Study reveals manifold applications of cytokine transcriptional response modules in COVID-19

In a recent bioRxiv* study, UK researchers used interleukin modules to investigate the pathology of coronavirus disease (COVID-19). The study also helps support the development of risk stratification methods and assists in the quantification of the biological effects of host-directed immunomodulatory treatments.

Cytokine response module expression in chronic inflammatory conditions. Geometric mean expression of IL-1 and IL-6 cytokine response modules in A) blood of patients with JIA compared to healthy controls, and B) in the synovium of RA patients compared to that of healthy controls. Transcriptomic datasets are designated adjacent to figure panels. * = p < 0.05 by Mann-Whitney test.  

COVID-19 disease, which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is related to a sequence of pathophysiological mechanisms and events that mobilize a plethora of biomolecules, predominantly immunological.

In most severe instances, the disease prognosis can be markedly worsened due to a hyperproduction of proinflammatory cytokines that preferentially target lung tissue, such as interleukins IL-1, IL-6, and IL-12, interferon-gamma, and tumor necrosis factor-alpha.

Although elevated IL-1 and IL-6 responses have been linked with disease severity, measuring individual cytokines at the protein or nucleic acid level may not accurately reflect their biological activity within multivariate immune systems that include redundancy and feedback loops.

Therefore, a much better approach would be the use of validated gene expression signatures or modules that represent the transcriptional response to cytokine stimulation. Such modules could measure functional cytokine activity within genome-wide transcriptomic data directly from clinical samples.

Since no such transcriptional modules have been published for the detection of human IL-1 or IL-6 bioactivity, Dr. Lucy CK Bell and Dr. Mahdad Noursadeghi from the University College London, together with Dr. Gabriele Pollara from the Royal Free London NHS Trust, have sought to address this gap and provide urgently needed analysis tools in COVID-19 research.

Appraising cytokine bioactivity

"In this study we utilized transcriptional modules derived from cytokine-stimulated cells to demonstrate that their expression, but not that of their cognate cytokine genes, provided a quantitative readout for cytokine bioactivity in vivo", study authors summarize their methodological approach.

They have decided to test the hypothesis that increased IL-1 and IL-6 bioactivity represents a hallmark of COVID-19 disease, primarily by using the peripheral blood transcriptome of three recovered patients with mild-to-moderate COVID-19 disease. This dataset was generated with the widely used Nanostring system.

Furthermore, the expression of transcriptional modules was obtained by calculating the geometric mean expression of all constituent genes. The scripts used enabled the absence of a constituent gene in the analyzed dataset, a scenario that did not hamper geometric mean calculation.

Finally, the researchers determined the expression of IL-1 and IL-6 response modules at the site of COVID-19 disease with the use of autopsy samples collected from pulmonary and non-pulmonary tissues. This helped in testing the hypothesis that cytokine activity would be highest in the lungs, which is the site of prevalent disease.

The elevated expression of IL-1 and IL-6

In a nutshell, the obtained results show that IL-1 and IL-6 transcriptional module expression can be detectable in COVID-19 patients in the blood and at the site of disease in the lung. Likewise, the module expression in the blood more precisely tracks the disease recovery in comparison to cognate cytokine gene expression.

More specifically, the elevated expression of IL-1 and IL-6 response modules in COVID-19, but not these cytokines per se, represents a feature of disease both in blood and affected organs.

However, these results should be considered preliminary, as the sample size was small with rather mild COVID-19 cases, and the experiments had their limits. Therefore, the use of larger datasets with a greater range of clinical severity, alongside other gene signatures found within the blood transcriptome in COVID-19, is warranted.

Diagnostic and therapeutic benefits

Our data support the elevated activity of the inflammatory cytokines IL-1 and IL-6 in COVID-19, and demonstrates the power of cytokine transcriptional response modules in providing a dynamic readout of the activity of these pathways in vivo",

This study supports the rationale for investigating the therapeutic benefit of neutralizing IL-1 and IL-6 in COVID-19, to reduce cytokine-induced pathological features at the site of disease.

Furthermore, IL-1 and IL-6 response modules may be used to measure cytokine bioactivity after immunomodulation, with drugs that target these cytokines (such as anakinra, tocilizumab, and canakinumab) – permitting, in turn, the correlation between clinical response and cytokine activity levels.

Finally, IL-1 and IL-6 response modules may be considered sensitive biomarkers to stratify disease severity in patients infected with SARS-CoV-2. Additional fundamental and translational research endeavors will be needed to make the full use of these findings.

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
  • Bell, L.C.K., Noursadeghi, M. & Pollara G. (2020). Transcriptional response modules characterise IL-1 and IL-6 activity in COVID-19. bioRxiv.

Dr. Tomislav Meštrović

Written by

Dr. Tomislav Meštrović

Dr. Tomislav Meštrović is a medical doctor (MD) with a Ph.D. in biomedical and health sciences, specialist in the field of clinical microbiology, and an Assistant Professor at Croatia's youngest university - University North. In addition to his interest in clinical, research and lecturing activities, his immense passion for medical writing and scientific communication goes back to his student days. He enjoys contributing back to the community. In his spare time, Tomislav is a movie buff and an avid traveler.


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