nf-core/nanostring: a pipeline for reproducible NanoString nCounter analysis

MOTIVATION

The NanoString™ nCounter® technology platform is a widely used targeted quantification platform for the analysis of gene expression of up to ∼800 genes. Whereas the software tools by the manufacturer can perform the analysis in an interactive and GUI driven approach, there is no portable and user-friendly workflow available that can be used to perform reproducible analysis of multiple samples simultaneously in a scalable fashion on different computing infrastructures.

RESULTS

Here, we present the nf-core/nanostring open-source pipeline to perform a comprehensive analysis including quality control and additional features such as expression visualization, annotation with additional metadata and input creation for differential gene expression analysis. The workflow features an easy installation, comprehensive documentation, open-source code with the possibility for further extensions, a strong portability across multiple computing environments and detailed quality metrics reporting covering all parts of the pipeline. nf-core/nanostring has been implemented in the Nextflow workflow language and supports Docker, Singularity, Podman container technologies as well as Conda environments, enabling easy deployment on any Nextflow supported compatible system, including most widely used cloud computing environments such as Google GCP or Amazon AWS.

AVAILABILITY AND IMPLEMENTATION

The source code, documentation and installation instructions as well as results for continuous tests are freely available at https://github.com/nf-core/nanostring and https://nf-co.re/nanostring.

A Novel Antagonistic CD73 Antibody for Inhibition of the Immunosuppressive Adenosine Pathway

Despite some impressive clinical results with immune checkpoint inhibitors, the majority of patients with cancer do not respond to these agents, in part due to immunosuppressive mechanisms in the tumor microenvironment. High levels of adenosine in tumors can suppress immune cell function, and strategies to target the pathway involved in its production have emerged. CD73 is a key enzyme involved in adenosine production. This led us to identify a novel humanized antagonistic CD73 antibody, mAb19, with distinct binding properties. mAb19 potently inhibits the enzymatic activity of CD73 in vitro, resulting in an inhibition of adenosine formation and enhanced T-cell activation. We then investigated the therapeutic potential of combining CD73 antagonism with other immune modulatory and chemotherapeutic agents. Combination of mAb19 with a PD-1 inhibitor increased T-cell activation in vitro Interestingly, this effect could be further enhanced with an agonist of the adenosine receptor ADORA3. Adenosine levels were found to be elevated upon doxorubicin treatment in vivo, which could be blocked by CD73 inhibition. Combining CD73 antagonism with doxorubicin resulted in superior responses in vivo Furthermore, a retrospective analysis of rectal cancer patient samples demonstrated an upregulation of the adenosine pathway upon chemoradiation, providing further rationale for combining CD73 inhibition with chemotherapeutic agents.This study demonstrates the ability of a novel CD73 antibody to enhance T-cell function through the potent suppression of adenosine levels. In addition, the data highlight combination opportunities with standard of care therapies as well as with an ADORA3 receptor agonist to treat patients with solid tumors.