Development and application of a high throughput cell based assay to identify apoptosis inducing proteins, and functional characterization of the candidate Vacuole Membrane Protein 1 (Vmp1)

The aim of the project was to identify and functionally characterize novel human proteins that dominantly induce apoptosis upon overexpression. To achieve this, a cell-based high throughput assay was developed. The assay is based on the detection of activated caspase-3 in cells overexpressing proteins tagged C- and N-terminally with YFP. Apoptotic cells were detected by staining with a specific antibody directed against the activated form of caspase-3. The assay was automated and data acquisition was done using a flow cytometer with an integrated 96-well plate reader. A total of 200 proteins have been screened in the assay, out of which five were identified to be significant activators of apoptosis. One of the candidates, Vacuole Membrane Protein 1 (Vmp1), which forms vacuoles in cells and subsequently induces apoptosis when overexpressed, has been functionally characterized in detail. It has been reported that VMP1 mRNA is differentially expressed in cancer, acute pancreatitis and kidney ischemia and that the overexpressed protein is localized to the Endoplasmic reticulum. But the function of this protein and its role in cancer and other diseases was previously unknown. In this study I show that the vacuoles are formed by the Endoplasmic reticulum due to accumulation of overexpressed Vmp1, and that Vmp1 is actually a plasma membrane protein involved in the formation of initial cell-cell contacts. Its function as a cell-cell adhesion protein was confirmed by identifying that Vmp1 interacts with the tight junction protein ZO-1, and that down regulation of Vmp1 induces cell detachment. Further, down regulation of Vmp1 resulted in a massive increase in the invasion potential of kidney cancer cells, which is consistent with the findings that VMP1 mRNA level is significantly lower in kidney metastases compared to primary tumours. Thus, these results are the first to show that Vmp1 is a cell adhesion protein, and that its expression level is a critical determinant of cancer cell invasiveness, metastasis formation and induction of apoptosis. In summary, I have established and applied a high throughput cell-based assay to screen for inducers of apoptosis. Functional characterization of one of the candidates from this screen revealed it to be a disease relevant regulator of cell-cell adhesion. This demonstrates the strength of this high throughput approach in the identification of proteins involved in diseases

Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts

Highthroughput cell-based assays with flow cytometric readout provide a powerful technique for identifying components of biologic pathways and their interactors. Interpretation of these large datasets requires effective computational methods. We present a new approach that includes data pre-processing, visualization, quality assessment, and statistical inference. The software is freely available in the Bioconductor package prada. The method permits analysis of large screens to detect the effects of molecular interventions in cellular systems

Remdesivir and three other drugs for hospitalised patients with COVID-19: final results of the WHO Solidarity randomised trial and updated meta-analyses.

BACKGROUND World Health Organization expert groups recommended mortality trials of four repurposed antiviral drugs - remdesivir, hydroxychloroquine, lopinavir, and interferon beta-1a - in patients hospitalized with coronavirus disease 2019 (Covid-19). METHODS We randomly assigned inpatients with Covid-19 equally between one of the trial drug regimens that was locally available and open control (up to five options, four active and the local standard of care). The intention-to-treat primary analyses examined in-hospital mortality in the four pairwise comparisons of each trial drug and its control (drug available but patient assigned to the same care without that drug). Rate ratios for death were calculated with stratification according to age and status regarding mechanical ventilation at trial entry. RESULTS At 405 hospitals in 30 countries, 11,330 adults underwent randomization; 2750 were assigned to receive remdesivir, 954 to hydroxychloroquine, 1411 to lopinavir (without interferon), 2063 to interferon (including 651 to interferon plus lopinavir), and 4088 to no trial drug. Adherence was 94 to 96% midway through treatment, with 2 to 6% crossover. In total, 1253 deaths were reported (median day of death, day 8; interquartile range, 4 to 14). The Kaplan-Meier 28-day mortality was 11.8% (39.0% if the patient was already receiving ventilation at randomization and 9.5% otherwise). Death occurred in 301 of 2743 patients receiving remdesivir and in 303 of 2708 receiving its control (rate ratio, 0.95; 95% confidence interval [CI], 0.81 to 1.11; P = 0.50), in 104 of 947 patients receiving hydroxychloroquine and in 84 of 906 receiving its control (rate ratio, 1.19; 95% CI, 0.89 to 1.59; P = 0.23), in 148 of 1399 patients receiving lopinavir and in 146 of 1372 receiving its control (rate ratio, 1.00; 95% CI, 0.79 to 1.25; P = 0.97), and in 243 of 2050 patients receiving interferon and in 216 of 2050 receiving its control (rate ratio, 1.16; 95% CI, 0.96 to 1.39; P = 0.11). No drug definitely reduced mortality, overall or in any subgroup, or reduced initiation of ventilation or hospitalization duration. CONCLUSIONS These remdesivir, hydroxychloroquine, lopinavir, and interferon regimens had little or no effect on hospitalized patients with Covid-19, as indicated by overall mortality, initiation of ventilation, and duration of hospital stay. (Funded by the World Health Organization; ISRCTN Registry number, ISRCTN83971151; ClinicalTrials.gov number, NCT04315948.)

From ORFeome to Biology: A Functional Genomics Pipeline

As several model genomes have been sequenced, the elucidation of protein function is the next challenge toward the understanding of biological processes in health and disease. We have generated a human ORFeome resource and established a functional genomics and proteomics analysis pipeline to address the major topics in the post-genome-sequencing era: the identification of human genes and splice forms, and the determination of protein localization, activity, and interaction. Combined with the understanding of when and where gene products are expressed in normal and diseased conditions, we create information that is essential for understanding the interplay of genes and proteins in the complex biological network. We have implemented bioinformatics tools and databases that are suitable to store, analyze, and integrate the different types of data from high-throughput experiments and to include further annotation that is based on external information. All information is presented in a Web database (http://www.dkfz.de/LIFEdb). It is exploited for the identification of disease-relevant genes and proteins for diagnosis and therapy