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 - Krebs, Markus A1 - Solimando, Antonio Giovanni A1 - Kalogirou, Charis A1 - Marquardt, André A1 - Frank, Torsten A1 - Sokolakis, Ioannis A1 - Hatzichristodoulou, Georgios A1 - Kneitz, Susanne A1 - Bargou, Ralf A1 - Kübler, Hubert A1 - Schilling, Bastian A1 - Spahn, Martin A1 - Kneitz, Burkhard T1 - miR-221-3p Regulates VEGFR2 Expression in High-Risk Prostate Cancer and Represents an Escape Mechanism from Sunitinib In Vitro JF - Journal of Clinical Medicine N2 - Downregulation of miR-221-3p expression in prostate cancer (PCa) predicted overall and cancer-specific survival of high-risk PCa patients. Apart from PCa, miR-221-3p expression levels predicted a response to tyrosine kinase inhibitors (TKI) in clear cell renal cell carcinoma (ccRCC) patients. Since this role of miR-221-3p was explained with a specific targeting of VEGFR2, we examined whether miR-221-3p regulated VEGFR2 in PCa. First, we confirmed VEGFR2/KDR as a target gene of miR-221-3p in PCa cells by applying Luciferase reporter assays and Western blotting experiments. Although VEGFR2 was mainly downregulated in the PCa cohort of the TCGA (The Cancer Genome Atlas) database, VEGFR2 was upregulated in our high-risk PCa cohort (n = 142) and predicted clinical progression. In vitro miR-221-3p acted as an escape mechanism from TKI in PC3 cells, as displayed by proliferation and apoptosis assays. Moreover, we confirmed that Sunitinib induced an interferon-related gene signature in PC3 cells by analyzing external microarray data and by demonstrating a significant upregulation of miR-221-3p/miR-222-3p after Sunitinib exposure. Our findings bear a clinical perspective for high-risk PCa patients with low miR-221-3p levels since this could predict a favorable TKI response. Apart from this therapeutic niche, we identified a partially oncogenic function of miR-221-3p as an escape mechanism from VEGFR2 inhibition. KW - microRNA-221 KW - high-risk Prostate Cancer KW - angiogenesis KW - Sunitinib KW - Tyrosine kinase inhibition Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-203168 SN - 2077-0383 VL - 9 IS - 3 ER - TY - JOUR A1 - Brumberg, Joachim A1 - Beckl, Melanie A1 - Dierks, Alexander A1 - Schirbel, Andreas A1 - Krebs, Markus A1 - Buck, Andreas A1 - Kübler, Hubert A1 - Lapa, Constantin A1 - Seitz, Anna Katharina T1 - Detection Rate of \(^{68}\)Ga-PSMA Ligand PET/CT in Patients with Recurrent Prostate Cancer and Androgen Deprivation Therapy JF - Biomedicines N2 - Prostate-specific membrane antigen (PSMA) ligand PET/CT enables the localization of tumor lesions in patients with recurrent prostate cancer, but it is unclear whether androgen deprivation therapy (ADT) influences diagnostic accuracy. The aim of this study was to evaluate the effect of ADT on the detection rate of \(^{68}\)Ga-PSMA ligand PET/CT. Thus, 399 patients with initial radical prostatectomy and 68Ga-PSMA ligand PET/CT during PSA relapse were retrospectively evaluated. Propensity score matching was used to create two balanced groups of 62 subjects who either did or did not receive ADT within six months before imaging. All \(^{68}\)Ga-PSMA ligand PET/CT were evaluated visually and with semiquantitative measures. The detection rate of tumor recurrence was significantly higher in the group with ADT (88.7% vs. 72.6%, p = 0.02) and improved with increasing PSA-levels in both groups. In subjects with pathological PET/CT and ADT, whole-body total lesion PSMA (p < 0.01) and PSMA-derived tumor volume (p < 0.01) were significantly higher than in those without ADT. More PSMA-positive lesions and higher PSMA-derived volumetric parameters in patients with ADT suggest that a better detection rate is related to a (biologically) more advanced disease stage. Due to high detection rates in patients with PSA-levels < 2 ng/mL, the withdrawal of ADT before PSMA ligand PET/CT cannot be recommended. KW - 68Ga-PSMA ligand PET/CT KW - androgen deprivation therapy KW - detection rate KW - recurrent prostate cancer Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-219301 SN - 2227-9059 VL - 8 IS - 11 ER - TY - THES A1 - Krebs, Markus Karl Ludwig T1 - microRNA-221 und ihr Einfluss auf Zytokin-vermittelte Signalwege im Hochrisiko-Karzinom der