DataSheet_1_Blood gene expression predicts intensive care unit admission in hospitalised patients with COVID-19.docx

BackgroundThe COVID-19 pandemic has created pressure on healthcare systems worldwide. Tools that can stratify individuals according to prognosis could allow for more efficient allocation of healthcare resources and thus improved patient outcomes. It is currently unclear if blood gene expression signatures derived from patients at the point of admission to hospital could provide useful prognostic information.MethodsGene expression of whole blood obtained at the point of admission from a cohort of 78 patients hospitalised with COVID-19 during the first wave was measured by high resolution RNA sequencing. Gene signatures predictive of admission to Intensive Care Unit were identified and tested using machine learning and topological data analysis, TopMD.ResultsThe best gene expression signature predictive of ICU admission was defined using topological data analysis with an accuracy: 0.72 and ROC AUC: 0.76. The gene signature was primarily based on differentially activated pathways controlling epidermal growth factor receptor (EGFR) presentation, Peroxisome proliferator-activated receptor alpha (PPAR-α) signalling and Transforming growth factor beta (TGF-β) signalling.ConclusionsGene expression signatures from blood taken at the point of admission to hospital predicted ICU admission of treatment naïve patients with COVID-19.</p

<i>Caspase-8</i>, association with Alzheimer’s Disease and functional analysis of rare variants

<div><p>The accumulation of amyloid beta (Aβ) peptide (Amyloid cascade hypothesis), an APP protein cleavage product, is a leading hypothesis in the etiology of Alzheimer's disease (AD). In order to identify additional AD risk genes, we performed targeted sequencing and rare variant burden association study for nine candidate genes involved in the amyloid metabolism in 1886 AD cases and 1700 controls. We identified a significant variant burden association for the gene encoding caspase-8, <i>CASP8</i> (p = 8.6x10^-5). For two CASP8 variants, p.K148R and p.I298V, the association remained significant in a combined sample of 10,820 cases and 8,881 controls. For both variants we performed bioinformatics structural, expression and enzymatic activity studies and obtained evidence for loss of function effects. In addition to their role in amyloid processing, caspase-8 and its downstream effector caspase-3 are involved in synaptic plasticity, learning, memory and control of microglia pro-inflammatory activation and associated neurotoxicity, indicating additional mechanisms that might contribute to AD. As caspase inhibition has been proposed as a mechanism for AD treatment, our finding that AD-associated CASP8 variants reduce caspase function calls for caution and is an impetus for further studies on the role of caspases in AD and other neurodegenerative diseases.</p></div

Age and ApoE4 genotypes for subjects in discovery sample.

<p>Age and ApoE4 genotypes for subjects in discovery sample.</p

SKAT TEST.

<p>SKAT TEST.</p

Variant count and association of <i>CASP8</i> K148R and I298V.

<p>Variant count and association of <i>CASP8</i> K148R and I298V.</p

Caspase-8 modeling and expression.

<p>(<b>A</b>) Schematic illustration of pro-caspase-8 protein and its p43, p18 and p10 fragments resulting from proteolytic processing and activation. (<b>B</b>) Protein folding (top) and 3D model (bottom) of caspase-8 DED₂ (left side) and p18 domain (right side). The K¹⁴⁸ and I²⁹⁸ variants are depicted in red color. F¹²² and L¹²³ of the hydrophobic FL motif within the DED₂ is shown in purple, and critical H³¹⁷ and C³⁶⁰ active site residues within the p18 domain are in green. (<b>C</b>) SK-N-BE(2) cells were transfected with expression vectors encoding WT-, K148R-, or I298V-caspase-8 and mock as control. Corresponding immunoblot analysis, 24 h post-transfection, indicating the expression levels for pro-caspase-8 and its p43, p18 and p10 fragments. For the LOAD caspase-8 variant, two clones (<i>a</i> and <i>b</i>) are presented.(<b>D</b>) Representative confocal images of SK-N-BE(2) cells transfected as described in panel C. The cleaved caspase-8 is labeled red and Hoechst counterstained nuclei are blue. Images were taken 24 h after transfection.</p

Caspase-8 enzymatic activity.

<p>SK-N-BE(2) cells were transfected with expression vectors encoding WT-, K148R-, or I298V-caspase-8 and mock as control. (A) Caspase-8 (LETDase) and (B) Caspase-3-like (DEVDase) activities were measured 24 h post-transfection. Data are presented as fold over mock untreated. Statistics and error bars: mean±s.d. n = 8 of biological replicates. Data was analyzed as comparison to Caspase-8 WT using two-sided student’s t-test. *P< 0.05; **P< 0.01 and ***P< 0.001.</p

Coverage, aggregated variant count and variant-burden test of association in discovery sample.

<p>Coverage, aggregated variant count and variant-burden test of association in discovery sample.</p

Most significant variants.

<p>Most significant variants.</p