinib against EGFR mutated lung cancer are two of the most prominent examples of such targeted cancer treatment. In the last decade, the rapid development and accessibility of novel technologies (such as array-CGH and deep-sequencing) has led to multiple genomic profiling studies with large patient cohorts, but only interrogating one tissue specimen per patient. Although intratumoral heterogeneity is a phenomenon that is widely accepted by clinicians and pathologist, it is usually not taken into consideration in the design of these studies. Heterogeneous tumors usually consist of multiple clonal tumor populations and these distinct populations can carry different genomic aberrations: a phenomenon called ?genomic heterogeneity?. This might be profoundly important since in the era of personalized medicine, the selection of patients for targeted therapeutics is more and more based on the presence of genomic aberrations. For this reason, in the last four years, we have developed an innovative and robust methodology for the detection and isolation of distinct clonal tumor populations from frozen patient biopsies. After separation, the distinct tumor populations are genomically characterized by array-CGH and deep sequencing. We have recently published this novel methodology and a proof of concept study in the journal PNAS. The primary objective of this study is the comprehensive analysis of the genomic heterogeneity in tumor biopsies from breast cancer patients. This study will provide novel information about the clonal composition of breast cancer, the population-specific genomic aberrations and their potential clinical relevance. Further, the analysis of multiple samples from the same patients (over time and during metastasis) will allow us to infer the genomic evolution and help us to understand which clonal populations and which specific genomic aberrations are responsible for the metastasis process and for the response to therapy in these breast cancer patients. The prevalence of novel population-specific genomic aberrations and the expression of the involved protein products will be determined by using a large tissue microarray with more than 2?300 breast cancer samples and complete clinical follow-up data. Profiling of anticancer-treatment effects in vitro using real-time impedance measurement on patient-derived samples Research Project | 1 Project MembersNo Description available Comprehensive Analysis of the genomic evolution of clonal populations in the progression of hormone sensitive prostate and breast cancers Research Project | 1 Project MembersThis study has two main focuses: first, the detection of novel gene fusions and second, the further development and application of a technology for the clonal analysis of solid tumor samples. The methodology relies on a unique combination of flow-sorting clonal tumor cell populations and the genomic characterization of the resulting populations by array-CGH or targeted sequencing. Due to the evidentiary success of this innovative methodology, we plan to apply it to a carefully selected, unique prostate and breast cancer cohort. For this purpose, multiple samples (primary/recurrence or primary/metastases) from single patients will be subjected to clonal flow-sorting and genomic analyses. Rigorous bioinformatic analyses and knowledge mining will be applied to the resulting data, followed by clinical validation using tissue microarrays and functional experiments in established cell line models. We are convinced that appliance of this cutting-edge technique to these unique samples will lead to novel and unprecedented results about the evolution of distinct clonal populations within a tumor and their response to the selective pressure caused by the therapeutic regimen. Further, inclusion of metastases from the same patients will allow us to interrogate which clonal tumor population was able to metastasize and how it propagated at the new anatomical site. We are confident that results from this proposed study can be translated into the clinics and can contribute to the development of personalized medicine in cancer treatment. Anschaffung eines BD INFLUX Flow Sorters Research Project | 1 Project MembersDer BD Influx Flow Sorter ist ein technisch hochmodernes Flow-Sort-Gerät, welches wir vor allem für die Isolierung von Tumorpopulationen aus Patientengewebe verwenden werden. Die Analyse und Charakterisierung von verschiedenen Populationen desselben Tumors ermöglicht neue, klinisch relevante Einblicke in die Entwicklung und Progression maligner Tumoren und schafft einen neuen Forschungsbereich mit zahlreichen Anwendungsmöglichkeiten Evaluation von potentiellen Zielgenen innerhalb des 10q22-Amplikons beim Prostata- und Mammakarzinom Research Project | 1 Project MembersBislang fehlt es an geeigneten Therapieformen zur erfolgreichen Behandlung von Patienten mit hormon-refraktärem Prostatakarzinom. Während einer Untersuchung haben wir 10q22 als eine der am häufigsten amplifizierten genomischen Regionen beim Prostatakarzinom identifiziert (Bloch et al, 2007). Die aussergewöhnlich hohe Inzidenz des 10q22-Amplikons (10-15%) beschränkt sich dabei ausschliesslich auf Fälle mit ungünstiger Prognose des hormon-refraktären Prostatakarzinoms. Dies lässt vermuten, dass das 10q22 Amplikon mindestens eines oder eventuell auch mehrere Gene beherbergt, welche für den ungünstigen Verlauf der Krankheit verantwortlich sind. Da sich jedoch die betroffene genomische Region über insgesamt 12 Mb erstreckt, ist es bislang noch niemandem gelungen das Zielgen zu identifizieren. Durch