Afatinib in Advanced NRG1 Fusion Cancers
Comprehensive molecular diagnosis using whole genome and RNA sequencing of patients with advanced cancers as part of the NCT/DKTK MASTER program led to the identification of cancer-driving NRG1 fusions in a significant proportion of KRAS wild type pancreatic cancers. NRG1 rearrangements drive cancer development through ErbB receptor-mediated signaling pathway activation, as was shown when patients with NRG1-rearranged pancreatic cancer responded to ErbB inhibitor treatment.
NRG1 fusions are very rare but have now been detected in a broad range of malignant diseases. During a Phase II study, we plan to investigate the effectiveness of the pan-Erb inhibitor afatinib in advanced NRG1-rearranged malignant cancers once standard treatment has failed, at a number of centers in Germany. Patients with NRG1-positive tumors who meet the eligibility criteria can take part in the trial and will receive afatinib monotherapy.
Dr. Christoph Heining
Senior Attending Physician, University of Tübingen
Prof. Dr. med. Richard Schlenk
Senior Physician of the Department of Hematology, Oncology and Rheumatology, University Hospital Heidelberg
In the multicenter “AMPLIFY NEOVAC” clinical study DKTK investigators explore a combination immunotherapy for treatment of aggressive brain tumors, malignant glioma. The approach is to boost tumor vaccination, previously developed within DKTK, with so-called immune checkpoint inhibitors (ICIs), which have shown impressive therapeutic activity for other tumors by unblocking the patient’s own immune system. In this trial the immunotherapy will be initiated before a planned resection. The aim of the study is to assess efficacy and to analyze intratumoral anti-tumor immune effects of the combined vaccination/ICI treatment using detailed molecular and immunological studies. These analyses are expected to reveal important mechanisms of response and resistance to targeted immunotherapy in brain tumors.
Despite increasing application and success of personalized treatment in medical oncology, little progress has been made in personalized surgical cancer therapy. The ARMANI trial presents the first prospective, randomized trial to evaluate effectiveness and safety of molecular-guided resection in patients with colorectal liver metastasis (CRLM). While CRLM might be removed independently of the liver’s segmental borders, retrospective data favor anatomic resections in the subgroup of patients with a mutation in the RAS oncogene. Therefore, the ARMANI trial will test the hypothesis, if an anatomic resection (AR) improves long-term outcome vs. a non-anatomical resection (NAR) in patients undergoing surgery for RAS-mutated CRLM. The trial will be carried out among 11 high-volume centers of hepato-biliary surgery in Germany. A total of 220 patients will be enrolled and randomized in a 1:1 ratio to undergo an AR vs. NAR. The primary endpoint is intrahepatic disease-free survival (iDFS). In addition, the study will provide important data on perioperative outcomes and quality of life for both surgical techniques. Given the trend among liver surgeons to aim for parenchymal-sparing operations to preserve liver parenchyma, a positive trial will be practice changing and present the first piece of high-level evidence on benefits of personalized surgical therapy guided by the tumor’s mutational profile in patients with CRLM.
Glioblastomas are particularly aggressive, and generally incurable, brain tumors. The CAR2BRAIN trial treats patients with an HER2-positive glioblastoma who have suffered a relapse. The research team uses genetically modified natural killer cells (NK cells) with a chimeric antigen receptor (CAR) that enables them to detect the HER2 antigen and selectively attack glioblastoma cells. Since the HER2 antigen is often formed by glioblastoma cells but is not detected in healthy brain tissue, it makes a good target for cellular immunotherapy.
The NK cells are injected into the edge of the surgical cavity during the resection operation. The idea is that they will attack any remaining tumor cells directly and also activate the patient’s own immune system against them. In the trial’s expansion cohort, CAR NK cells will also be repeatedly administered into the resection cavity via a reservoir and catheter. The DKTK’s ‘upgrade project’ will enable a detailed characterization of the immune architecture changes triggered by the CAR NK cell therapy in the blood, reservoir fluid and tumor tissue. In addition, the immune response produced by the CAR NK therapy alone will be compared with the result of a combined therapy that also involves immune checkpoint blockade.
