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Abstract
Cell lineage decisions occur in three-dimensional spatial patterns that are difficult to identify by eye. There is an ongoing effort to replicate such patterns using mathematical modeling. One approach uses long ranging cell-cell communication to replicate common spatial arrangements like checkerboard and engulfing patterns. In this model, the cell-cell communication has been implemented as a signal that disperses throughout the tissue. On the other hand, machine learning models have been developed for pattern recognition and pattern reconstruction tasks. We combined synthetic data generated by the mathematical model with spatial summary statistics and deep learning algorithms to recognize and reconstruct cell fate patterns in organoids of mouse embryonic stem cells. Application of Moran’s index and pair correlation functions for in vitro and synthetic data from the model showed local clustering and radial segregation. To assess the patterns as a whole, a graph neural network was developed and trained on synthetic data from the model. Application to in vitro data predicted a low signal dispersion value. To test this result, we implemented a multilayer perceptron for the prediction of a given cell fate based on the fates of the neighboring cells. The results show a 70% accuracy of cell fate imputation based on the nine nearest neighbors of a cell. Overall, our approach combines deep learning with mathematical modeling to link cell fate patterns with potential underlying mechanisms.
Author summary
Mammalian embryo development relies on organized differentiation of stem cells into different lineages. Particularly at the early stages of embryogenesis, cells of different fates form three-dimensional spatial patterns that are difficult to identify by eye. Pattern quantification and mathematical modeling have produced first insights into potential mechanisms for the cell fate arrangements. However, these approaches have relied on classifications of the patterns such as inside-out or random, or used summary statistics such as pair correlation functions or cluster radii. Deep neural networks allow characterizing patterns directly. Since the tissue context can be readily reproduced by a graph, we implemented a graph neural network to characterize the patterns of embryonic stem cell organoids as a whole. In addition, we implemented a multilayer perceptron model to reconstruct the fate of a given cell based on its neighbors. To train and test the models, we used synthetic data generated by our mathematical model for cell-cell communication. This interplay of deep learning and mathematical modeling in combination with summary statistics allowed us to identify a potential mechanism for cell fate determination in mouse embryonic stem cells. Our results agree with a mechanism with a dispersion of the intercellular signal that links a cell’s fate to those of the local neighborhood.
Immune checkpoint blockade therapy is beneficial and even curative for some cancer patients. However, the majority don’t respond to immune therapy. Across different tumor types, pre-existing T cell infiltrates predict response to checkpoint-based immunotherapy. Based on in vitro pharmacological studies, mouse models and analyses of human melanoma patients, we show that the cytokine GDF-15 impairs LFA-1/β2-integrin-mediated adhesion of T cells to activated endothelial cells, which is a pre-requisite of T cell extravasation. In melanoma patients, GDF-15 serum levels strongly correlate with failure of PD-1-based immune checkpoint blockade therapy. Neutralization of GDF-15 improves both T cell trafficking and therapy efficiency in murine tumor models. Thus GDF-15, beside its known role in cancer-related anorexia and cachexia, emerges as a regulator of T cell extravasation into the tumor microenvironment, which provides an even stronger rationale for therapeutic anti-GDF-15 antibody development.
Land-use intensification is a major driver of biodiversity loss. However, understanding how different components of land use drive biodiversity loss requires the investigation of multiple trophic levels across spatial scales. Using data from 150 agricultural grasslands in central Europe, we assess the influence of multiple components of local- and landscape-level land use on more than 4,000 above- and belowground taxa, spanning 20 trophic groups. Plot-level land-use intensity is strongly and negatively associated with aboveground trophic groups, but positively or not associated with belowground trophic groups. Meanwhile, both above- and belowground trophic groups respond to landscape-level land use, but to different drivers: aboveground diversity of grasslands is promoted by diverse surrounding land-cover, while belowground diversity is positively related to a high permanent forest cover in the surrounding landscape. These results highlight a role of landscape-level land use in shaping belowground communities, and suggest that revised agroecosystem management strategies are needed to conserve whole-ecosystem biodiversity.