unsere Analyse eines multi-tumor Tissue Microarrays (TMA) mit über 2?000 Tumoren aus mehr als 120 unterschiedlichen Tumortypen, haben wir das 10q22-Amplifikation nun erstmals auch bei anderen Tumortypen nachweisen können (Mammakarzinom, Ovarialkarzinom und Tumoren des Endometriums). Die Inzidenz lag insgesamt lediglich bei 1.9%, doch interessanterweise waren in allen Fällen östrogenregulierte Tumortypen betroffen, welche mittels Anti-Östrogen Therapie behandelt werden können. Anhand einer weiteren TMA Untersuchung von 1?200 Mammatumoren mit klinischen Verlaufsdaten wurde der Nachweis des 10q22 Amplikons beim Mammakarzinom bestätigt. Die Inzidenz lag diesmal bei 1.9% und war mit hohem Tumor Grad, schneller Wachstumsrate und schlechter Prognose assoziiert. Im Rahmen unserer bisherigen funktionellen Untersuchungen ist es uns zudem gelungen die Wachstumsrate mehrerer Mammakarzinom- und Prostatakarzinom-Zelllinien durch gezielte Behandlung mit KCNMA1-spezifischer siRNA und durch Zugabe von KCNMA1-Blocker (Paxilline) deutlich zu reduzieren. Ein weiteres potentielles Zielgen des 10q22-Amplikons (RAI17) wurde ebenfalls in diese Untersuchungen mit eingeschlossen und lieferte ähnliche Ergebnisse. Durch hoch auflösende Array CGH mittels 10q22-amplifizierten Mammatumoren konnte auch gezeigt werden, dass beide Gene immer gemeinsam amplifiziert werden. Erste Untersuchungen in Bezug auf RAI17 haben ausserdem ergeben, dass die Amplifikation mit erhöhter mRNA Expression assoziiert ist. Im Rahmen des 10q22 Projektes werden erstmals beide potentiellen Zielgene des 10q22 Amplikons beim Prostata- und Mammakarzinom näher untersucht. Dabei stellt sich nicht zuletzt die Frage nach der Ursache für das Auftreten der Amplifikation bei Tumortypen mit ungünstiger Prognose. Unser spezielles Augenmerk liegt deshalb auf der Erforschung der molekularen Mechanismen, welche durch die 10q22 Amplifikation beeinflusst werden, sowie auf der Suche nach möglichen Therapieformen. SAKK 08/07: Docetaxel and cetuximab in patients with docetaxel-resistant hormone-refractory prostate cancer. A multicenter phase II trial. Immunohistochemical analysis of biomarkers Research Project | 1 Project MembersSAKK 08/07 Evaluation of the ALK FISH probe in NSCLC specimens Research Project | 1 Project MembersNo Description available 12 12 OverviewResearch Publications Projects & Collaborations
Projects & Collaborations 15 foundShow per page10 10 20 50 Exploring the genomic, epigenomic and transcriptomic landscapes of adenosquamous and pleomorphic lung cancer Research Project | 2 Project MembersLung cancer remains the leading cause of cancer related death worldwide with approximately 1.8 million new cases and 1.6 million deaths per year. Fortunately, there have been significant improvements in the last decade. Better treatment options guided by the discovery of targetable genomic alterations have been identified and improved patient's survival. However, personalized medicine with targeted therapeutics is suitable for less than 20-30% of Western patients. Landmark studies investigating the genomics of non-small cell lung cancer (NSCLC) have focused mainly on the most frequent types of NSCLC, namely lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). In contrast, rare but clinically relevant subtypes of NSCLCs, such as adenosquamous carcinoma (ASC) and pleomorphic carcinoma (PMC), have not yet been thoroughly investigated, despite affecting large patient numbers globally. The here proposed study draws upon the experiences and developments made in the previous SNF studies with LUAD (310030_138513) and LUSC (320030_162781), especially for the potential of whole-exome sequencing (WES) for the analysis of tumor evolution. Over the course of said studies, we have improved our bioinformatic pipeline and approaches from genomic analysis of targeted panel sequencing (310030_138513) to WES (320030_162781). Always in the context with our refined technology of multiparameter ploidy profiling (MPP), which allows separation of tumor population with high purity enabling the genomic analysis of complex tumor samples and tumors with low tumor cell content. The main aim of this study is to explore the molecular and genetic background of tumor heterogeneity and evolution in ASC and PMC in a comprehensive manner. For this purpose, we will analyze the morphological distinct tumor components of the two rare NSCLC subtypes ASC and PMC, which are defined by their distinct morphological heterogeneity and aggressive clinical behavior. We selected 20 patients with ASC and 20 patients with PMC from our pathology archive. In both cohorts, tumor regions will be separated by histology (adenosquamous carcinoma and squamous cell carcinoma components in ASC; adenocarcinoma or squamous cell carcinoma and spindle and/or giant cell components in PMC) using macrodissection or the above-mentioned MPP approach in tumor specimens with low tumor cell proportion. DNA of all separated tumor regions will be tested for the presence of mutations, insertions- and deletions, copy number aberrations and mirrored allelic imbalances using WES. Further, epigenomic and transcriptomic profiles will be assessed using DNA methylation arrays and genome-wide gene expression arrays, respectively. This will allow us to elucidate the genomic, epigenomic and transcriptomic background of morphologically different histologies in the two rare NSCLC subtypes, ASC and PMC that are defined by the striking intratumoral heterogeneity of their morphology. Importantly, we will be able to define to which