Clonal hematopoiesis is a hallmark of hematologic malignancy, but can also be seen in healthy elderly people. This so-called “clonal hematopoiesis of indeterminate potential” (CHIP) is considered as a risk factor for stem cell-driven hematological diseases, including the myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). In this project, DKTK scientists join forces to investigate the role of the bone/bone marrow niche in the evolution of CHIP in elderly patients. The aim of the interdisciplinary study is to comprehensively characterize all components of the stem cell niches in the bone marrow in blood-healthy elderly people and patients with MDS/AML. For this purpose, an extensive collection of biosamples from the BoHemE study (Bone and Hematology in the Elderly) is available. With the help of high-throughput technologies, the CHOICE team will trace the molecular and cellular changes in the hematological compartment and the bone marrow microenvironment in CHIP towards MDS/AML. The researchers aim to define factors and key mechanisms that drive clonal hematopoiesis and malignant evolution of the mutant blood stem cells. The project also aims to elucidate the relationship between bone health and impaired hematopoiesis. Functional investigations using patient-derived xenograft models and 3D cell culture models are planned to evaluate the impact of an altered microenvironment on stem cell clonal evolution. The findings from the CHOICE project could help to better predict and perhaps prevent the transformation of a pre-leukemic clone to leukemia in CHIP patients.
Precision medicine in oncological surgery: Identification of predictive biomarkers for individualized surgical treatment of gastrointestinal tumors.
In the treatment of gastrointestinal tumors, especially in colorectal and pancreatic cancer (CRC and PDAC), local recurrences and long-distance metastases present a major clinical challenge. By now research has focused primarily on molecular biomarkers to initiate a personalized treatment in the sense of precision oncology. However, these treatments are almost exclusively of systemic nature, while localised forms of therapy such as surgery or radiotherapy are much less individualized. Surgical resection as part of a multimodal therapy concept is the central element of the treatment of gastrointestinal tumors. It is known that tumors prone to local recurrence can often be curatively removed by radical surgery, while tumors prone to distant metastases may be treated better by more gentle surgery in combination with early systemic therapy. However, the technique of surgical resection is largely independent of the patient.
The aim of this DKTK-wide research project is to introduce personalized oncology in surgery. To this end, molecular biomarkers that predict the recurrence behavior of GI tumors at an early stage need to be identified, so that this knowledge can be incorporated into the surgical decision. Despite the enormous clinical potential, the area is heavily under-researched. To address this enormous task, all surgical departments of the DKTK framework as well as selected non-surgical groups with unique expertise have formed a consortium which is unparalleled in surgical expertise and annual caseload. Parallel transcriptomic, proteomic and immunopeptidomic analyses from a large cohort of surgical patients together with a detailed follow-up allow to build up a comprehensive database. In specific scientific projects, the "DKTK Surgery" initiative will identify and validate molecular biomarkers in primary tumors as well as circulating tumor cells that allow the physician to predict the recurrence pattern (local vs. distant) in CRC and PDAC. This will enable patient-tailored surgical treatments for two of the most common and deadly solid cancers.
A particularly aggressive form of breast cancer is the so-called triple negative breast cancer (TNBC). Patients with this type of tumor usually receive treatment with chemotherapy before surgical removal. While in some cases this treatment sequence leads to a massive reduction in the size of the tumor, it offers little or no benefit to other patients. In the past, attempts have been made to identify subgroups of TNBC based on RNA sequencing that respond differently to chemotherapy. However, these postulated groups are still not clinically applied in the diagnostic routine.
A new method to classify malignant tumor diseases is the analysis of genome wide DNA methylation. DNA methylation is a dynamic modification of genetic information that can influence gene activity. By using artificial intelligence, complex patterns can be recognized in the DNA methylation profile of tumors, which can provide information about the origin of a tumor cell. In recent studies, new, prognostically relevant tumor subgroups have been found, particularly in the area of brain tumors.
In cooperation with the German Breast Group (GBG), the extensive analysis of the DNA methylation profile of 400 patients from the GeparOcto (G8) study will be used to identify possible new subclasses of TNBCs and evaluate their significance in terms of predicting the response to chemotherapy. This analysis will be complemented by RNA sequencing in order to be able to make a comparison with the groups postulated so far.
Prof. Dr. med. David Capper
Charité – Universitätsmedizin Berlin
The German-wide INFORM (for children with relapsed cancers) and MASTER (for young adults with refractory cancers and patients with rare tumors) registry studies stratify patients based on genome and transcriptome sequencing signatures as well as epigenetic profiling for experimental therapies. Both programs follow their patients to obtain a comprehensive assessment about the usefulness of broad individualized molecular profiling in patient care. However, data for the functionally and therapeutically important layer of the proteome is currently not included.
