Fig. 4: A six-gene hypoxia signature identified cells under hypoxic conditions and is associated with typhoid and other infectious disease-related pathologies.

a Dot plot showing expression of six hypoxia-associated genes, specific and shared across the four hypoxic subsets (from Fig. 3e–g). Dot size represents the percentage of cells in a subset expressing a given gene, and dot color indicates relative expression levels (legend at the bottom). Hypoxic subsets from each cell type are indicated in purple. b, c PBMCs from a healthy donor were either subjected to hypoxic conditions (15 h or 22 h in a hypoxia chamber), or ex vivo infected with S. Typhi for 4 h, 8 h, and 24 h. b Heat map showing the expression levels of the six-gene hypoxia signature in PBMCs under hypoxic conditions (left) or following ex vivo infection (right). c Quantification of the hypoxia signature fold-change relative to matched naïve samples for both hypoxic conditions (3 biological replicates for each condition) and ex vivo infection (4 biological replicates for each condition, except 24 h with 3 biological replicates). The signature is significantly elevated only under hypoxic conditions. Mean signature and SE values are shown. d Heat map of expression levels of the hypoxia signature in a dataset of isolated blood monocytes from sepsis patients during active sepsis (n = 8), post-recovery (n = 8), and from healthy controls (n = 6). HILPDA is not included in the heat map as the measurement platform used in this dataset lacks a probe for this gene. Box plot comparing six-gene hypoxia signature across conditions indicates significant induction of the signature only during sepsis; a p-value was calculated using two-sided one-way ANOVA (F(2,19) = 19.61, p = 2.4 × 10⁻⁵). The box represents the median and 25^th and 75^th percentiles, whiskers encompass all data points. The color bar below the heatmap indicates relative expression levels.