extent each of the three 'Omic' profiles contribute to the morphological heterogeneity and to decipher the evolution of these tumors. This may not only provide new fundamental insights into the molecular mechanisms of morphological tumor heterogeneity in general but also pinpoint new therapeutic avenues in these NSCLC subtypes, which are known for their aggressive clinical behavior. We anticipate that the here proposed study will lead to a better understanding of the evolution and the underlying clonal composition of rare NSCLC subtypes and thus contribute to the further development of personalized cancer medicine in patients with ASC and PMC. Defining the driver population in prostate cancer Research Project | 1 Project MembersTumor heterogeneity is a hallmark of cancer. It occurs due to genetic instability fostering random mutations eventually developing into genetically and phenotypically different clones of a tumor. The inherent potential to kill patients is restricted to a small cancer population that maintains a balance of a well-selected set of mutations and defense mechanisms to withstand therapeutic pressure. We call these cell populations driver cell populations in order to distinguish them from the bulk tumor mass. We postulate that the driver cancer cell population in prostate cancer consists of androgen independent stem cell like cells. At the time of surgery for localized disease these cells are either dormant and need to acquire the ability to proliferate, or already hold the ability to proliferate without androgen stimulus ? or both. Here, we propose to analyze these potential driver populations in a xenograft model of human prostate cancer. Tumors will be processed by DNA content based sorting of cancer cells, and the sorted populations will be subjected to genomic analysis before xenografting, before and after castration, and after in vivo passaging. Consequently, this will allow us to characterize the heterogeneity of a single tumor in a so far unmatched resolution and to identify a castration resistant cell population within the tumor at the time of surgery. Assuming that the castration resistant cell population represents a potential driver population in prostate cancer, the identification of the specific mutations within this population may contribute to the basic understanding of meaningful genetic changes associated with prostate cancer. This should have critical impact on the future design of new therapies. The genomic analysis clonal tumor populations in NSCLC: Evolution over time and during metastasis in non-small cell lung cancers (NSCLC) Research Project | 1 Project MembersBei der Entstehung des Bronchialkarzinoms ereignen sich sogenannte genomische Aberrationen, wie Genvermehrungen (Amplifikationen), Genverluste (Deletionen), Translokationen (Ortsveränderung von Genen) oder Mutationen (Änderung der DNA-Sequenz). Da diese Aberrationen spezifisch für den Tumor sind und das Tumorwachstum antreiben, sind die Proteinprodukte dieser Aberrationen vielversprechende Angriffsziele von zielgerichteten Krebsmedikamenten. Ein Beispiel hierfür ist die EML4-ALK Translokation. Patienten, deren Bronchialkarzinom diese Aberration aufweist, können mit dem Medikament Crizotinib behandelt werden, da es spezifisch die Aktivität des aus dieser Aberration resultierenden Proteins hemmt. Es ist demnach von grossem Interesse, neue genomische Aberrationen zu entdecken, welche die Prognose oder das Ansprechen auf zielgerichtete Medikamente vorhersagen können. Die meisten Tumoren sind heterogen, d.h. sie bestehen aus verschiedenen klonalen Tumorpopulationen, die zum Teil eigenständige morphologische Charakteristiken und genomische Aberrationen aufweisen. Unter Berücksichtigung dieser Eigenschaft haben wir einen technologischen Ansatz entwickelt, um die verschiedenen Populationen innerhalb eines Tumors voneinander zu trennen und separat genomisch zu untersuchen. Dies erlaubt uns populationsspezifische genomische Aberrationen zu bestimmen. In diesem Forschungsprojekt werden wir diese neue Methode auf Tumorgewebe von Patienten mit nicht-kleinzelligem Bronchialkarzinom anwenden. Wir werden uns dabei auf Patienten konzentrieren, von welchen wir mehrere Tumorproben analysieren können: entweder Primärtumor und Rezidiv, oder Primärtumor und Metastase. Damit möchten wir die Charakteristiken der verschiedenen klonalen Tumorpopulationen untersuchen und bestimmen, wie sich die einzelnen Populationen über Zeit und Ort entwickelt haben und welche genomische Aberrationen sie erwerben mussten, um der Therapie zu widerstehen. Durch die Kultivierung und genomische Analyse von malignen Pleuraergüssen von Patienten mit Bronchialkarzinom möchten wir neue potentielle Zielgene auch funktionell in vitro untersuchen. Diese Studie wird dazu beitragen, die genomischen Aberrationen in vivo und in vitro zu bestimmen, welche für ein Therapieversagen bei gewissen Patienten mit nicht-kleinzelligem Bronchialkarzinom verantwortlich sind. Genomic analysis of flow-sorted clonal tumor populations from breast cancer patients: Assessment of the clinically relevant genomic heterogeneity and clonal evolution Research Project | 1 Project MembersBreast carcinomas are composed of different clonal populations with distinct population-specific genomic aberrations. This so-called genomic heterogeneity impacts the response to therapeutic regimens. The development of therapy resistance and metastases in breast cancer are clonal processes that are driven by genomic aberrations. It is generally accepted that cancer is caused and