TY - JOUR A1 - Lichthardt, Sven A1 - Kerscher, Alexander A1 - Dietz, Ulrich A. A1 - Jurowich, Christian A1 - Kunzmann, Volker A1 - von Rahden, Burkhard H. A. A1 - Germer, Christoph-Thomas A1 - Wiegering, Armin T1 - Original article: role of adjuvant chemotherapy in a perioperative chemotherapy regimen for gastric cancer JF - BMC Cancer N2 - Background Multimodal treatment strategies – perioperative chemotherapy (CTx) and radical surgery – are currently accepted as treatment standard for locally advanced gastric cancer. However, the role of adjuvant postoperative CTx (postCTx) in addition to neoadjuvant preoperative CTx (preCTx) in this setting remains controversial. Methods Between 4/2006 and 12/2013, 116 patients with locally advanced gastric cancer were treated with preCTx. 72 patients (62 %), in whom complete tumor resection (R0, subtotal/total gastrectomy with D2-lymphadenectomy) was achieved, were divided into two groups, one of which receiving adjuvant therapy (n = 52) and one without (n = 20). These groups were analyzed with regard to survival and exclusion criteria for adjuvant therapy. Results Postoperative complications, as well as their severity grade, did not correlate with fewer postCTx cycles administered (p = n.s.). Long-term survival was shorter in patients receiving postCTx in comparison to patients without postCTx, but did not show statistical significance. In per protocol analysis by excluding two patients with perioperative death, a shorter 3-year survival rate was observed in patients receiving postCTx compared to patients without postCTx (3-year survival: 71.2 % postCTx group vs. 90.0 % non-postCTx group; p = 0.038). Conclusion These results appear contradicting to the anticipated outcome. While speculative, they question the value of post-CTx. Prospectively randomized studies are needed to elucidate the role of postCTx. KW - gastric cancer KW - chemotherapy KW - neoadjuvant KW - multimodal KW - complication KW - adjuvant KW - risk factor KW - survival Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-147743 VL - 16 IS - 650 ER - TY - JOUR A1 - Pelz, Joerg O. W. A1 - Chua, Terence C. A1 - Esquivel, Jesus A1 - Stojadinovic, Alexander A1 - Doerfer, Joerg A1 - Morris, David L. A1 - Maeder, Uwe A1 - Germer, Christoph-Thomas A1 - Kerscher, Alexander G. T1 - Evaluation of Best Supportive Care and Systemic Chemotherapy as Treatment Stratified according to the retrospective Peritoneal Surface Disease Severity Score (PSDSS) for Peritoneal Carcinomatosis of Colorectal Origin N2 - Background: We evaluate the long-term survival of patients with peritoneal carcinomatosis (PC) treated with systemic chemotherapy regimens, and the impact of the of the retrospective peritoneal disease severity score (PSDSS) on outcomes. Methods: One hundred sixty-seven consecutive patients treated with PC from colorectal cancer between years 1987-2006 were identified from a prospective institutional database. These patients either received no chemotherapy, 5-FU/Leucovorin or Oxaliplatin/Irinotecan-based chemotherapy. Stratification was made according to the retrospective PSDSS that classifies PC patients based on clinically relevant factors. Survival analysis was performed using the Kaplan-Meier method and comparison with the log-rank test. Results: Median survival was 5 months (95% CI, 3-7 months) for patients who had no chemotherapy, 11 months (95% CI, 6-9 months) for patients treated with 5 FU/LV, and 12 months (95% CI, 4-20 months) for patients treated with Oxaliplatin/Irinotecan-based chemotherapy. Survival differed between patients treated with chemotherapy compared to those patients who did not receive chemotherapy (p = 0.026). PSDSS staging was identified as an independent predictor for survival on multivariate analysis [RR 2.8 (95%CI 1.5-5.4); p < 0.001]. Conclusion: A trend towards improved outcomes is demonstrated from treatment of patients with PC from colorectal cancer using modern systemic chemotherapy. The PSDSS appears to be a useful tool in patient selection and prognostication in PC of colorectal origin. KW - Krebs KW - peritoneal carcinomatosis KW - colorectal cancer Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-67875 ER - TY - JOUR A1 - Seyfried, Florian A1 - von Rahden, Burkhard H. A1 - Miras, Alexander D. A1 - Gasser, Martin A1 - Maeder, Uwe A1 - Kunzmann, Volker A1 - Germer, Christoph-Thomas A1 - Pelz, Jörg O. W. A1 - Kerscher, Alexander G. T1 - Incidence, time course and independent risk factors for metachronous