RNA sequencing transcriptome analysis of lesional to perilesional cortex at 5 days after traumatic brain injury
C57BL6/N male mice (14-week-old) were subjected to a controlled cortical impact (CCI) to induce a unilateral traumatic brain injury (TBI). After surgery, mice were treated and monitored for 5 days after TBI (5 dpi).  There were four treatment groups, each consisting in five male mice (n = 5 per group). Group-1 received the CSF1R antagonist, PLX3397 (pexidartinib) via food pellets (290 mg per kilogram of pellets, feeding at libitum). Group-2 received the interleukin-1 receptor antagonist (IL1RA), anakinra  (100 mg/kg body weight subcutaneously at 5 min, 24h, 48h, and 72h after CCI). Group-3 received both PLX3397 and anakinra (PLX3397+anakinra), and Group-4 got vehicle p.o. and s.c.. A control group was subjected to sham-surgy (n = 4)which included anesthesia, skin incision and suture but no skull penetration. PLX3397 leads to a depletion of microglial cells which was confirmed by immunohistochemistry. Lesional to perilesional cortical tissue was obtained 5 dpi (Brgema: +0.64 mm to -2.86 mm) to assess differential gene and transcript expression, microglia depletion and cortical reorganization. Behavioral scores for well-being and motor functions were obatined repeatedly during the observation time. Histology of brain lesion size, indices of neuronal damage and neuroinflammation were obtained at 5 days after TBI. Neuroinflammatory markers tended to be lower in PLX3397 treated mice, there was almost no effects of anakinra alone but inflammation and lesion volume were strongly reduced in the PLX3397+anakinra group, which was associated with better neurological outcome suggesting synergistic effects of PLX3997 and anakinra after TBI. Overall design: Total RNA was extracted from lesional-perilesional cortex 5d after TBI in mice treated with PLX3397 (n = 5), anakinra (n = 5), PLX3397+anakinra (n = 5) or vehicle (n = 5) from d1-d5 and from sham treated mice (n = 4). mRNA was analyzed by RNA sequencing in 5 biological replicates per treatment group using an Illumina NovaSeq 6000 system.