driven by a sequential accumulation of genomic aberrations (so-called mutations) in cancer-relevant genes. These mutations might affect only one or a few nucleotides (small scale mutations) or larger segments with an effect on the structure of a chromosome, as it is the case for deletions, amplifications and translocations. Although hundreds of these mutations have been reported in cancer and in breast cancer in particular, the impact of these mutations on cancer development has not been completely elucidated yet. Nevertheless, the detection of a genomic aberration can impact the cancer treatment decision and predict therapeutic response. Trastuzumab against HER2 amplified breast cancer and erlotinib against EGFR mutated lung cancer are two of the most prominent examples of such targeted cancer treatment. In the last decade, the rapid development and accessibility of novel technologies (such as array-CGH and deep-sequencing) has led to multiple genomic profiling studies with large patient cohorts, but only interrogating one tissue specimen per patient. Although intratumoral heterogeneity is a phenomenon that is widely accepted by clinicians and pathologist, it is usually not taken into consideration in the design of these studies. Heterogeneous tumors usually consist of multiple clonal tumor populations and these distinct populations can carry different genomic aberrations: a phenomenon called ?genomic heterogeneity?. This might be profoundly important since in the era of personalized medicine, the selection of patients for targeted therapeutics is more and more based on the presence of genomic aberrations. For this reason, in the last four years, we have developed an innovative and robust methodology for the detection and isolation of distinct clonal tumor populations from frozen patient biopsies. After separation, the distinct tumor populations are genomically characterized by array-CGH and deep sequencing. We have recently published this novel methodology and a proof of concept study in the journal PNAS. The primary objective of this study is the comprehensive analysis of the genomic heterogeneity in tumor biopsies from breast cancer patients. This study will provide novel information about the clonal composition of breast cancer, the population-specific genomic aberrations and their potential clinical relevance. Further, the analysis of multiple samples from the same patients (over time and during metastasis) will allow us to infer the genomic evolution and help us to understand which clonal populations and which specific genomic aberrations are responsible for the metastasis process and for the response to therapy in these breast cancer patients. The prevalence of novel population-specific genomic aberrations and the expression of the involved protein products will be determined by using a large tissue microarray with more than 2?300 breast cancer samples and complete clinical follow-up data. Profiling of anticancer-treatment effects in vitro using real-time impedance measurement on patient-derived samples Research Project | 1 Project MembersNo Description available Comprehensive Analysis of the genomic evolution of clonal populations in the progression of hormone sensitive prostate and breast cancers Research Project | 1 Project MembersThis study has two main focuses: first, the detection of novel gene fusions and second, the further development and application of a technology for the clonal analysis of solid tumor samples. The methodology relies on a unique combination of flow-sorting clonal tumor cell populations and the genomic characterization of the resulting populations by array-CGH or targeted sequencing. Due to the evidentiary success of this innovative methodology, we plan to apply it to a carefully selected, unique prostate and breast cancer cohort. For this purpose, multiple samples (primary/recurrence or primary/metastases) from single patients will be subjected to clonal flow-sorting and genomic analyses. Rigorous bioinformatic analyses and knowledge mining will be applied to the resulting data, followed by clinical validation using tissue microarrays and functional experiments in established cell line models. We are convinced that appliance of this cutting-edge technique to these unique samples will lead to novel and unprecedented results about the evolution of distinct clonal populations within a tumor and their response to the selective pressure caused by the therapeutic regimen. Further, inclusion of metastases from the same patients will allow us to interrogate which clonal tumor population was able to metastasize and how it propagated at the new anatomical site. We are confident that results from this proposed study can be translated into the clinics and can contribute to the development of personalized medicine in cancer treatment. Anschaffung eines BD INFLUX Flow Sorters Research Project | 1 Project MembersDer BD Influx Flow Sorter ist ein technisch hochmodernes Flow-Sort-Gerät, welches wir vor allem für die Isolierung von Tumorpopulationen aus Patientengewebe verwenden werden. Die Analyse und Charakterisierung von verschiedenen Populationen desselben Tumors ermöglicht neue, klinisch relevante Einblicke in die Entwicklung und Progression maligner Tumoren und schafft einen neuen Forschungsbereich mit zahlreichen Anwendungsmöglichkeiten Evaluation von potentiellen Zielgenen innerhalb des 10q22-Amplikons beim Prostata- und Mammakarzinom Research Project | 1 Project MembersBislang fehlt es an geeigneten Therapieformen zur erfolgreichen Behandlung von Patienten mit