Prostata T1 - microRNA-221 and its influence on cytokine-mediated signaling pathways in high-risk prostate cancer N2 - Der klinische Verlauf von Prostatakarzinom(PCa)-Erkrankungen ist extrem unterschiedlich und lässt sich mit den bisher üblichen Verfahren wie der feingeweblichen Beurteilung der Prostatastanzbiopsie bzw. des OP-Präparates und der PSA-Wert-Bestimmung nur unzureichend vorhersagen. Für eine bessere Versorgung von PCa-Patienten sind deshalb neuartige Marker notwendig, die das individuelle Progressions-Risiko bestimmen. Ein hoffnungsvoller Ansatz sind miRNA-Vertreter als Prognose-Parameter. Besonders interessant in dieser Hinsicht ist miR-221, die im PCa-Gewebe signifikant niedriger exprimiert wird. Jedoch existieren für diese in den meisten Neoplasien als Onkogen betrachtete miRNA kaum Erklärungsansätze für eine tumorsuppressive Funktion im PCa. Die vorliegende Arbeit konnte mit Hilfe von Microarray-basierten Expressionsanalysen und deren bioinformatischer Auswertung sowie zell- und molekularbiologischen Experimenten erstmals zeigen, dass miR-221 das protektive Interferon-Signal in PCa-Zellen stärkt und auf diese Weise deren Proliferation hemmt. Daneben konnten zwei prominente Inhibitoren dieses Signals, IRF2 und SOCS3, als neue Zielgene von miR-221 in vitro nachgewiesen und eine Korrelation von miR-221 mit diesen Zielgenen auch in PCa-Nativmaterial identifiziert werden. Somit konnte erstmals ein Mechanismus der – vorher lediglich aufgrund der Herabregulation in PCa-Nativmaterial postulierten – tumorsuppressiven Funktion von miR-221 im Rahmen der PCa-Entstehung und -Progression dargestellt werden. Eine Aktivierung des JAK / STAT-vermittelten Interferon-Signals durch miR-221 erscheint auch in einem breiteren infektiologischen Kontext interessant – sind doch zahlreiche Virenarten wie das HI-Virus, Hepatitis- und Herpesviren in der Lage, die zelluläre miR-221-Expression zu vermindern und auf diese Weise wohl das antivirale Interferon-Signal zu umgehen. Die Erhöhung der zellulären miR-221-Spiegel könnte nach diesem Prinzip auch Interferon-basierte Therapie-Strategien unterstützen bzw. erst ermöglichen. Für das PCa müssen weitere experimentelle sowie klinisch-translationale Untersuchungen zeigen, ob miR-221 als Bestandteil einer Biomarker-Signatur dazu beiträgt, Patienten mit einem letalen PCa frühzeitig zu identifizieren und der dringend notwendigen Primärtherapie bzw. einer adjuvanten Behandlung zuzuführen. Im Gegenzug könnte zahlreichen Patienten, deren (hohe) miR-221-Expression im Tumorgewebe einen günstigeren Verlauf prognostiziert, die übermäßige Therapie erspart werden. N2 - The clinical course of prostate cancer (PCa) is extremely heterogeneous and cannot be predicted sufficiently with usual procedures such as histological examination of prostate biopsies and surgical specimen or determination of PSA values. For a better treatment of PCa patients, novel markers are necessary which predict individual progression risk. MicroRNAs are promising biomarker candidates and miR-221 – which is significantly downregulated in prostate cancer tissue – seems especially interesting. However, as this specific microRNA plays an oncogenic role in various malignancies, no potential tumor suppressive functions are known. By using Microarray-based gene expression analysis, bioinformatical algorithms, cell culture and molecular biology techniques, this thesis could show that miR-221 strengthens interferon signaling in PCa cells thereby serving as a tumor suppressor. Moreover, two prominent inhibitors of this signal, IRF2 and SOCS3, were introduced as new miR-221 target genes in vitro and a negative correlation of these targets and miR-221 was shown for PCa specimen. Altogether, this is the first miR-221-mediated mechanism fitting in with the previously postulated tumor suppressor role of miR-221 in PCa. An activation of JAK / STAT-mediated interferon signaling by miR-221 also seems interesting from an infectious diseases perspective. Several viruses like HIV and members of the Hepatitis and Herpes family are able to lower the cellular miR-221 expression, thereby possibly weakening the antiviral interferon signal. For PCa, further experimental as well as clinical-translational approaches have to