Aim of the INFORM / MASTER project is to perform comprehensive quantitative proteome expression profiling in a set of initially 200 sarcoma patients included in the INFORM or MASTER program. The profiling data will be discussed in the molecular tumor board, and treatment recommendations based on the newly integrated proteogenomic profiling data will be compared to “conventional” genomic profiling. By this approach, information will be obtained, if a) proteomic profiling is feasible in the context of large-scale personalized patient stratification programs, b) the additional proteomic information adds to or changes current recommendation practice in molecular tumor boards, c) recommendations based on proteomes or proteogenomes correlate stronger with response to selected experimental therapies in sarcomas than those based on genomics/epigenomics/transcriptomics alone (exploratory) and d) which recurrently altered non-genomically activated signalling pathways do exist in sarcomas.
JIP – Joint Imaging Platform
Distributed IT Infrastructure for Multicenter Cohort Analysis in Imaging
The Joint Imaging Platform aims to introduce a technical infrastructure which enables modern and decentralized research in the field of imaging within DKTK. The main focus is on using and evaluating modern machine learning methods for oncological (medical) research projects. In line with CCP-IT and RadPlanBio, JIP also constitutes a strategic initiative within DKTK. The common infrastructure will strengthen the cooperation between the participating hospitals as well as multicenter studies.
Imaging procedures within radiology and nuclear medicine play an increasingly important role in cancer research, both in diagnostics and treatment monitoring of oncological diseases. This field is developing constantly and quickly. The enormous progress in the evolution of artificial intelligence also leads to considerable development in radiological research. The automatic analysis of image data, such as tumor characterization by means of Radiomics, enables the extraction of the most diverse and highly complex information. Afterwards, this information can be correlated with clinical data in order to obtain new findings regarding diseases or even to evaluate the individual treatment situation (Precision Medicine).
In this context, the JIP complies with the highest data protection requirements as it focuses on the distribution of processing methods (algorithms) instead of personal data. The local image data are protected with a state-of-the-art encryption system and are stored within the clinical IT infrastructure of the individual locations at any time. In case data exchange might be necessary within the context of multicenter studies, this can be done – upon the patients‘ agreement - in a pseudonymized way.
More information can be accessed via the website of the "Joint Imaging Platform".
In healthy cells, a number of different processes ensure that damage or mutations to DNA are repaired efficiently. In cancer cells of various tumor entities, however, genes whose products are involved in one of these repair processes can also suffer somatic mutation. These cells then lose some of their DNA repair ability.
If it is the homologous recombination repair system that is affected in this way, the cells are particularly sensitive to a group of drugs called Poly(ADP-ribose) polymerase inhibitors (PARP inhibitors). PARP inhibitors prevent cancer cells from being able to repair themselves, e.g. as a result of DNA damage caused by chemotherapy treatments, and are already used to treat a number of different types of cancer. One such form of acquired sensitivity to a particular group of drugs is called synthetic lethality.
However, we do not know all the genes or mutations involved in synthetic lethality where PARP inhibitors are concerned. Other biological processes besides mutations, such as hypermethylation of a gene promoter involved in homologous recombination, may contribute to their inactivation. This means that it is not possible using current technical methods, including high-throughput technologies, to systematically identify all the causes of loss of homologous recombination function. On the other hand, these methods can identify a large number of ‘passenger’ mutations that arise following the repair defect. We have developed an integrated genomic biomarker that can detect the fingerprint of this repair defect on the genome of tumor cells with the help of pattern recognition, thereby increasing precision levels when detecting DNA repair defects. Subsequently, we designed a clinical trial in which patients who have tested positive with this biomarker, are treated with a synergistic combination of a PARP inhibitor and matched drug.
In future, as well as conducting a broad, in-depth genomic characterization of the samples from these treated patients, we hope to (i) gain a better understanding of the biological process of DNA repair via homologous recombination, (ii) improve the precision of our biomarker, (iii) improve predictions of the effectiveness of synthetic lethality drugs in DNA repair defect cases, (iv) investigate resistance development mechanisms to these drugs and prevent them occurring in patients, and (v) find new synergistic therapies.
The DKTK project 'Molecular Stratification Program' at the National Center for Tumour Diseases (NCT) in Heidelberg focuses on customized therapies. The term 'stratification' refers to the initiative to assign patients with the same initial diagnosis to subgroups according to molecular results in order to be able to offer them a tailored therapy. The project promotes the development of a central database containing gene defects and changes in gene activity of tumour cells. The tumour profiles will help hospitals to tailor therapy for individual patients.