hormon-refraktärem Prostatakarzinom. Während einer Untersuchung haben wir 10q22 als eine der am häufigsten amplifizierten genomischen Regionen beim Prostatakarzinom identifiziert (Bloch et al, 2007). Die aussergewöhnlich hohe Inzidenz des 10q22-Amplikons (10-15%) beschränkt sich dabei ausschliesslich auf Fälle mit ungünstiger Prognose des hormon-refraktären Prostatakarzinoms. Dies lässt vermuten, dass das 10q22 Amplikon mindestens eines oder eventuell auch mehrere Gene beherbergt, welche für den ungünstigen Verlauf der Krankheit verantwortlich sind. Da sich jedoch die betroffene genomische Region über insgesamt 12 Mb erstreckt, ist es bislang noch niemandem gelungen das Zielgen zu identifizieren. Durch unsere Analyse eines multi-tumor Tissue Microarrays (TMA) mit über 2?000 Tumoren aus mehr als 120 unterschiedlichen Tumortypen, haben wir das 10q22-Amplifikation nun erstmals auch bei anderen Tumortypen nachweisen können (Mammakarzinom, Ovarialkarzinom und Tumoren des Endometriums). Die Inzidenz lag insgesamt lediglich bei 1.9%, doch interessanterweise waren in allen Fällen östrogenregulierte Tumortypen betroffen, welche mittels Anti-Östrogen Therapie behandelt werden können. Anhand einer weiteren TMA Untersuchung von 1?200 Mammatumoren mit klinischen Verlaufsdaten wurde der Nachweis des 10q22 Amplikons beim Mammakarzinom bestätigt. Die Inzidenz lag diesmal bei 1.9% und war mit hohem Tumor Grad, schneller Wachstumsrate und schlechter Prognose assoziiert. Im Rahmen unserer bisherigen funktionellen Untersuchungen ist es uns zudem gelungen die Wachstumsrate mehrerer Mammakarzinom- und Prostatakarzinom-Zelllinien durch gezielte Behandlung mit KCNMA1-spezifischer siRNA und durch Zugabe von KCNMA1-Blocker (Paxilline) deutlich zu reduzieren. Ein weiteres potentielles Zielgen des 10q22-Amplikons (RAI17) wurde ebenfalls in diese Untersuchungen mit eingeschlossen und lieferte ähnliche Ergebnisse. Durch hoch auflösende Array CGH mittels 10q22-amplifizierten Mammatumoren konnte auch gezeigt werden, dass beide Gene immer gemeinsam amplifiziert werden. Erste Untersuchungen in Bezug auf RAI17 haben ausserdem ergeben, dass die Amplifikation mit erhöhter mRNA Expression assoziiert ist. Im Rahmen des 10q22 Projektes werden erstmals beide potentiellen Zielgene des 10q22 Amplikons beim Prostata- und Mammakarzinom näher untersucht. Dabei stellt sich nicht zuletzt die Frage nach der Ursache für das Auftreten der Amplifikation bei Tumortypen mit ungünstiger Prognose. Unser spezielles Augenmerk liegt deshalb auf der Erforschung der molekularen Mechanismen, welche durch die 10q22 Amplifikation beeinflusst werden, sowie auf der Suche nach möglichen Therapieformen. SAKK 08/07: Docetaxel and cetuximab in patients with docetaxel-resistant hormone-refractory prostate cancer. A multicenter phase II trial. Immunohistochemical analysis of biomarkers Research Project | 1 Project MembersSAKK 08/07 Evaluation of the ALK FISH probe in NSCLC specimens Research Project | 1 Project MembersNo Description available 12 12
Exploring the genomic, epigenomic and transcriptomic landscapes of adenosquamous and pleomorphic lung cancer Research Project | 2 Project MembersLung cancer remains the leading cause of cancer related death worldwide with approximately 1.8 million new cases and 1.6 million deaths per year. Fortunately, there have been significant improvements in the last decade. Better treatment options guided by the discovery of targetable genomic alterations have been identified and improved patient's survival. However, personalized medicine with targeted therapeutics is suitable for less than 20-30% of Western patients. Landmark studies investigating the genomics of non-small cell lung cancer (NSCLC) have focused mainly on the most frequent types of NSCLC, namely lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). In contrast, rare but clinically relevant subtypes of NSCLCs, such as adenosquamous carcinoma (ASC) and pleomorphic carcinoma (PMC), have not yet been thoroughly investigated, despite affecting large patient numbers globally. The here proposed study draws upon the experiences and developments made in the previous SNF studies with LUAD (310030_138513) and LUSC (320030_162781), especially for the potential of whole-exome sequencing (WES) for the analysis of tumor evolution. Over the course of said studies, we have improved our bioinformatic pipeline and approaches from genomic analysis of targeted panel sequencing (310030_138513) to WES (320030_162781). Always in the context with our refined technology of multiparameter ploidy profiling (MPP), which allows separation of tumor population with high purity enabling the genomic analysis of complex tumor samples and tumors with low tumor cell content. The main aim of this study is to explore the molecular and genetic background of tumor heterogeneity and evolution in ASC and PMC in a comprehensive manner. For this purpose, we will analyze the morphological distinct tumor components of the two rare NSCLC subtypes ASC and PMC, which are defined by their distinct morphological heterogeneity and aggressive clinical behavior. We selected 20 patients with ASC and 20 patients with PMC from our pathology archive. In both cohorts, tumor regions will be separated by histology (adenosquamous carcinoma and squamous cell carcinoma components in ASC; adenocarcinoma or squamous cell carcinoma and spindle and/or giant cell components in PMC) using macrodissection or the above-mentioned MPP approach in tumor specimens with low tumor cell proportion. DNA of all separated tumor regions