determine whether miR-221 could be a part of a clinically relevant biomarker signature. This could help to identify and subsequently treat patients with a high-risk PCa, whereas many patients – with a prognostically favorable high miR-221 expression in tumor tissue – could be spared an overtreatment. KW - miRNS KW - Prostatakrebs KW - Interferon KW - microRNA-221 KW - Interferonsignal KW - Biomarker KW - Hochrisikokarzinom der Prostata Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-137644 ER - TY - JOUR A1 - Vergho, Daniel Claudius A1 - Kneitz, Susanne A1 - Kalogirou, Charis A1 - Burger, Maximilian A1 - Krebs, Markus A1 - Rosenwald, Andreas A1 - Spahn, Martin A1 - Löser, Andreas A1 - Kocot, Arkadius A1 - Riedmiller, Hubertus A1 - Kneitz, Burkhard T1 - Impact of miR-21, miR-126 and miR-221 as Prognostic Factors of Clear Cell Renal Cell Carcinoma with Tumor Thrombus of the Inferior Vena Cava N2 - Clear cell renal cell carcinoma (ccRCC) characterized by a tumor thrombus (TT) extending into the inferior vena cava (IVC) generally indicates poor prognosis. Nevertheless, the risk for tumor recurrence after nephrectomy and thrombectomy varies. An applicable and accurate prediction system to select ccRCC patients with TT of the IVC (ccRCC/TT) at high risk after nephrectomy is urgently needed, but has not been established up to now. To our knowledge, a possible role of microRNAs (miRs) for the development of ccRCC/TT or their impact as prognostic markers in ccRCC/TT has not been explored yet. Therefore, we analyzed the expression of the previously described onco-miRs miR-200c, miR-210, miR-126, miR-221, let-7b, miR-21, miR-143 and miR-141 in a study collective of 74 ccRCC patients. Using the expression profiles of these eight miRs we developed classification systems that accurately differentiate ccRCC from non-cancerous renal tissue and ccRCC/TT from tumors without TT. In the subgroup of 37 ccRCC/TT cases we found that miR-21, miR-126, and miR-221 predicted cancer related death (CRD) accurately and independently from other clinico-pathological features. Furthermore, a combined risk score based on the expression of miR-21, miR-126 and miR-221 was developed and showed high sensitivity and specificity to predict cancer specific survival (CSS) in ccRCC/TT. Using the combined risk score we were able to classify ccRCC/TT patients correctly into high and low risk cases. The risk stratification by the combined risk score (CRS) will benefit from further cohort validation and might have potential for clinical application as a molecular prediction system to identify high- risk ccRCC/TT patients. KW - forecasting KW - metastasis KW - renal cancer KW - renal cell carcinoma KW - kidneys KW - surgical oncology KW - surgical and invasive medical procedures KW - regression analysis Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-113633 ER - TY - JOUR A1 - Kneitz, Burkhard A1 - Kalogirou, Charis A1 - Spahn, Martin A1 - Krebs, Markus A1 - Joniau, Steven A1 - Lerut, Evelyne A1 - Burger, Maximilian A1 - Scholz, Claus-Jürgen A1 - Kneitz, Susanne A1 - Riedmiller, Hubertus T1 - MiR-205 Is Progressively Down-Regulated in Lymph Node Metastasis but Fails as a Prognostic Biomarker in High-Risk Prostate Cancer JF - International Journal of Molecular Sciences N2 - The treatment of high-risk prostate cancer (HRPCa) is a tremendous challenge for uro-oncologists. The identification of predictive moleculobiological markers allowing risk assessment of lymph node metastasis and systemic progression is essential in establishing effective treatment. In the current study, we investigate the prognostic potential of miR-205 in HRPCa study and validation cohorts, setting defined clinical endpoints for both. We demonstrate miR-205 to be significantly down-regulated in over 70% of the HRPCa samples analysed and that reconstitution of miR-205 causes inhibition of proliferation and invasiveness in prostate cancer (PCa) cell lines. Additionally, miR-205 is increasingly down-regulated in lymph node metastases compared to the primary tumour indicating that miR-205 plays a role in migration of PCa cells from the original location into extraprostatic tissue. Nevertheless, down-regulation of miR-205 in primary PCa was not correlated to the