Background: The rapid progress of psychosomatic research in cardiology and also the increasing impact of psychosocial issues in the clinical daily routine have prompted the Clinical Commission of the German Heart Society (DGK) to agree to an update of the first state of the art paper on this issue which was originally released in 2008.
Methods: The circle of experts was increased, general aspects were implemented and the state of the art was updated. Particular emphasis was dedicated to coronary heart diseases (CHD), heart rhythm diseases and heart failure because to date the evidence-based clinical knowledge is most advanced in these particular areas. Differences between men and women and over the life span were considered in the recommendations as were influences of cognitive capability and the interactive and synergistic impact of classical somatic risk factors on the affective comorbidity in heart disease patients.
Results: A IA recommendation (recommendation grade I and evidence grade A) was given for the need to consider psychosocial risk factors in the estimation of coronary risks as etiological and prognostic risk factors. Furthermore, for the recommendation to routinely integrate psychosocial patient management into the care of heart surgery patients because in these patients, comorbid affective disorders (e.g. depression, anxiety and post-traumatic stress disorder) are highly prevalent and often have a malignant prognosis. A IB recommendation was given for the treatment of psychosocial risk factors aiming to prevent the onset of CHD, particularly if the psychosocial risk factor is harmful in itself (e.g. depression) or constrains the treatment of the somatic risk factors. Patients with acute and chronic CHD should be offered anti-depressive medication if these patients suffer from medium to severe states of depression and in this case medication with selective reuptake inhibitors should be given. In the long-term course of treatment with implanted cardioverter defibrillators (ICDs) a subjective health technology assessment is warranted. In particular, the likelihood of affective comorbidities and the onset of psychological crises should be carefully considered.
Conclusions: The present state of the art paper presents an update of current empirical evidence in psychocardiology. The paper provides evidence-based recommendations for the integration of psychosocial factors into cardiological practice and highlights areas of high priority. The evidence for estimating the efficiency for psychotherapeutic and psychopharmacological interventions has increased substantially since the first release of the policy document but is, however, still weak. There remains an urgent need to establish curricula for physician competence in psychodiagnosis, communication and referral to ensure that current psychocardiac knowledge is translated into the daily routine.
Background: Pioglitazone, an oral anti-diabetic that stimulates the PPAR-gamma transcription factor, increased survival of mice with amyotrophic lateral sclerosis (ALS).
Methods/Principal Findings: We performed a phase II, double blind, multicentre, placebo controlled trial of pioglitazone in ALS patients under riluzole. 219 patients were randomly assigned to receive 45 mg/day of pioglitazone or placebo (one: one allocation ratio). The primary endpoint was survival. Secondary endpoints included incidence of non-invasive ventilation and tracheotomy, and slopes of ALS-FRS, slow vital capacity, and quality of life as assessed using EUROQoL EQ-5D. The study was conducted under a two-stage group sequential test, allowing to stop for futility or superiority after interim analysis. Shortly after interim analysis, 30 patients under pioglitazone and 24 patients under placebo had died. The trial was stopped for futility; the hazard ratio for primary endpoint was 1.21 (95% CI: 0.71-2.07, p = 0.48). Secondary endpoints were not modified by pioglitazone treatment. Pioglitazone was well tolerated.
Conclusion/Significance: Pioglitazone has no beneficial effects on the survival of ALS patients as add-on therapy to riluzole.
Highly efficient single-photon sources (SPS) can increase the secure key rate of quantum key distribution (QKD) systems compared to conventional attenuated laser systems. Here we report on a free space QKD test using an electrically driven quantum dot single-photon source (QD SPS) that does not require a separate laser setup for optical pumping and thus allows for a simple and compact SPS QKD system. We describe its implementation in our 500 m free space QKD system in downtown Munich. Emulating a BB84 protocol operating at a repetition rate of 125 MHz, we could achieve sifted key rates of 5-17 kHz with error ratios of 6-9% and g((2))(0)-values of 0.39-0.76.