will be tested for the presence of mutations, insertions- and deletions, copy number aberrations and mirrored allelic imbalances using WES. Further, epigenomic and transcriptomic profiles will be assessed using DNA methylation arrays and genome-wide gene expression arrays, respectively. This will allow us to elucidate the genomic, epigenomic and transcriptomic background of morphologically different histologies in the two rare NSCLC subtypes, ASC and PMC that are defined by the striking intratumoral heterogeneity of their morphology. Importantly, we will be able to define to which extent each of the three 'Omic' profiles contribute to the morphological heterogeneity and to decipher the evolution of these tumors. This may not only provide new fundamental insights into the molecular mechanisms of morphological tumor heterogeneity in general but also pinpoint new therapeutic avenues in these NSCLC subtypes, which are known for their aggressive clinical behavior. We anticipate that the here proposed study will lead to a better understanding of the evolution and the underlying clonal composition of rare NSCLC subtypes and thus contribute to the further development of personalized cancer medicine in patients with ASC and PMC.
Defining the driver population in prostate cancer Research Project | 1 Project MembersTumor heterogeneity is a hallmark of cancer. It occurs due to genetic instability fostering random mutations eventually developing into genetically and phenotypically different clones of a tumor. The inherent potential to kill patients is restricted to a small cancer population that maintains a balance of a well-selected set of mutations and defense mechanisms to withstand therapeutic pressure. We call these cell populations driver cell populations in order to distinguish them from the bulk tumor mass. We postulate that the driver cancer cell population in prostate cancer consists of androgen independent stem cell like cells. At the time of surgery for localized disease these cells are either dormant and need to acquire the ability to proliferate, or already hold the ability to proliferate without androgen stimulus ? or both. Here, we propose to analyze these potential driver populations in a xenograft model of human prostate cancer. Tumors will be processed by DNA content based sorting of cancer cells, and the sorted populations will be subjected to genomic analysis before xenografting, before and after castration, and after in vivo passaging. Consequently, this will allow us to characterize the heterogeneity of a single tumor in a so far unmatched resolution and to identify a castration resistant cell population within the tumor at the time of surgery. Assuming that the castration resistant cell population represents a potential driver population in prostate cancer, the identification of the specific mutations within this population may contribute to the basic understanding of meaningful genetic changes associated with prostate cancer. This should have critical impact on the future design of new therapies.
The genomic analysis clonal tumor populations in NSCLC: Evolution over time and during metastasis in non-small cell lung cancers (NSCLC) Research Project | 1 Project MembersBei der Entstehung des Bronchialkarzinoms ereignen sich sogenannte genomische Aberrationen, wie Genvermehrungen (Amplifikationen), Genverluste (Deletionen), Translokationen (Ortsveränderung von Genen) oder Mutationen (Änderung der DNA-Sequenz). Da diese Aberrationen spezifisch für den Tumor sind und das Tumorwachstum antreiben, sind die Proteinprodukte dieser Aberrationen vielversprechende Angriffsziele von zielgerichteten Krebsmedikamenten. Ein Beispiel hierfür ist die EML4-ALK Translokation. Patienten, deren Bronchialkarzinom diese Aberration aufweist, können mit dem Medikament Crizotinib behandelt werden, da es spezifisch die Aktivität des aus dieser Aberration resultierenden Proteins hemmt. Es ist demnach von grossem Interesse, neue genomische Aberrationen zu entdecken, welche die Prognose oder das Ansprechen auf zielgerichtete Medikamente vorhersagen können. Die meisten Tumoren sind heterogen, d.h. sie bestehen aus verschiedenen klonalen Tumorpopulationen, die zum Teil eigenständige morphologische Charakteristiken und genomische Aberrationen aufweisen. Unter Berücksichtigung dieser Eigenschaft haben wir einen technologischen Ansatz entwickelt, um die verschiedenen Populationen innerhalb eines Tumors voneinander zu trennen und separat genomisch zu untersuchen. Dies erlaubt uns populationsspezifische genomische Aberrationen zu bestimmen. In diesem Forschungsprojekt werden wir diese neue Methode auf Tumorgewebe von Patienten mit nicht-kleinzelligem Bronchialkarzinom anwenden. Wir werden uns dabei auf Patienten konzentrieren, von welchen wir mehrere Tumorproben analysieren können: entweder Primärtumor und Rezidiv, oder Primärtumor und Metastase. Damit möchten wir die Charakteristiken der verschiedenen klonalen Tumorpopulationen untersuchen und bestimmen, wie sich die einzelnen Populationen über Zeit und Ort entwickelt haben und welche genomische Aberrationen sie erwerben mussten, um der Therapie zu widerstehen. Durch die Kultivierung und genomische Analyse von malignen Pleuraergüssen von Patienten mit Bronchialkarzinom möchten wir neue potentielle Zielgene auch funktionell in vitro untersuchen. Diese Studie wird dazu beitragen, die genomischen Aberrationen in vivo und in vitro zu bestimmen, welche für ein Therapieversagen bei gewissen Patienten mit nicht-kleinzelligem Bronchialkarzinom verantwortlich sind.
