Cell-free genome analysis reveals pathophysiological response to hypoxia at high altitude

Extreme physiological stress induced by hypobaric hypoxia at high altitude (HA) alters nucleosome organization across the genome, affecting multiple tissues and cell types. Investigating hypoxic responses is essential to understand inter-individual differences in susceptibility, their impact on vital organs, underlying epigenetic modifications, and the clinical consequences of compromised oxygen delivery. Remarkably, the fragmentation pattern of cell-free (cf) DNA in high-altitude pulmonary edema (HAPE), a life-threatening, non-cardiogenic form of pulmonary edema that occurs in susceptible individuals traveling to altitudes >2500m asl, can identify disease-specific changes in nucleosome positioning attributable to hypoxia-induced gene activation or repression. The present case-control study profiled cfDNA fragmentation patterns in 42 healthy HA acclimatized sojourners designated as controls and HAPE patients, further subdivided into mild (n=40), moderate (n=40), and severe (n=37) categories. The windowed protection score employed for tissue deconvolution analysis showed a greater contribution of cfDNA fragments from immune cells, the adrenal gland, spleen, pancreas, liver, and the esophageal muscularis mucosa in HAPE, indicating the systemic impact of the disease, even though its main symptoms are localized in the lungs. In addition, severe HAPE patients exhibited tissue contributions from lung fibroblasts, renal epithelium, and thyroid tissue, suggesting extensive tissue damage in these patients. The positive correlations of cfDNA concentration, peripheral oxygen saturation, respiratory rate, and pulse rate with tissue-specific fragmentation scores enhanced the translational value of the study. Furthermore, motif enrichment analysis, using HAPE-specific open chromatin regions and their integration with in-house RNA-seq data, revealed significant enrichment of oxygen-sensing, inflammatory, and immune-signaling pathways in HAPE.