Biodiversity, a multidimensional property of natural systems, is difficult to quantify partly because of the multitude of indices proposed for this purpose. Indices aim to describe general properties of communities that allow us to compare different regions, taxa, and trophic levels. Therefore, they are of fundamental importance for environmental monitoring and conservation, although there is no consensus about which indices are more appropriate and informative. We tested several common diversity indices in a range of simple to complex statistical analyses in order to determine whether some were better suited for certain analyses than others. We used data collected around the focal plant Plantago lanceolata on 60 temperate grassland plots embedded in an agricultural landscape to explore relationships between the common diversity indices of species richness (S), Shannon's diversity (H'), Simpson's diversity (D-1), Simpson's dominance (D-2), Simpson's evenness (E), and Berger-Parker dominance (BP). We calculated each of these indices for herbaceous plants, arbuscular mycorrhizal fungi, aboveground arthropods, belowground insect larvae, and P.lanceolata molecular and chemical diversity. Including these trait-based measures of diversity allowed us to test whether or not they behaved similarly to the better studied species diversity. We used path analysis to determine whether compound indices detected more relationships between diversities of different organisms and traits than more basic indices. In the path models, more paths were significant when using H', even though all models except that with E were equally reliable. This demonstrates that while common diversity indices may appear interchangeable in simple analyses, when considering complex interactions, the choice of index can profoundly alter the interpretation of results. Data mining in order to identify the index producing the most significant results should be avoided, but simultaneously considering analyses using multiple indices can provide greater insight into the interactions in a system.
Synthese siliciumhaltiger Wirkstoffe und Synthese-Bausteine des 4-Silapiperidin-Typs:
Im Rahmen der systematischen Untersuchungen unseres Arbeitskreises zur C/Si-Bioisosterie wurde für bereits bekannte σ-Rezeptor-Antagonisten eine neue verbesserte Syntheseroute entwickelt, wobei die Endprodukte jeweils in einer sechsstufigen Synthese dargestellt und als entsprechende Hydrochloride isoliert wurden.
Ein weiteres Teilprojekt der vorliegenden Arbeit betraf die Entwicklung einer Syntheseroute zur Darstellung von Sila-L-741,626, dem Sila-Analogon des selektiven D2-Dopamin-Rezeptorantagonisten L-741,626.
In einem weiteren Teilprojekt der vorliegenden Arbeit wurde ein neuer, säurefreier Weg zu 4 Silapiperidin-Bausteinen mit NH-Funktion entwickelt, der eine Staudinger-Reaktion als ringschließenden Syntheseschritt beinhaltet. Am Beispiel einer Modellverbindung, die in zwei alternativen jeweils fünfstufigen Synthesen ausgehend von Dichlordiphenylsilan dargestellt und als Hydrochlorid isoliert wurde, konnte die neue Syntheseroute erfolgreich ausgearbeitet werden. Die anhand der Modellverbindung erfolgreich getestete Syntheseroute konnte im Folgenden auf ein Zielmolekül angewendet werden, das anstatt einer inerten Phenyl-Gruppe die säurelabilere 4-Methoxyphenyl- (MOP-) Gruppe trägt.
Synthese siliciumhaltiger Wirkstoffe und Synthese-Bausteine des 4-Silacyclohexan-1-on- und (4-Silacyclohexan-1-yl)amin-Typs:
Im Zusammenhang mit unseren systematischen Untersuchungen zur C/Si-Bioisosterie wurde Sila-pramiverin dargestellt. Dies gelang in einer vierstufigen Synthese, ausgehend von Dichlordiphenylsilan. Im Zuge dieser Synthese fand Brown’s DCME-Prozess Anwendung, um in einer Eintopf-Reaktion das entsprechende 4-Silacyclohexan-1-on und daraus durch anschließende reduktive Aminierung mit Isopropylamin Sila-pramiverin erstmals darzustellen.
Analog zur Synthese von Sila-pramiverin konnten ebenfalls Synthese-Bausteine des 4 Silacyclohexan-1-on-Typs sowie des (4-Silacyclohexan-1-yl)amin-Typs unter Verwendung der 4 Methoxyphenyl- (MOP ), 2,6-Dimethoxyphenyl- (DMOP-) bzw. 2,4,6-Trimethoxyphenyl- (TMOP-) Schutzgruppe dargestellt werden.