Genomic analysis of flow-sorted clonal tumor populations from breast cancer patients: Assessment of the clinically relevant genomic heterogeneity and clonal evolution Research Project | 1 Project MembersBreast carcinomas are composed of different clonal populations with distinct population-specific genomic aberrations. This so-called genomic heterogeneity impacts the response to therapeutic regimens. The development of therapy resistance and metastases in breast cancer are clonal processes that are driven by genomic aberrations. It is generally accepted that cancer is caused and driven by a sequential accumulation of genomic aberrations (so-called mutations) in cancer-relevant genes. These mutations might affect only one or a few nucleotides (small scale mutations) or larger segments with an effect on the structure of a chromosome, as it is the case for deletions, amplifications and translocations. Although hundreds of these mutations have been reported in cancer and in breast cancer in particular, the impact of these mutations on cancer development has not been completely elucidated yet. Nevertheless, the detection of a genomic aberration can impact the cancer treatment decision and predict therapeutic response. Trastuzumab against HER2 amplified breast cancer and erlotinib against EGFR mutated lung cancer are two of the most prominent examples of such targeted cancer treatment. In the last decade, the rapid development and accessibility of novel technologies (such as array-CGH and deep-sequencing) has led to multiple genomic profiling studies with large patient cohorts, but only interrogating one tissue specimen per patient. Although intratumoral heterogeneity is a phenomenon that is widely accepted by clinicians and pathologist, it is usually not taken into consideration in the design of these studies. Heterogeneous tumors usually consist of multiple clonal tumor populations and these distinct populations can carry different genomic aberrations: a phenomenon called ?genomic heterogeneity?. This might be profoundly important since in the era of personalized medicine, the selection of patients for targeted therapeutics is more and more based on the presence of genomic aberrations. For this reason, in the last four years, we have developed an innovative and robust methodology for the detection and isolation of distinct clonal tumor populations from frozen patient biopsies. After separation, the distinct tumor populations are genomically characterized by array-CGH and deep sequencing. We have recently published this novel methodology and a proof of concept study in the journal PNAS. The primary objective of this study is the comprehensive analysis of the genomic heterogeneity in tumor biopsies from breast cancer patients. This study will provide novel information about the clonal composition of breast cancer, the population-specific genomic aberrations and their potential clinical relevance. Further, the analysis of multiple samples from the same patients (over time and during metastasis) will allow us to infer the genomic evolution and help us to understand which clonal populations and which specific genomic aberrations are responsible for the metastasis process and for the response to therapy in these breast cancer patients. The prevalence of novel population-specific genomic aberrations and the expression of the involved protein products will be determined by using a large tissue microarray with more than 2?300 breast cancer samples and complete clinical follow-up data.
Profiling of anticancer-treatment effects in vitro using real-time impedance measurement on patient-derived samples Research Project | 1 Project MembersNo Description available
Comprehensive Analysis of the genomic evolution of clonal populations in the progression of hormone sensitive prostate and breast cancers Research Project | 1 Project MembersThis study has two main focuses: first, the detection of novel gene fusions and second, the further development and application of a technology for the clonal analysis of solid tumor samples. The methodology relies on a unique combination of flow-sorting clonal tumor cell populations and the genomic characterization of the resulting populations by array-CGH or targeted sequencing. Due to the evidentiary success of this innovative methodology, we plan to apply it to a carefully selected, unique prostate and breast cancer cohort. For this purpose, multiple samples (primary/recurrence or primary/metastases) from single patients will be subjected to clonal flow-sorting and genomic analyses. Rigorous bioinformatic analyses and knowledge mining will be applied to the resulting data, followed by clinical validation using tissue microarrays and functional experiments in established cell line models. We are convinced that appliance of this cutting-edge technique to these unique samples will lead to novel and unprecedented results about the evolution of distinct clonal populations within a tumor and their response to the selective pressure caused by the therapeutic regimen. Further, inclusion of metastases from the same patients will allow us to interrogate which clonal tumor population was able to metastasize and how it propagated at the new anatomical site. We are confident that results from this proposed study can be translated into the clinics and can contribute to the development of personalized medicine in cancer treatment.