peritoneal carcinomatosis of gastric origin – a longitudinal experience from a prospectively collected database of 1108 patients JF - BMC Cancer N2 - Background Comprehensive evidence on the incidence, time course and independent risk factors of metachronous peritoneal carcinomatosis (metaPC) in gastric cancer patients treated with curative intent in the context of available systemic combination chemotherapies is lacking. Methods Data from a prospectively collected single-institutional Center Cancer Registry with 1108 consecutive patients with gastric adenocarcinoma (GC), clinical, histological and survival data were analyzed for independent risk factors and prognosis with focus on the development of metaPC. Findings were then stratified to the time periods of treatment with surgery alone, 5-Fluorouracil-only and contemporary combined systemic perioperative chemotherapy strategies, respectively. Results Despite R0 D2 gastrectomy (n = 560), 49.6% (±5.4%) of the patients were diagnosed with tumour recurrence and 15.5% (±1.8%) developed metaPC after a median time of 17.7 (15.1-20.3) months after surgery resulting in a tumour related mortality of 100% with a median survival of 3.0 months (2.1 – 4.0). Independent risk factors for the development of metaPC were serosa positive T-category, nodal positive-status, signet cell and undifferentiated gradings (G3/G4). Contemporary systemic combination chemotherapy did not improve the incidence and prognosis of metaPC (p = 0.54). Conclusions Despite significant improvements in the overall survival for the complete cohort with gastric cancer over time, those patients with metaPC did not experience the same benefits. The lack of change in the incidence, and persistent poor prognosis of metaPC after curative surgery expose the need for further prevention and/or improved treatment options for this devastating condition. KW - recurrence survival KW - metachronous KW - peritoneal carcinomatosis KW - gastric cancer KW - risk factors KW - perioperative chemotherapy Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-125014 VL - 15 IS - 73 ER - TY - JOUR A1 - Duhr, Carolin D. A1 - Kenn, Werner A1 - Kickuth, Ralph A1 - Kerscher, Alexander G. A1 - Germer, Christoph-Thomas A1 - Hahn, Dietbert A1 - Pelz, Joerg O. W. T1 - Optimizing of preoperative computed tomography for diagnosis in patients with peritoneal carcinomatosis JF - World Journal of Surgical Oncology N2 - Background and Objective This study evaluates whether Computer Tomography is an effective procedure for preoperative staging of patients with Peritoneal Carcinomatosis. Method A sample of 37 patients was analyzed with contrast enhanced abdominal Computer Tomography, followed by surgical staging. All Computer Tomography scans were evaluated 3 times by 2 radiologists with one radiologist reviewing 2 times. The efficacy of Computer Tomography was evaluated using the Spearman correlation coefficient. Correlations were analyzed by abdominopelvic region to assess results of the Peritoneal Carcinomatosis Index (PCI) aggregating the 13 regions. Surgical findings were compared to radiological findings. Results Results indicate high correlations between the surgical and radiological Peritoneal Carcinomatosis Indices. Analyses of the intra-class correlation between the first and second reading of one radiologist suggest high intra-observer reliability. Correlations by abdominopelvic region show higher values in the upper and middle regions and relatively lower values in the lower regions and the small bowel (correlation coefficients range between 0.418 and 0.726, p < 0.010; sensitivities range between 50% and 96%; and specificities range between 62% and 100%). Conclusion Computer Tomography represents an effective procedure in the preoperative staging of patients with PC. However, results by abdominopelvic region show lower correlation, therefore suggest lower efficacy. These results are supported by analyses of sensitivity and accuracy by lesion size. This suggests that Computer Tomography is an effective procedure for pre-operative staging but less for determining a tumor's accurate extent. KW - Carcinomatosis KW - diagnosis KW - PCI Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-138024 VL - 9 IS - 171 ER - TY - THES A1 - Kerscher, Alexander Georg T1 - Entwicklung einer mikroskopierbaren Perfusions-Kulturkammer für die Kultivierung, die In-Vitro-Vitalitäts- und die Funktionsdiagnostik von endokrinen Zellen T1 - A perfusion-culture system to cultivate