Passage of SARS-CoV-2 in cells expressing human and mouse ACE2 selects for mouse-adapted and ACE2-independent viruses

Human ACE2 (hACE2) is required for cell attachment and entry of SARS-CoV-2. Mouse ACE2 (mACE2) does not support infection of early SARS-CoV-2 isolates. Herein we describe a new system for generating mouse-adapted SARS-CoV-2 in vitro by serial passaging virus in co-cultures of cell lines expressing hACE2 and mACE2. Mouse-adapted viruses emerged with a series of spike protein amino acid changes, all of which have been reported in human isolates. Mouse-adapted viruses replicated to high titers in C57BL/6J mouse lungs and nasal turbinates, and caused severe lung histopathology. Remarkably, one mouse-adapted virus was able to replicate efficiently in ACE2-negative cell lines, a characteristic not described for any SARS-CoV-2 variants. ACE2-independent entry by SARS-CoV-2 represents a new biology for SARS-CoV-2 with potential widespread implications for disease and intervention development.

RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes

Recent advances in single-cell RNA sequencing technologies have made detection of transcripts in single cells possible. The level of resolution provided by these technologies can be used to study changes in transcript usage across cell populations and help investigate new biology. Here, we introduce RNA-Scoop, an interactive cell cluster and transcriptome visualization tool to analyze transcript usage across cell categories and clusters. The tool allows users to examine differential transcript expression across clusters and investigate how usage of specific transcript expression mechanisms varies across cell groups.

The promise and perils of immunotherapy

Advances in understanding the ways in which the immune system fails to control tumor growth or prevent autoimmunity have led to the development of powerful therapeutic strategies to treat these diseases. In contrast to conventional therapies that have a broadly suppressive effect, immunotherapies are more akin to targeted therapies because they are mechanistically driven and are typically developed with the goal of “drugging” a specific underlying pathway or phenotype. This means that their effects and toxicities are, at least in theory, more straightforward to anticipate. The development of functionalized antibodies, genetically engineered T cells, and immune checkpoint inhibitors continues to accelerate, illuminating new biology and bringing new treatment to patients. In the following sections, we provide an overview of immunotherapeutic concepts, highlight recent advances in the field of immunotherapies, and discuss controversies and future directions, particularly as these pertain to hematologic oncology or blood-related diseases. We conclude by illustrating how original research published in this journal fits into and contributes to the overall framework of advances in immunotherapy.

Proximity interactome analysis of Lassa polymerase reveals eRF3a/GSPT1 as a druggable target for host directed antivirals.

Completion of the Lassa virus (LASV) life cycle critically depends on the activities of the virally encoded RNA-dependent RNA polymerase in replication and transcription of the negative-sense RNA viral genome in the cytoplasm of infected cells. We hypothesized that interactions with an array of cellular proteins may enable LASV polymerase to execute distinct viral RNA biosynthetic processes. To investigate this hypothesis, we applied proximity proteomics to define the interactome of LASV polymerase in cells, under conditions that recreate viral transcription and replication. We engineered a LASV polymerase-biotin ligase TurboID fusion protein that retained polymerase activity and successfully biotinylated the proximal proteome, which allowed us to identify 42 high-confidence hits that interact with LASV polymerase. We performed an siRNA screen to evaluate the role of the identified interactors in LASV infection, which uncovered six host factors for which their depletion affected LASV infection. We found that one polymerase interactor, eukaryotic peptide chain release factor subunit 3a (eRF3a/GSPT1), physically and functionally associated with LASV polymerase, exhibiting proviral activity. Accordingly, pharmacological targeting of GSPT1 resulted in strong inhibition of LASV infection. In summary, our work demonstrates the feasibility of using proximity proteomics to illuminate and characterize yet to be defined, host-pathogen interactomes, which can reveal new biology and uncover novel targets for the development of antivirals against LASV.

Mechanisms of Attenuation by Genetic Recoding of Viruses

ABSTRACT The development of safe and effective vaccines against viruses is central to disease control. With advancements in DNA synthesis technology, the production of synthetic viral genomes has fueled many research efforts that aim to generate attenuated viruses by introducing synonymous mutations. Elucidation of the mechanisms underlying virus attenuation through synonymous mutagenesis is revealing interesting new biology that can be exploited for vaccine development. Here, we review recent advancements in this field of synthetic virology and focus on the molecular mechanisms of attenuation by genetic recoding of viruses. We highlight the action of the zinc finger antiviral protein (ZAP) and RNase L, two proteins involved in the inhibition of viruses enriched for CpG and UpA dinucleotides, that are often the products of virus recoding algorithms. Additionally, we discuss current challenges in the field as well as studies that may illuminate how other host functions, such as translation, are potentially involved in the attenuation of recoded viruses.