Web resources bring new insight into COVID-19

Date:
September 22, 2020
Source:
Baylor College of Medicine
Summary:
Two new web resources put at researchers' fingertips information
about cellular genes whose expression is affected by coronavirus
infection and place these data points in the context of the complex
network of host molecular signaling pathways.



FULL STORY ========================================================================== Researchers around the world are a step closer to a better understanding
of the intricacies of COVID-19 thanks to two new web resources developed
by investigators at Baylor College of Medicine and the University
of California San Diego. The resources are freely available through
the Signaling Pathways Project (Baylor) and the Network Data Exchange
(UCSD). They put at researchers' fingertips information about cellular
genes whose expression is affected by coronavirus infection and place
these data points in the context of the complex network of host molecular signaling pathways. Using this resource has the potential to accelerate
the development of novel therapeutic strategies.


==========================================================================
The study appears in the journal Scientific Data.

"Our motivation for developing this resource is to contribute to making research about COVID-19 more accessible to the scientific community. When researchers have open access to each other's work, discoveries move
forward more efficiently," said leading author Dr. Neil McKenna,
associate professor of molecular and cellular biology and member of the
Dan L Duncan Comprehensive Cancer Center at Baylor.

The Signaling Pathway Project For years, the scientific community has
been generating and archiving molecular datasets documenting how genes
are expressed as cells conduct their normal functions, or in association
with disease. However, usually this information is not easily accessible.

In 2019, McKenna and his colleagues developed the Signaling Pathways
Project, a web-based platform that integrates molecular datasets published
in the scientific literature into consensus regulatory signatures, or
what they are calling consensomes, that rank genes according to their
rates of differential expression.



==========================================================================
In the current study, the researchers generated consensomes for genes
affected by infection with three major coronaviruses, Middle East
respiratory syndrome coronavirus (MERS) and severe acute respiratory
syndrome coronaviruses 1 (SARS1) and 2 (SARS2, which causes COVID-19).

McKenna and his colleagues provide a resource that assists researchers in making the most out of coronavirus' datasets. The resource identifies the
genes whose expression is most consistently affected by the infection
and integrates those responses with data about the cells' molecular
signaling pathways, in a sense getting a better picture of what happens
inside a cell infected by coronavirus and how the cell responds.

"The collaboration with UCSD makes our analyses available as intuitive Cytoscape-style networks," says McKenna. "Because using these resources
does not require training in meta-analysis, they greatly lower the
barriers to usability by bench researchers." Providing new insights
into COVID-19 The consensus strategy, the researchers explain, can bring
to light previously unrecognized links or provide further support for
suspected connections between coronavirus infection and human signaling pathways, ultimately simplifying the generation of hypotheses to be
tested in the laboratory.



==========================================================================
For example, the connection between pregnancy and susceptibility to
COVID-19 has been difficult to evaluate due to lack of clinical data,
but McKenna and colleagues' approach has provided new insights into
this puzzle.

"We found evidence that progesterone receptor signaling antagonizes
SARS2- induced inflammatory signaling mediated by interferon in the
airway epithelium.

This finding suggests the hypothesis that the suppression of
the interferon response to SARS2 infection by elevated circulating
progesterone during pregnancy may contribute to the asymptomatic clinical course," McKenna said.

Consistent with their hypothesis, while this paper was being reviewed,
a clinical trial was launched to evaluate progesterone as a treatment
for COVID- 19 in men.

Scott A. Ochsner at Baylor College of Medicine and Rudolf T. Pillich at
the University of California San Diego were also authors of this work.

This study was supported by the National Institute of Diabetes,
Digestive and Kidney Diseases NIDDK Information Network (DK097748),
the National Cancer Institute (CA125123, CA184427) and by the Brockman
Medical Research Foundation.

The Signaling Pathways Project website is hosted by the Dan L Duncan Comprehensive Cancer Center.


========================================================================== Story Source: Materials provided by Baylor_College_of_Medicine. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. Scott A. Ochsner, Rudolf T. Pillich, Neil J. McKenna. Consensus
transcriptional regulatory networks of coronavirus-infected
human cells.

Scientific Data, 2020; 7 (1) DOI: 10.1038/s41597-020-00628-6 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/09/200922083905.htm

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