Transcriptomic study on the effect of Igf1r deficiency in control and bleomycin-challenged mouse lungs.
Acute lung injury (ALI), ARDS and COVID-19 usually involve a “cytokine storm”. IGF1R (Insulin-like growth factor receptor 1) maintains lung homeostasis and is implicated in these pulmonary inflammatory diseases. In mice, widespread IGF1R  deficiency was reported to counteract respiratory inflammation and alveolar damage after bleomycin (BLM)-induced ALI. To explore the molecular mechanisms mediated by Igf1r signaling after BLM challenge, we performed RNA-sequencing in lungs of IGF1R-deficient mice after BLM or saline (SAL) instillation. Transcriptomic analysis identified differentially expressed genes between BLM-challenged and SAL-treated control lungs, detecting biological processes and signaling pathways involved in ALI pathobiology. Igf1r depletion in BLM-challenged mice reversed large part of the transcriptional changes triggered by BLM, counteracting the transcriptomic profile of the inflammatory "cytokine storm". Data mining also identified changes in the expression of gene clusters with key roles in DNA damage, metabolic reprogramming, mitochondrial homeostasis, and epigenetics. Exploration of these functional groups, together with validation studies, provide new insights into the molecular mechanisms underlying the attenuating effect of Igf1r deficiency on ALI. These findings allow a more comprehensive view of IGF1R signaling at the transcriptional level, reinforcing its important role in promoting ALI and postulating it as a global epigenetic regulator in ARDS. Overall design: In order to evaluate the effect of generalized Igf1r deficiency in the context of BLM-mediated ALI on the transcriptome, lung RNA samples from the following four groups of mice were sequenced, (3 samples per group, 12 samples in total): 1) SAL-treated Igf1rfl/fl 2) SAL-treated UBC-CreERT2; Igf1r?/? (Igf1r-deficient; CreERT2) 3) BLM-challenged Igf1rfl/fl (Igf1rfl/fl-BLM)4) BLM-challenged CreERT2 (CreERT2-BLM)  Three differential gene expression comparisons were established between experimental groups: i) CreERT2 vs Igf1rfl/fl ("mutation") ii) Igf1rfl/fl-BLM vs Igf1rfl/fl ("injury") iii) CreERT2-BLM vs Igf1rfl/fl-BLM lungs ("attenuation")  Analysis of differenial gene expression, gene set enrichment analysis (GSEA) and intensive data mining were performed to thoroughly explore transcriptomic data. Additional experimental techniques were used to further investigate transcriptomic results.