In this project, we aim to understand PET/CT-based imaging features and their molecular and clinical correlates pre/post therapy in gastroesophageal junction (GEJ) adenocarcinoma. In the DKTK-funded MEMORI trial we evaluated PET-directed chemo- (CTX) or salvage radiochemotherapy (CRT) and assembled sequential high-quality tumor tissue at PET/CT imaging time points pre/post therapy. The fully recruited trial, met its primary endpoint of improved negative surgical margins (R0 rate) upon salvage intensified CRT not responding to standard neoadjuvant CTX determined by PET response 14 days after CTX initiation. Salvage CRT also led to a highly increased rate of pathologic complete remissions (pCR) suggesting high local activity of CRT. However, an important result from the trial was distant recurrence in a subgroup of patients despite high R0 resection and pCR rates. Thus, current standard-of care PET/CT or histological diagnostics do not identify high- risk patients with bad outcome and their distinguishing tumor features remain unknown.
We here aim to investigate molecular subtypes and tumor metabolism patterns in the MEMORI patient cohort. We will focus on understanding therapy-induced molecular dynamics. We will correlate these findings with PET-CT derived metabolic and anatomical imaging data using standard (SUVmax/mean) and advanced (radiomics) techniques leveraging the infrastructure provided by the Joint Imaging Platform (JIP) to perform an integrated analysis of clinical, molecular and imaging data. The available clinical and multimodal imaging data combined with available tumor tissue before, during and after neoadjuvant therapy are a unique opportunity to address fundamental questions of imaging and tissue- based features in tumor metabolism, heterogeneity and therapy response.
Prof Dr Jens Sieveke
University Medicine Essen/ DKFZ
Image-based subtyping of locally advanced pancreatic cancer
Pancreatic ductal adenocarcinoma (PDAC) has a very poor prognosis because the tumor is often already at an advanced stage when first diagnosed and because of resistance to conventional chemotherapy treatments. The genome, transcriptome and proteome of these tumors are highly heterogeneous. This heterogeneity is reflected in a complex tissue architecture with different molecular phenotypes: the classic phenotype with a somewhat better response rate, and the particularly aggressive quasi-mesenchymal phenotype.
There are currently no reliable biomarkers to differentiate between these subtypes in routine clinical practice. This again is partly because of the high degree of heterogeneity, which makes it harder to ensure representative sampling and draw histopathological and molecular conclusions. Medical imaging provides information on total tumor volume. Recent developments in the field of machine learning (e.g. radiomics) are showing promising results in terms of non-invasive tumor characterization and risk stratification based on medical imaging. Translational development and testing of these kinds of prognostic models require a standardized data matrix.
The NEOLAP phase II clinical trial (NCT02125136) is one of the biggest randomized prospective trials that aims to evaluate intensified neoadjuvant chemotherapy in locally advanced PDAC. The image datasets, tumor samples and clinical information collected prospectively for the NEOLAP trial offer a unique opportunity to develop and test the image-based algorithms mentioned above.
Prof. Dr. Jens Sieveke
University Medicine Essen/ DKFZ
Dr. Jens Kleesiek
Next Gen LOGGIC
Pediatric low-grade gliomas (pLGGs), including pilocytic astrocytomas (PAs), are the most common childhood brain tumors. While the overall survival rate is very good, progression-free survival, especially in subtotal resection cases, is low. Chemotherapy is currently the standard treatment, but it is associated with secondary damage. Moreover, tumor-associated morbidity is particularly high in cases that cannot be fully resected and do not respond well to conservative therapy. Despite the very good overall survival rate, therefore, there is a need to establish new therapy approaches to significantly improve the quality of life of patients with this chronic disease. The researchers working on the DKTK’s Next Gen LOGGIC project aim to generate preclinical data in collaboration with the LOGGIC pLGG trial that will form the basis for next-generation clinical trials. Working with the Berlin, Düsseldorf, Freiburg and Heidelberg sites, they are investigating the signaling pathways, the proteome and the response to novel low-molecular substances in pLGG models and primary tumors. Integration with the molecular and clinical data from LOGGIC Core and the ongoing clinical trial for pLGGs (LOGGIC trial) ensures the translational value of the preclinical data.
The multi-center first-user study to investigate the safety, tolerance and effectiveness of the bispecific PSMAxCD3 antibody CC-1 in patients with prostate cancer is being carried out at University Hospital Tübingen in its Clinical Collaboration Unit Translational Immunology, and at other DKTK sites in Germany.