Anschaffung eines BD INFLUX Flow Sorters Research Project | 1 Project MembersDer BD Influx Flow Sorter ist ein technisch hochmodernes Flow-Sort-Gerät, welches wir vor allem für die Isolierung von Tumorpopulationen aus Patientengewebe verwenden werden. Die Analyse und Charakterisierung von verschiedenen Populationen desselben Tumors ermöglicht neue, klinisch relevante Einblicke in die Entwicklung und Progression maligner Tumoren und schafft einen neuen Forschungsbereich mit zahlreichen Anwendungsmöglichkeiten
Evaluation von potentiellen Zielgenen innerhalb des 10q22-Amplikons beim Prostata- und Mammakarzinom Research Project | 1 Project MembersBislang fehlt es an geeigneten Therapieformen zur erfolgreichen Behandlung von Patienten mit hormon-refraktärem Prostatakarzinom. Während einer Untersuchung haben wir 10q22 als eine der am häufigsten amplifizierten genomischen Regionen beim Prostatakarzinom identifiziert (Bloch et al, 2007). Die aussergewöhnlich hohe Inzidenz des 10q22-Amplikons (10-15%) beschränkt sich dabei ausschliesslich auf Fälle mit ungünstiger Prognose des hormon-refraktären Prostatakarzinoms. Dies lässt vermuten, dass das 10q22 Amplikon mindestens eines oder eventuell auch mehrere Gene beherbergt, welche für den ungünstigen Verlauf der Krankheit verantwortlich sind. Da sich jedoch die betroffene genomische Region über insgesamt 12 Mb erstreckt, ist es bislang noch niemandem gelungen das Zielgen zu identifizieren. Durch unsere Analyse eines multi-tumor Tissue Microarrays (TMA) mit über 2?000 Tumoren aus mehr als 120 unterschiedlichen Tumortypen, haben wir das 10q22-Amplifikation nun erstmals auch bei anderen Tumortypen nachweisen können (Mammakarzinom, Ovarialkarzinom und Tumoren des Endometriums). Die Inzidenz lag insgesamt lediglich bei 1.9%, doch interessanterweise waren in allen Fällen östrogenregulierte Tumortypen betroffen, welche mittels Anti-Östrogen Therapie behandelt werden können. Anhand einer weiteren TMA Untersuchung von 1?200 Mammatumoren mit klinischen Verlaufsdaten wurde der Nachweis des 10q22 Amplikons beim Mammakarzinom bestätigt. Die Inzidenz lag diesmal bei 1.9% und war mit hohem Tumor Grad, schneller Wachstumsrate und schlechter Prognose assoziiert. Im Rahmen unserer bisherigen funktionellen Untersuchungen ist es uns zudem gelungen die Wachstumsrate mehrerer Mammakarzinom- und Prostatakarzinom-Zelllinien durch gezielte Behandlung mit KCNMA1-spezifischer siRNA und durch Zugabe von KCNMA1-Blocker (Paxilline) deutlich zu reduzieren. Ein weiteres potentielles Zielgen des 10q22-Amplikons (RAI17) wurde ebenfalls in diese Untersuchungen mit eingeschlossen und lieferte ähnliche Ergebnisse. Durch hoch auflösende Array CGH mittels 10q22-amplifizierten Mammatumoren konnte auch gezeigt werden, dass beide Gene immer gemeinsam amplifiziert werden. Erste Untersuchungen in Bezug auf RAI17 haben ausserdem ergeben, dass die Amplifikation mit erhöhter mRNA Expression assoziiert ist. Im Rahmen des 10q22 Projektes werden erstmals beide potentiellen Zielgene des 10q22 Amplikons beim Prostata- und Mammakarzinom näher untersucht. Dabei stellt sich nicht zuletzt die Frage nach der Ursache für das Auftreten der Amplifikation bei Tumortypen mit ungünstiger Prognose. Unser spezielles Augenmerk liegt deshalb auf der Erforschung der molekularen Mechanismen, welche durch die 10q22 Amplifikation beeinflusst werden, sowie auf der Suche nach möglichen Therapieformen.
SAKK 08/07: Docetaxel and cetuximab in patients with docetaxel-resistant hormone-refractory prostate cancer. A multicenter phase II trial. Immunohistochemical analysis of biomarkers Research Project | 1 Project MembersSAKK 08/07
Evaluation of the ALK FISH probe in NSCLC specimens Research Project | 1 Project MembersNo Description available
