Direct image to subtype prediction for brain tumors using deep learning

Background: Deep Learning (DL) can predict molecular alterations of solid tumors directly from routine histopathology slides. Since the 2021 update of the World Health Organization (WHO) diagnostic criteria, the classification of brain tumors integrates both histopathological and molecular information. We hypothesize that DL can predict molecular alterations as well as WHO subtyping of brain tumors from hematoxylin and eosin-stained histopathology slides. // Methods: We used weakly supervised DL and applied it to three large cohorts of brain tumor samples, comprising N = 2845 patients. // Results: We found that the key molecular alterations for subtyping, IDH and ATRX, as well as 1p19q codeletion, were predictable from histology with an area under the receiver operating characteristic curve (AUROC) of 0.95, 0.90, and 0.80 in the training cohort, respectively. These findings were upheld in external validation cohorts with AUROCs of 0.90, 0.79, and 0.87 for prediction of IDH, ATRX, and 1p19q codeletion, respectively. // Conclusions: In the future, such DL-based implementations could ease diagnostic workflows, particularly for situations in which advanced molecular testing is not readily available

Die Bedeutung des P-Glycoproteins an der Blut-Hirn-Schranke in der Therapie des Morbus Alzheimer mittels aktiver Immunisierung gegen β-Amyloid 1-42

Einleitung: Die Immunisierung gegen β-Amyloid in der Therapie des Morbus Alzheimer führt im Mausmodell zur Verbesserung von β-Amyloid-Clearance und Kognition. In klinischen Studien an Alzheimer-Patienten wurde eine gesteigerte β-Amyloid-Clearance beobachtet, jedoch blieb die Verbesserung der Kognition aus. Stattdessen fand sich eine verstärkte Amyloidangiopathie kombiniert mit einer Zunahme intrazerebraler Blutungen. Die alters-korrelierte Dysfunktion von P-Glycoprotein, welches β-Amyloid aktiv über die Blut-Hirn-Schranke transportiert, könnte diese Phänomene erklären. Material und Methoden: Zunächst wurde ein transgenes Alzheimer-Mausmodell mit kombiniertem Knockout von P-Glycoprotein generiert. Versuchstiere dieses Stammes wurden zusammen mit einer Kontrollgruppe mit funktionalem P-Glycoprotein über einen Zeitraum von 56 Wochen aktiv seriell gegen β-Amyloid 1-42 immunisiert. Dann wurden die Anti-β-Amyloid-Antikörperbildung, die β-Amyloid-Last im Hirngewebe und an den Hirngefäßen, die mikrogliale Aktivität sowie Mikroblutungen und entzündliche Veränderungen an Gefäßen und Meningen qualitativ und quantitativ evaluiert. Ergebnisse: Bei Tieren mit intaktem P-Glycoprotein führte die Immunisierung zur signifikanten Reduktion der senilen Plaques sowie des löslichen und unlöslichen β-Amyloids. Bei Tieren mit Knockout von P-Glycoprotein war dieser Effekt wesentlich abgeschwächt, gleichzeitig bestand eine stärkere intrazerebrale Amyloidangiopathie als bei Tieren mit intaktem P-Glycoprotein. Die mikrogliale Aktivität und entzündliche Veränderungen waren in beiden Stämmen identisch ausgeprägt. Diskussion: Der Knockout von P-Glycprotein an der Blut-Hirn-Schranke führt im transgenen Mausmodell nach aktiver Immunisierungstherapie gegen β-Amyloid 1-42 zu einer gestörten β-Amyloid-Clearence. Rückkopplungseffekte zwischen der Dysfunktion von P-Glycoprotein und der Amyloidangiopathie bilden dabei einen selbstverstärkenden Feedback-Mechanismus. Dies kann die diskrepanten Ergebnisse einer Anti-β-Amyloid-Immunisierungstherapie zwischen Tiermodell und klinischen Studien mit Alzheimer-Patienten erklären. Gleichzeitig ergibt sich ein Behandlungs- und Präventionsansatz für den Morbus Alzheimer durch eine Kombinationstherapie aus Anti-Aβ-Immunisierung und P-Glycoprotein-Induktion.Background: Immunization against β-amyloid as a treatment of Alzheimer´s disease leads to an improvement of the clearence of β-amyloid and cognition in a transgenic mouse models of alzheimer´s disease. However, despite a greater β-amyloid clearence in clinical studies with patients with Alzheimer´s disease no improvement of cognitive function was observed. Instead, an increased amyloidangiopathy along with increased intracerebral hemorrhages was found. An age-related decline of the function of P-glycoprotein, which actively removes β-amyloid from the brain across the blood-brain barrier may explain these phenomena. Methods and Material: At first, a transgenic mouse model of Alzheimer's disease carrying a knockout mutation of P-glycoprotein was generated. These animals along with a control group with functional P-glycoprotein were actively serial immunized against β-amyloid 1-42 over the course of 56 weeks. Anti-β-amyloid-antibody formation, β-amyloid burden in brain tissue and brain vessels, microglial activity and microbleedings as well as inflammatory changes at intracerebral vessels and meninges were qualitively and quantatively evaluated. Results: In animals with intact P-gylcoprotein the immunization led to a significant reduction of both, senile plaques and soluble as well as insoluble β-amyloid. In animals with knockout of P-gylcoprotein this effect was markedly diminished. Concurrently, an increased intracerebral amyloid angiopathy was observed in animals lacking P-glycoprotein compared to those with functional P-glycoprotein. Microglial activity as well as inflammatory changes were identical in both strains. Discussion: The knockout of P-glycoprotein at the blood-brain barrier leads to a disturbance in the clearance of β-amyloid after active immunization against β-amyloid 1-42 in a transgenic mouse model of Alzheimer's disease. A link between amyloid angiopathy and the dysfunction of P-glycoprotein gives rise to a self-energizing feedback loop. This may explain the discrepancy in the results of an anti-β-amyloid immunization therapy between animal models and human patients with Alzheimer's disease in clinical studies. A combined therapy using an anti-β-amyloid immunization and an induction of P-glycoprotein may be a promising treatment in the therapy and prevention of Alzheimer's disease