Bispecific antibodies are protein molecules with two different binding sites. In the case of the bispecific PSMAxCD3 antibody CC-1, one binding site addresses the prostate-specific membrane antigen (PSMA), which presents on the surface of aggressive prostate cancer cells. The other arm binds to a protein that is responsible for activating defense cells called T cells. When the antibody binds to the two binding sites, it activates the body’s immune response. In addition, CC-1 has a special characteristic: it also binds to the tumor’s blood vessels, creating a dual anti-tumor effect.
A serious side effect of the bispecific antibodies currently available is excessive activation of the immune system. This causes cytokine release syndrome (CRS). CRS can lead to a wide range of symptoms, including in particular fever and cardiovascular problems. When CRS occurs, the patient is usually treated with tocilizumab, an antibody that lessens the excessive immune system response.
For the study, the CC-1 antibody was optimized to minimize the risk of an unwanted immune activation. In addition, patients participating in the trial are given tocilizumab as a preventative measure to start with, in order to prevent CRS occurring in the first place.
Prof. Dr. med. Richard Schlenk
Senior Physician of the Department of Hematology, Oncology and Rheumatology, University Hospital Heidelberg
Anti-angiogenic agents are a key element of drug therapy for patients with metastatic colorectal cancer (mCRC). Despite intensive efforts over recent years, there is still a lack of biomarkers that can predict whether these medicines will be effective. Complex interactions between the tumor cells and the surrounding stroma have made it harder to identify suitable biomarkers.
The aim of the RAMTAS study-related research project is to identify a molecular signature in patients with mCRC that can predict a response to anti-angiogenic therapy. To this end, researchers are analyzing tumor and blood samples from a phase II clinical trial (RAMTAS, NCT03520946) that was held at Arbeitsgemeinschaft Internistische Onkologie (AIO) that investigates the use of a monoclonal antibody against vascular endothelial growth factor receptor 2 (VEGFR-2). This receptor plays a key role in tumor neoangiogenesis and is an attractive target structure for modern molecular drugs.
There is a particular focus on the analysis of somatic gene mutations, gene expression profiles and post-translational protein modifications. In addition, IT-assisted machine learning and data mining make it possible to increase our understanding of the complex interactions between the individual profiles and to explore and validate the prognostic value regarding the effectiveness of the anti-angiogenic agent.
The SoraTram trial is a basket study designed to evaluate a new concept for treating a wide range of tumors with kinase-inactivating BRAF mutations. The BRAF enzyme is an important link in the RAS/RAF/MEK/ERK signaling chain that promotes cell division and, as a result of mutations, is present in a hyperactive state in many tumors. Drugs that inhibit the hyperactive oncoprotein BRAF V600E are already used to treat a number of cancers. The sequencing of tumor genomes has also identified increasing numbers of non-V600E mutations. In most cases, the clinical significance of these and their susceptibility to drugs have not yet been described. A sub-group of these non-V600E BRAF mutations inhibit the enzyme activity of the BRAF kinase. Paradoxically, however, these inactive BRAF mutants activate the ERK signaling chain and stimulate the onset of tumors. Preclinical models have shown that sorafenib, a drug that was approved several years ago for the treatment of kidney and liver cancer, can block the paradoxical effect of kinase-inactive BRAF mutants. The combination of sorafenib and the inhibitor trametinib is even more effective at blocking tumor growth. The effectiveness of this SoraTram combination has already been demonstrated in an index case with a metastatic melanoma. (1)
The SoraTram study, which is planned to run at all DKTK sites, aims to
• identify patients in the DKTK MASTER network with tumors harboring non-V600 BRAF mutations
• characterize mutations in terms of their susceptibility to BRAF, CRAF and MEK inhibitors and combinations of these
• treat 30 DKTK MASTER patients harboring non-V600 BRAF mutations that respond to CRAF/MEK inhibition following in vitro testing, with sorafenib and trametinib in a prospective multicenter Phase II trial
Comprehensive tumor sequencing in the DKTK network, especially through the MASTER program, is currently identifying many novel BRAF mutations whose significance remains unclear. These will be validated and verified during the study, both in terms of their kinase-inactivating potential and their oncogenic potential and susceptibility to pharmacological intervention. The cataloging of all non-V600E mutations can then be used for personalized therapy recommendations.
(1) Hoefflin R, Geißler AL, Fritsch R, Claus R, Wehrle J, Metzger P, et al. Personalized clinical decision making through implementation of a molecular tumor board – a German single-center experience. JCO Precision Oncology. 2018; DOI: 10.1200/PO.18.00105 JCO Precision Oncology - published online August 16, 2018