and test the vitality and functional dynamics of endocrine Cells and tissues N2 - Als Therapie des Diabetes mellitus Typ II stellt die Xenotransplantation von porzinen Langerhans-Inseln in mikroverkapselter Form eine attraktive Alternative zu den täglichen Insulininjektionen dar. Kultivierung und Funktionsdiagnostik der isolierten porzinen Langerhans-Inseln sind technisch anspruchsvoll und bieten noch immer Potential für Verbesserungen. Werden die Zellen in Zellkulturflaschen über mehrere Tage kultiviert, sinkt die Vitalität unter ein akzeptables Niveau. Bei der Beurteilung der Vitalität und Funktion der Inseln gehen wertvolle Zellen für eine spätere Transplantation verloren. Dies schränkt eine ausgiebige Diagnostik vor der Transplantation ein. Ziel der Arbeit ist es, eine Möglichkeit zur Verbesserung der Kulturbedingungen zu finden und exakte Ergebnisse bei der Funktions- und Vitalitätsdiagnostik ohne Verlust von Zellen zu erreichen. Vorversuche konnten beweisen, dass eine Verbesserung der Vitalität von Langerhans-Inseln in Kultur an der Methode der Kultivierung in Zellkulturflaschen scheitert. Stattdessen wurde das Prinzip der Perfusionskultur in spezialisierten Behältnissen für die systematische Verbesserung der Kulturbedingungen und zur genaueren Diagnostik mittels Mikroskopie und Funktionsdiagnostik gewählt. Mit einem solchen System ist sowohl Kultivierung als auch Funktions- und Vitalitätsdiagnostik in einem Behälter möglich. Beim Prinzip der Perfusionskultur befindet sich das Medium stets in Bewegung um die Zellen und Gewebe und sorgt so für einen kontinuierlichen Zustrom exakt definierten Mediums und permanenten Abtransport der Stoffwechselprodukte. Im Rahmen dieser Arbeit wurde für die Anforderungen im eigenen Labor ein maßgeschneidertes System mit mehreren Versionen von Behältnissen für Perfusionskulturen entwickelt, deren jeweils neuere Version auf den Erfahrungen mit den Vorversionen aufbaut. In die Entwicklung fließen ebenso umfangreiche theoretische Überlegungen ein, sowie systematische Tests zu den physikalischen Eigenschaften der Behältnisse. Die zuletzt entwickelte ist die Version V6SMTE, die in der Arbeit „Würzburger Kammer“ genannt wird. Dieser Behälter ist aus Edelstahl, mit einem Deckglas zur makro- und mikroskopischen Begutachtung, Zu- und Abläufen und einem Anschluss zum Entfernen von Gasblasen. Im Inneren befindet sich ein Einsatz, der eine stufenlose Regulierung des Volumens um die Zellen ermöglicht, so dass für Kultur und Funktionsprüfung bzw. Mikroskopie jeweils optimale Bedingungen erreicht werden. Weiterhin kann über einen Temperatursensor die Temperatur im Inneren des Behälters gemessen und über Heizelemente an der Außenwand computergesteuert reguliert werden. Die Zellen und Gewebe können auf unterschiedlichen Trägermaterialien eingesetzt werden. Während der Kultur kann ein Deckel geöffnet und die Zellen manipuliert werden. Das System ist unabhängig vom Brutschrank, ist sterilisierbar und wieder verwendbar. Kultiviert wurde endokrines Gewebe (isolierte Langerhans-Inseln, humanes Nebenschilddrüsengewebe). Dieses wurde zur Funktionsprüfung mit verschiedenen Mediatoren stimuliert, das Medium fraktioniert aufgefangen und sein Hormongehalt mit ELISA oder RIA bestimmt. Die Zellen wurden nativ und mit Fluoreszenzfarbstoffen (FDA, PI) gefärbt mit bis zu 400facher Vergrößerung unter dem Auflichtmikroskop beurteilt. Im Zuge der Auswertung der anfallenden Proben auf ihren Insulingehalt wurde für diese Arbeit ein Insulin-ELISA entwickelt, der bei vergleichbarer Genauigkeit deutlich günstiger ist, als der bisher verwendete kommerzielle ELISA. Mit der Würzburger Kammer kultivierte Langerhans-Inseln zeigten eine vergleichbare Vitalität im Vergleich zur Zellkulturflasche, die mit der Würzburger Kammer gewonnenen Perifusionskurven sind in hohem Maß reproduzierbar, Zusammenhänge von Höhe der Glukoseexposition und Kultivierungsdauer mit der Insulinausschüttungskurve konnten eindrucksvoll beschrieben werden. Erstmals wurde auch im eigenen Labor die aus der Literatur bekannte paradoxe Insulinausschüttung beschrieben. Beispielhaft für andere endokrine Gewebe wurde humanes Nebenschilddrüsengewebe erfolgreich in der Würzburger Kammer kultiviert und Vitalitäts- und Funktionsdiagnostik unterzogen. Das Kultursystem ermöglicht die Kultivierung und eine komplette Analyse von Funktion, Vitalität und Morphologie von endokrinen Zellen. Es kann somit in idealer Weise zur Verbesserung der Kulturbedingungen und zur Beurteilung von endokrinen