In einer Machbarkeitsstudie wurde zudem unter selektiver Abspaltung der 4 Methoxyphenyl- (MOP ), 2,6-Dimethoxyphenyl- (DMOP-) bzw. 2,4,6-Trimethoxyphenyl- (TMOP-) Schutzgruppe der phenylierten 4 Silacyclohexan-1-one mittels Chlorwasserstoff das entsprechende Chlorsilan dargestellt.
Synthese siliciumhaltiger Synthese-Bausteine des 4-Silatetrahydropyran-Typs:
Eine fast gänzlich unerforschte Klasse siliciumhaltiger Heterocyclen stellen 4 Silatetrahydropyrane dar. Im Rahmen der vorliegenden Arbeit konnte zunächst anhand einer Modellstudie das 4,4-Diphenyl-4-silatetrahydropyran dargestellt werden. Die für die Modellverbindung ausgearbeitete Syntheseroute konnte schließlich auf die Synthese der 4 Methoxyphenyl- (MOP-) und 2,6-Dimethoxyphenyl- (DMOP-) substituierten 4 Silatetra¬hydropyrane übertragen werden. Diese konnten jeweils in einer vierstufigen Synthese dargestellt werden. Lediglich die Synthese der 2,4,6-Trimethoxyphenyl- (TMOP-) substituierten 4 Silatetra¬hyropyrane gelang aufgrund der Instabilität der mesylierten Zwischenstufen nicht.
Head and neck squamous cell carcinoma (HNSCC) is known to overexpress a variety of receptor tyrosine kinases, such as the HGF receptor Met. Like other malignancies, HNSCC involves a mutual interaction between the tumor cells and surrounding tissues and cells. We hypothesized that activation of HGF/Met signaling in HNSCC influences glucose metabolism and therefore substantially changes the tumor microenvironment. To determine the effect of HGF, we submitted three established HNSCC cell lines to mRNA sequencing. Dynamic changes in glucose metabolism were measured in real time by an extracellular flux analyzer. As expected, the cell lines exhibited different levels of Met and responded differently to HGF stimulation. As confirmed by mRNA sequencing, the level of Met expression was associated with the number of upregulated HGF-dependent genes. Overall, Met stimulation by HGF leads to increased glycolysis, presumably mediated by higher expression of three key enzymes of glycolysis. These effects appear to be stronger in Met\(^{high}\)-expressing HNSCC cells. Collectively, our data support the hypothesized role of HGF/Met signaling in metabolic reprogramming of HNSCC.
Squamous cell carcinomas (SCC) frequently have an exceptionally high mutational burden. As consequence, they rapidly develop resistance to platinum-based chemotherapy and overall survival is limited. Novel therapeutic strategies are therefore urgently required. SCC express ∆Np63, which regulates the Fanconi Anemia (FA) DNA-damage response in cancer cells, thereby contributing to chemotherapy-resistance. Here we report that the deubiquitylase USP28 is recruited to sites of DNA damage in cisplatin-treated cells. ATR phosphorylates USP28 and increases its enzymatic activity. This phosphorylation event is required to positively regulate the DNA damage repair in SCC by stabilizing ∆Np63. Knock-down or inhibition of USP28 by a specific inhibitor weakens the ability of SCC to cope with DNA damage during platin-based chemotherapy. Hence, our study presents a novel mechanism by which ∆Np63 expressing SCC can be targeted to overcome chemotherapy resistance. Limited treatment options and low response rates to chemotherapy are particularly common in patients with squamous cancer. The SCC specific transcription factor ∆Np63 enhances the expression of Fanconi Anemia genes, thereby contributing to recombinational DNA repair and Cisplatin resistance. Targeting the USP28-∆Np63 axis in SCC tones down this DNA damage response pathways, thereby sensitizing SCC cells to cisplatin treatment.