Detecting drug resistance in pancreatic cancer organoids guides optimized chemotherapy treatment

Drug combination therapies for cancer treatment show high efficacy but often induce severe side effects, resulting in dose or cycle number reduction. We investigated the impact of neoadjuvant chemotherapy (neoCTx) adaptions on treatment outcome in 59 patients with pancreatic ductal adenocarcinoma (PDAC). Resections with tumor-free margins were significantly more frequent when full-dose neoCTx was applied. We determined if patient-derived organoids (PDOs) can be used to personalize poly-chemotherapy regimens by pharmacotyping of treatment-naïve and post-neoCTx PDAC PDOs. Five out of ten CTx-naïve PDO lines exhibited a differential response to either the FOLFIRINOX or the Gem/Pac regimen. NeoCTx PDOs showed a poor response to the neoadjuvant regimen that had been administered to the respective patient in 30% of cases. No significant difference in PDO response was noted when comparing modified treatments in which the least effective single drug was removed from the complete regimen.Drug testing of CTx-naïve PDAC PDOs and neoCTx PDOs may be useful to guide neoadjuvant and adjuvant regimen selection, respectively. Personalizing poly-chemotherapy regimens by omitting substances with low efficacy could potentially result in less severe side effects, thereby increasing the fraction of patients receiving a full course of neoadjuvant treatment

NCT/DKFZ MASTER handbook of interpreting whole-genome, transcriptome, and methylome data for precision oncology

Abstract Analysis of selected cancer genes has become an important tool in precision oncology but cannot fully capture the molecular features and, most importantly, vulnerabilities of individual tumors. Observational and interventional studies have shown that decision-making based on comprehensive molecular characterization adds significant clinical value. However, the complexity and heterogeneity of the resulting data are major challenges for disciplines involved in interpretation and recommendations for individualized care, and limited information exists on how to approach multilayered tumor profiles in clinical routine. We report our experience with the practical use of data from whole-genome or exome and RNA sequencing and DNA methylation profiling within the MASTER (Molecularly Aided Stratification for Tumor Eradication Research) program of the National Center for Tumor Diseases (NCT) Heidelberg and Dresden and the German Cancer Research Center (DKFZ). We cover all relevant steps of an end-to-end precision oncology workflow, from sample collection, molecular analysis, and variant prioritization to assigning treatment recommendations and discussion in the molecular tumor board. To provide insight into our approach to multidimensional tumor profiles and guidance on interpreting their biological impact and diagnostic and therapeutic implications, we present case studies from the NCT/DKFZ molecular tumor board that illustrate our daily practice. This manual is intended to be useful for physicians, biologists, and bioinformaticians involved in the clinical interpretation of genome-wide molecular information