here is increasing evidence that SARS-CoV-2 not only affects the respiratory tract but also impacts the CNS, resulting in neurological symptoms such as loss of smell and taste, headache , fatigue, nausea and vomiting in more than one-third of individuals with COVID-19 (refs. 1,2). Moreover, acute cerebrovascular disease and impaired consciousness have been reported 3. While Olfactory transmucosal SARS-CoV-2 invasion as a port of central nervous system entry in individuals with COVID-19

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Despite our rapidly growing knowledge about the human genome, we do not know all of the genes required for some of the most basic functions of life. To start to fill this gap we developed a high-throughput phenotypic screening platform combining potent gene silencing by RNA interference, time-lapse microscopy and computational image processing. We carried out a genome-wide phenotypic profiling of each of the ,21,000 human protein-coding genes by two-day live imaging of fluorescently labelled chromosomes. Phenotypes were scored quantitatively by computational image processing, which allowed us to identify hundreds of human genes involved in diverse biological functions including cell division, migration and survival. As part of the Mitocheck consortium, this study provides an in-depth analysis of cell division phenotypes and makes the entire high-content data set available as a resource to the community.To target the ,21,000 protein-coding genes in the human genome, we used a chemically synthesized short interfering RNA (siRNA) library designed to uniquely target each gene with 2-3 independent sequences (Supplementary Methods). The siRNAs in this library were tested individually and reduced the messenger RNAs of targeted genes to below 30% of original levels (to an average of 13%) for 97% of more than 1,000 genes tested (Supplementary Table 1). To allow high-throughput phenotyping of each individual siRNA in triplicates by live-cell imaging, we used a previously established workflow for solid-phase transfection using siRNA microarrays coupled to automatic time-lapse microscopy 1 . As a high-content phenotypic assay we chose to monitor fluorescent chromosomes in a human cell line stably expressing core histone 2B tagged with green fluorescent protein (GFP) 1 . After seeding on the siRNA microarrays, on average 67 (630) cells for each siRNA of the library were imaged in triplicates for 2 days, thus documenting many of their basic functions such as cell division, proliferation, survival and migration. Image processing reveals mitotic hitsThis resulted in a large data set of ,190,000 time-lapse movies providing time-resolved records of over 19 million cell divisions. To automatically score and annotate phenotypes in this large data set, we developed a computational pipeline 2 ( Fig. 1) extending previously established methods of morphology recognition by supervised machine learning [3][4][5][6] . In brief, after segmentation, about 200 quantitative features were extracted from each nucleus and used for classification into one of 16 morphological classes ( Fig. 1 and Supplementary Movies 1-30) by a support vector machine classifier previously trained on a set of ,3,000 manually annotated nuclei (Supplementary Methods). This classifier automatically recognizes changes in nuclear morphology due to the cell cycle, cell death or other phenotypic changes with an overall accuracy of 87% (Supplementary Fig. 1) and allows us to convert each time-lapse movie into a phenotypic profile that quantifies the response to each siRNA ...

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Chromosome segregation and cell division are essential, highly ordered processes that depend on numerous protein complexes. Results from recent RNA interference (RNAi) screens indicate that the identity and composition of these protein complexes is incompletely understood. Using gene tagging on bacterial artificial chromosomes, protein localization and tandem affinity purificationmass spectrometry, the MitoCheck consortium has analyzed about 100 human protein complexes, many of which had not or only incompletely been characterized. This work has led to the discovery of previously unknown, evolutionarily conserved subunits of the anaphase-promoting complex (APC/C) and the γ-tubulin ring complex (γ-TuRC), large complexes which are essential †

The SARS-CoV-2 pandemic affecting the human respiratory system severely challenges public health and urgently demands for increasing our understanding of COVID-19 pathogenesis, especially host factors facilitating virus infection and replication. SARS-CoV-2 was reported to enter cells via binding to ACE2, followed by its priming by TMPRSS2. Here, we investigate ACE2 and TMPRSS2 expression levels and their distribution across cell types in lung tissue (twelve donors, 39,778 cells) and in cells derived from subsegmental bronchial branches (four donors, 17,521 cells) by single nuclei and single cell RNA sequencing, respectively. While TMPRSS2 is strongly expressed in both tissues, in the subsegmental bronchial branches ACE2 is predominantly expressed in a transient secretory cell type. Interestingly, these transiently differentiating cells show an enrichment for pathways related to RHO GTPase function and viral processes suggesting increased vulnerability for SARS-CoV-2 infection. Our data provide a rich resource for future investigations of COVID-19 infection and pathogenesis.

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