Zellen vor der Transplantation herangezogen werden. N2 - Therapy of the diabetes mellitus typ II by xenotransplantation of microencapsuled porcine Islets of Langerhans is an attractive alternative to daily injections of insulin. However cultivation and functional diagnostics of these isolated porcine Islets of Langerhans are challenging and there is still potential for improvement. Islets cultivated in culture-flasks for more than only 3 days suffer from bad vitality and altered functionality. Cells used for performing vitality-staining and perifusion to test the functionality have to be dropped away and cannot be used for later transplantation. This delimitates quantity and quality of diagnostic procedures prior to transplantation. Goal of this study is to find a way of obtaining accurate information about vitality and viability of the Islets of Langerhans without losing cells on diagnostics and to use this information on the improvement of culture conditions. Preliminary results showed that an improvement of culture conditions cannot be achieved with cultivation of Islets of Langerhans in culture-flasks. Instead of that the perfusion-culture concept showed to be most promising for that problem because with this concept cultivation of cells as well as functional and vitality diagnostics can be performed within one single container. To meet the demands in our laboratory a special container named “Würzburger Kammer” has been developed for this study. It is made of high-grade steel with a cover slip for macro- and microscopic observation and a variable internal space to have optimum conditions for cultivation as well as perifusion and microscopy. Temperature inside the container can be controlled by a regulating system consisting of a microprocessor and a temperature sensor inside the container and a heating unit outside the container. Different carrier materials can be inserted. The top of the container can be opened while the perfusion container is in operation and cells can be manipulated. The system is a self-contained device, which has not to be operated in an incubator. Perifusion as a test for the function of the Islets of Langerhans can easily be performed by changing the media and collecing fractionated samples afterwards. Microscopy can be done with a magnification factor of up to 400. To analyse the samples collected during the perifusion for the concentration of insulin a low-priced enzyme-linked-immuno-assay was developed. In this study we proved that with the “Würzburger Kammer” it is possible to cultivate isolated porcine Islets of Langerhans as well as human Parathyroid cells and that precise vitality and functional diagnostics can be performed by microscopy and perifusion. The results of these tests were more accurate and reliable than former tests using microscopy slides and doing perifusion without the “Würzburger Kammer”. So this perfusion culture system helps to improve quality of cultivation and diagnostics of islets of Langerhans prior to transplantation and allows for better results in transplantation one day. KW - Zellkultur KW - Perfusionskultur KW - Tissue Engineering KW - endokrin KW - Langerhans KW - Inselzellen KW - Perifusion KW - Nebenschilddrüsen KW - Verkapselung KW - Cellculture KW - endocrine KW - perifusion KW - perfusion-culture KW - container KW - Insulin KW - vitality-staining KW - parathyroid cells KW - tissue engineering Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-20282 ER - TY - JOUR A1 - Wiegering, Armin A1 - Isbert, Christoph A1 - Dietz, Ulrich A. A1 - Kunzmann, Volker A1 - Ackermann, Sabine A1 - Kerscher, Alexander A1 - Maeder, Uwe A1 - Flentje, Michael A1 - Schlegel, Nicolas A1 - Reibetanz, Joachim A1 - Germer, Christoph-Thomas A1 - Klein, Ingo T1 - Multimodal therapy in treatment of rectal cancer is associated with improved survival and reduced local recurrence - a retrospective analysis over two decades N2 - Background The management of rectal cancer (RC) has substantially changed over the last decades with the implementation of neoadjuvant chemoradiotherapy, adjuvant therapy and improved surgery such as total mesorectal excision (TME). It remains unclear in which way these approaches overall influenced the rate of local recurrence and overall survival. Methods Clinical, histological and survival data of 658 out of 662 consecutive patients with RC were analyzed for treatment and prognostic factors from a prospectively expanded single-institutional database. Findings were then