synchronous presence of metastasis and failed to predict the outcome for HRPCa patients. Moreover, we found a tendency for miR-205 up-regulation to correlate with an adverse outcome of PCa patients suggesting a pivotal role of miR-205 in tumourigenesis. Overall, we showed that miR-205 is involved in the development and metastasis of PCa, but failed to work as a useful clinical biomarker in HRPCa. These findings might have implications for the use of miR-205 as a prognostic or therapeutic target in HRPCa. KW - high-risk prostate cancer KW - microRNA KW - miR-205 KW - prognosis KW - biomarker Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-97321 ER - TY - JOUR A1 - Hartrampf, Philipp E. A1 - Heinrich, Marieke A1 - Seitz, Anna Katharina A1 - Brumberg, Joachim A1 - Sokolakis, Ioannis A1 - Kalogirou, Charis A1 - Schirbel, Andreas A1 - Kübler, Hubert A1 - Buck, Andreas K. A1 - Lapa, Constantin A1 - Krebs, Markus T1 - Metabolic Tumour Volume from PSMA PET/CT Scans of Prostate Cancer Patients during Chemotherapy — Do Different Software Solutions Deliver Comparable Results? JF - Journal of Clinical Medicine N2 - (1) Background: Prostate-specific membrane antigen (PSMA)-derived tumour volume (PSMA-TV) and total lesion PSMA (TL-PSMA) from PSMA PET/CT scans are promising biomarkers for assessing treatment response in prostate cancer (PCa). Currently, it is unclear whether different software tools for assessing PSMA-TV and TL-PSMA produce comparable results. (2) Methods: \(^{68}\)Ga-PSMA PET/CT scans from n = 21 patients with castration-resistant PCa (CRPC) receiving chemotherapy were identified from our single-centre database. PSMA-TV and TL-PSMA were calculated with Syngo.via (Siemens) as well as the freely available Beth Israel plugin for FIJI (Fiji Is Just ImageJ) before and after chemotherapy. While statistical comparability was illustrated and quantified via Bland-Altman diagrams, the clinical agreement was estimated by matching PSMA-TV, TL-PSMA and relative changes of both variables during chemotherapy with changes in serum PSA (ΔPSA) and PERCIST (Positron Emission Response Criteria in Solid Tumors). (3) Results: Comparing absolute PSMA-TV and TL-PSMA as well as Bland–Altman plotting revealed a good statistical comparability of both software algorithms. For clinical agreement, classifying therapy response did not differ between PSMA-TV and TL-PSMA for both software solutions and showed highly positive correlations with BR. (4) Conclusions: due to the high levels of statistical and clinical agreement in our CRPC patient cohort undergoing taxane chemotherapy, comparing PSMA-TV and TL-PSMA determined by Syngo.via and FIJI appears feasible. KW - prostate-specific membrane antigen (PSMA) KW - metabolic tumour volume (MTV) KW - total lesion PSMA KW - biomarker KW - software KW - comparability KW - agreement Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-205893 SN - 2077-0383 VL - 9 IS - 5 ER - TY - JOUR A1 - Krebs, Markus A1 - Behrmann, Christoph A1 - Kalogirou, Charis A1 - Sokolakis, Ioannis A1 - Kneitz, Susanne A1 - Kruithof-de Julio, Marianna A1 - Zoni, Eugenio A1 - Rech, Anne A1 - Schilling, Bastian A1 - Kübler, Hubert A1 - Spahn, Martin A1 - Kneitz, Burkhard T1 - miR-221 Augments TRAIL-mediated apoptosis in prostate cancer cells by inducing endogenous TRAIL expression and targeting the functional repressors SOCS3 and PIK3R1 JF - BioMed Research International N2 - miR-221 is regarded as an oncogene in many malignancies, and miR-221-mediated resistance towards TRAIL was one of the first oncogenic roles shown for this small noncoding RNA. In contrast, miR-221 is downregulated in prostate cancer (PCa), thereby implying a tumour suppressive function. By using proliferation and apoptosis assays, we show a novel feature of miR-221 in PCa cells: instead of inducing TRAIL resistance, miR-221 sensitized cells towards TRAIL-induced proliferation inhibition and apoptosis induction. Partially responsible for this effect was the interferon-mediated gene signature, which among other things contained an endogenous overexpression of the TRAIL encoding gene TNFSF10. This TRAIL-friendly environment was provoked by downregulation of the established miR-221 target gene SOCS3. Moreover, we introduced PIK3R1 as