stratified according to time of diagnosis in patient groups treated between 1993 and 2001 and 2002 and 2010. Results The study population included 658 consecutive patients with rectal cancer between 1993 and 2010. Follow up data was available for 99.6% of all 662 treated patients. During the time period between 2002 and 2010 significantly more patients underwent neoadjuvant chemoradiotherapy (17.6% vs. 60%) and adjuvant chemotherapy (37.9% vs. 58.4%). Also, the rate of reported TME during surgery increased. The rate of local or distant metastasis decreased over time, and tumor related 5-year survival increased significantly with from 60% to 79%. Conclusion In our study population, the implementation of treatment changes over the last decade improved the patient’s outcome significantly. Improvements were most evident for UICC stage III rectal cancer. KW - Rectal cancer KW - Improved survival KW - TME Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-110606 ER - TY - JOUR A1 - Stangl, Stephanie A1 - Haas, Kirsten A1 - Eichner, Felizitas A. A1 - Grau, Anna A1 - Selig, Udo A1 - Ludwig, Timo A1 - Fehm, Tanja A1 - Stübner, Tanja A1 - Rashid, Asarnusch A1 - Kerscher, Alexander A1 - Bargou, Ralf A1 - Hermann, Silke A1 - Arndt, Volker A1 - Meyer, Martin A1 - Wildner, Manfred A1 - Faller, Hermann A1 - Schrauder, Michael G. A1 - Weigel, Michael A1 - Schlembach, Ulrich A1 - Heuschmann, Peter U. A1 - Wöckel, Achim T1 - Development and proof-of-concept of a multicenter, patient-centered cancer registry for breast cancer patients with metastatic disease — the “Breast cancer care for patients with metastatic disease” (BRE-4-MED) registry JF - Pilot and Feasibility Studies N2 - Background: Patients with metastatic breast cancer (MBC) are treated with a palliative approach with focus oncontrolling for disease symptoms and maintaining high quality of life. Information on individual needs of patients andtheir relatives as well as on treatment patterns in clinical routine care for this specific patient group are lacking or arenot routinely documented in established Cancer Registries. Thus, we developed a registry concept specifically adaptedfor these incurable patients comprising primary and secondary data as well as mobile-health (m-health) data. Methods: The concept for patient-centered “Breast cancer care for patients with metastatic disease”(BRE-4-MED)registry was developed and piloted exemplarily in the region of Main-Franconia, a mainly rural region in Germanycomprising about 1.3 M inhabitants. The registry concept includes data on diagnosis, therapy, progression, patient-reported outcome measures (PROMs), and needs of family members from several sources of information includingroutine data from established Cancer Registries in different federal states, treating physicians in hospital as well as inoutpatient settings, patients with metastatic breast cancer and their family members. Linkage with routine cancerregistry data was performed to collect secondary data on diagnosis, therapy, and progression. Paper and online-basedquestionnaires were used to assess PROMs. A dedicated mobile application software (APP) was developed to monitorneeds, progression, and therapy change of individual patients. Patient’s acceptance and feasibility of data collection inclinical routine was assessed within a proof-of-concept study. Results: The concept for the BRE-4-MED registry was developed and piloted between September 2017 and May 2018.In total n= 31 patients were included in the pilot study, n= 22 patients were followed up after 1 month. Recordlinkage with the Cancer Registries of Bavaria and Baden-Württemberg demonstrated to be feasible. The voluntary APP/online questionnaire was used by n= 7 participants. The feasibility of the registry concept in clinical routine waspositively evaluated by the participating hospitals. Conclusion: The concept of the BRE-4-MED registry provides evidence that combinatorial evaluation of PROMs, needsof family members, and raising clinical parameters from primary and secondary data sources as well as m-healthapplications are feasible and accepted in an incurable cancer collective. KW - Metastatic breast cancer KW - Patient-centered registry KW - Patient’s needs KW - m-Health KW - Health care service research Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-229149 VL - 6 ER - TY - JOUR A1 - Loda, Sophia A1 - Krebs, Jonathan A1 - Danhof, Sophia A1 - Schreder, Martin A1 - Solimando, Antonio G. A1 - Strifler, Susanne A1 - Rasche, Leo A1 - Kortüm, Martin A1 - Kerscher, Alexander A1 - Knop, Stefan A1 - Puppe, Frank A1 - Einsele, Hermann A1 - Bittrich, Max T1 - Exploration of artificial intelligence use with ARIES in multiple myeloma research JF - Journal of Clinical Medicine N2 - Background: Natural language processing (NLP) is a powerful tool supporting the generation of Real-World Evidence (RWE). There is no NLP system that enables the extensive querying of parameters specific to multiple myeloma (MM) out of unstructured medical reports. We therefore created a MM-specific ontology to accelerate the information extraction (IE) out of unstructured text. Methods: Our MM ontology consists of extensive MM-specific and hierarchically structured attributes and values. We implemented “A Rule-based Information Extraction System” (ARIES) that uses this ontology. We evaluated ARIES on 200 randomly selected medical reports of patients diagnosed with MM. Results: Our system achieved a high F1-Score of 0.92 on the evaluation dataset with a precision of 0.87 and recall of 0.98. Conclusions: Our rule-based IE system enables the comprehensive querying of medical reports. The IE accelerates the extraction of data and enables clinicians to faster generate RWE on hematological issues. RWE helps clinicians to make decisions in an evidence-based manner. Our tool easily accelerates the integration of research evidence into everyday clinical practice. KW - natural language processing KW - ontology KW - artificial intelligence KW - multiple myeloma KW - real world evidence Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-197231 SN - 2077-0383 VL - 8 IS - 7 ER - TY - JOUR A1 - Marquardt, André A1 - Solimando, Antonio Giovanni A1 - Kerscher, Alexander A1 - Bittrich, Max A1 - Kalogirou, Charis A1 - Kübler, Hubert A1 - Rosenwald, Andreas A1 - Bargou, Ralf A1 - Kollmannsberger, Philip A1 - Schilling, Bastian A1 - Meierjohann, Svenja A1 - Krebs, Markus T1 - Subgroup-Independent Mapping of Renal Cell Carcinoma — Machine Learning Reveals Prognostic Mitochondrial Gene Signature Beyond Histopathologic Boundaries JF - Frontiers in Oncology N2 - Background: Renal cell carcinoma (RCC) is divided into three major histopathologic groups—clear cell (ccRCC), papillary (pRCC) and chromophobe RCC (chRCC). We performed a comprehensive re-analysis of publicly available RCC datasets from the TCGA (The Cancer Genome Atlas) database, thereby combining samples from all three subgroups, for an exploratory transcriptome profiling of RCC subgroups. Materials and Methods: We used FPKM (fragments per kilobase per million) files derived from the ccRCC, pRCC and chRCC cohorts of the TCGA database, representing transcriptomic data of 891 patients. Using principal component analysis, we visualized datasets as t-SNE plot for cluster detection. Clusters were characterized by machine learning, resulting gene signatures were validated by correlation analyses in the TCGA dataset and three external datasets (ICGC RECA-EU, CPTAC-3-Kidney, and GSE157256). Results: Many RCC samples co-clustered according to histopathology. However, a substantial number of samples clustered independently from histopathologic origin (mixed subgroup)—demonstrating divergence between histopathology and transcriptomic data. Further analyses of mixed subgroup via machine learning revealed a predominant mitochondrial gene signature—a trait previously known for chRCC—across all histopathologic subgroups. Additionally, ccRCC samples from mixed subgroup presented an inverse correlation of mitochondrial and angiogenesis-related genes in the TCGA and in three external validation cohorts. Moreover, mixed subgroup affiliation was associated with a highly significant shorter overall survival for patients with ccRCC—and a highly significant longer overall survival for chRCC patients. Conclusions: Pan-RCC clustering according to RNA-sequencing data revealed a distinct histology-independent subgroup characterized by strengthened mitochondrial and weakened angiogenesis-related gene signatures. Moreover, affiliation to mixed subgroup went along with a significantly shorter overall survival for ccRCC and a longer overall survival for chRCC patients. Further research could offer a therapy stratification by specifically addressing the mitochondrial metabolism of such tumors and its microenvironment. KW - kidney cancer KW - pan-RCC KW - machine learning KW - mitochondrial DNA KW - mtDNA KW - mTOR Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-232107 SN - 2234-943X VL - 11 ER - TY - JOUR A1 - Marquardt, André A1 - Kollmannsberger, Philip A1 - Krebs, Markus A1 - Argentiero, Antonella A1 - Knott, Markus A1 - Solimando, Antonio Giovanni A1 - Kerscher, Alexander Georg T1 - Visual clustering of transcriptomic data from primary and metastatic tumors — dependencies and novel pitfalls JF - Genes N2 - Personalized oncology is a rapidly evolving area and offers cancer patients therapy options that are more specific than ever. However, there is still a lack of understanding regarding transcriptomic similarities or differences of metastases and corresponding primary sites. Applying two unsupervised dimension reduction methods (t-Distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP)) on three datasets of metastases (n = 682 samples) with three different data transformations (unprocessed, log10 as well as log10 + 1 transformed values), we visualized potential underlying clusters. Additionally, we analyzed two datasets (n = 616 samples) containing metastases and primary tumors of one entity, to point out potential familiarities. Using these methods, no tight link between the site of resection and cluster formation outcome could be demonstrated, or for datasets consisting of solely metastasis or mixed datasets. Instead, dimension reduction methods and data transformation significantly impacted visual clustering results. Our findings strongly suggest data transformation to be considered as another key element in the interpretation of visual clustering approaches along with initialization and different parameters. Furthermore, the results highlight the need for a more thorough examination of parameters used in the analysis of clusters. KW - visual clustering KW - t-SNE KW - UMAP KW - transcriptomic analysis KW - cancer KW - metastasis Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-281872 SN - 2073-4425 VL - 13 IS - 8 ER - TY - JOUR A1 - Lüke, Florian A1 - Haller, Florian A1 - Utpatel, Kirsten A1 - Krebs, Markus A1 - Meidenbauer, Norbert A1 - Scheiter, Alexander A1 - Spoerl, Silvia A1 - Heudobler, Daniel A1 - Sparrer, Daniela A1 - Kaiser, Ulrich A1 - Keil, Felix A1 - Schubart, Christoph A1 - Tögel, Lars A1 - Einhell, Sabine A1 - Dietmaier, Wolfgang A1 - Huss, Ralf A1 - Dintner, Sebastian A1 - Sommer, Sebastian A1 - Jordan, Frank A1 - Goebeler, Maria-Elisabeth A1 - Metz, Michaela A1 - Haake, Diana A1 - Scheytt, Mithun A1 - Gerhard-Hartmann, Elena A1 - Maurus, Katja A1 - Brändlein, Stephanie A1 - Rosenwald, Andreas A1 - Hartmann, Arndt A1 - Märkl, Bruno A1 - Einsele, Hermann A1 - Mackensen, Andreas A1 - Herr, Wolfgang A1 - Kunzmann, Volker A1 - Bargou, Ralf A1 - Beckmann, Matthias W. A1 - Pukrop, Tobias A1 - Trepel, Martin A1 - Evert, Matthias A1 - Claus, Rainer A1 - Kerscher, Alexander T1 - Identification of disparities in personalized cancer care — a joint approach of the German WERA consortium JF - Cancers N2 - (1) Background: molecular tumor boards (MTBs) are crucial instruments for discussing and allocating targeted therapies to suitable cancer patients based on genetic findings. Currently, limited evidence is available regarding the regional impact and the outreach component of MTBs; (2) Methods: we analyzed MTB patient data from four neighboring Bavarian tertiary care oncology centers in Würzburg, Erlangen, Regensburg, and Augsburg, together constituting the WERA Alliance. Absolute patient numbers and regional distribution across the WERA-wide catchment area were weighted with local population densities; (3) Results: the highest MTB patient numbers were found close to the four cancer centers. However, peaks in absolute patient numbers were also detected in more distant and rural areas. Moreover, weighting absolute numbers with local population density allowed for identifying so-called white spots—regions within our catchment that were relatively underrepresented in WERA MTBs; (4) Conclusions: investigating patient data from four neighboring cancer centers, we comprehensively assessed the regional impact of our MTBs. The results confirmed the success of existing collaborative structures with our regional partners. Additionally, our results help identifying potential white spots in providing precision oncology and help establishing a joint WERA-wide outreach strategy. KW - precision oncology KW - MTB KW - patient access KW - cancer care KW - outreach KW - real world data KW - outcomes research Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-290311 SN - 2072-6694 VL - 14 IS - 20 ER -