a target gene of miR-221 in PCa cells. Proliferation assays showed that siRNA-mediated downregulation of SOCS3 and PIK3R1 mimicked the effect of miR-221 on TRAIL sensitivity. Finally, Western blotting experiments confirmed lower amounts of phospho-Akt after siRNA-mediated downregulation of PIK3R1 in PC3 cells. Our results further support the tumour suppressing role of miR-221 in PCa, since it sensitises PCa cells towards TRAIL by regulating the expression of the oncogenes SOCS3 and PIK3R1. Given the TRAIL-inhibiting effect of miR-221 in various cancer entities, our results suggest that the influence of miR-221 on TRAIL-mediated apoptosis is highly context- and entity-dependent. KW - Cancer Cell Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-202480 VL - 2019 ER - TY - JOUR A1 - Argentiero, Antonella A1 - Solimando, Antonio Giovanni A1 - Krebs, Markus A1 - Leone, Patrizia A1 - Susca, Nicola A1 - Brunetti, Oronzo A1 - Racanelli, Vito A1 - Vacca, Angelo A1 - Silvestris, Nicola T1 - Anti-angiogenesis and immunotherapy: novel paradigms to envision tailored approaches in renal cell-carcinoma JF - Journal of Clinical Medicine N2 - Although decision making strategy based on clinico-histopathological criteria is well established, renal cell carcinoma (RCC) represents a spectrum of biological ecosystems characterized by distinct genetic and molecular alterations, diverse clinical courses and potential specific therapeutic vulnerabilities. Given the plethora of drugs available, the subtype-tailored treatment to RCC subtype holds the potential to improve patient outcome, shrinking treatment-related morbidity and cost. The emerging knowledge of the molecular taxonomy of RCC is evolving, whilst the antiangiogenic and immunotherapy landscape maintains and reinforces their potential. Although several prognostic factors of survival in patients with RCC have been described, no reliable predictive biomarkers of treatment individual sensitivity or resistance have been identified. In this review, we summarize the available evidence able to prompt more precise and individualized patient selection in well-designed clinical trials, covering the unmet need of medical choices in the era of next-generation anti-angiogenesis and immunotherapy. KW - renal cell carcinoma KW - angiogenesis KW - immune-checkpoint inhibitor KW - tumor microenvironment KW - molecular subtypes KW - prognostic-biomarkers KW - predictive factors Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-205846 SN - 2077-0383 VL - 9 IS - 5 ER - TY - JOUR A1 - Solimando, Antonio Giovanni A1 - Kalogirou, Charis A1 - Krebs, Markus T1 - Angiogenesis as therapeutic target in metastatic prostate cancer – narrowing the gap between bench and bedside JF - Frontiers in Immunology N2 - Angiogenesis in metastatic castration-resistant prostate cancer (mCRPC) has been extensively investigated as a promising druggable biological process. Nonetheless, targeting angiogenesis has failed to impact overall survival (OS) in patients with mCRPC despite promising preclinical and early clinical data. This discrepancy prompted a literature review highlighting the tumor heterogeneity and biological context of Prostate Cancer (PCa). Narrowing the gap between the bench and bedside appears critical for developing novel therapeutic strategies. Searching clinicaltrials.gov for studies examining angiogenesis inhibition in patients with PCa resulted in n=20 trials with specific angiogenesis inhibitors currently recruiting (as of September 2021). Moreover, several other compounds with known anti-angiogenic properties – such as Metformin or Curcumin – are currently investigated. In general, angiogenesis-targeting strategies in PCa include biomarker-guided treatment stratification – as well as combinatorial approaches. Beyond established angiogenesis inhibitors, PCa therapies aiming at PSMA (Prostate Specific Membrane Antigen) hold the promise to have a substantial anti-angiogenic effect – due to PSMA´s abundant expression in tumor vasculature. KW - prostate adenocarcinoma KW - PCa KW - angiogenesis inhibitors KW - TKI KW - immunotherapy KW - tumor microenvironment KW - clinical trials KW - PSMA Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-263061 SN - 1664-3224 VL - 13 ER -