Exploratory multi-tissue profiling after regenerative peripheral nerve interface reconstruction in rats

Abstract Background Regenerative peripheral nerve interface (RPNI) reconstruction provides a target for regenerating axons, but its associated responses across peripheral and central tissues remain incompletely characterized. Methods Thirteen male rats were randomized to Sham ( n = 3), unreconstructed Stump ( n = 5), or RPNI ( n = 5). Four tissues per animal underwent RNA sequencing at 8 weeks. DESeq2 used all 52 libraries; an overlapping 36-library subset provided sensitivity analysis. Thalamic histology and selected-transcript qRT-PCR each used three animals per group from the same cohort. Autotomy was scored at weeks 4 and 8. Public rat nerve and mouse dorsal root ganglion (DRG) datasets provided exploratory context. Results Direct RPNI–Stump comparisons identified 189, 67, 2 and 6 differentially expressed genes in nerve, DRG, thalamus and hippocampus, respectively (FDR < 0.05; |log2 fold change|≥1). Thalamic Iba1-positive cell-body and TUNEL-positive nuclear counts were lower in RPNI (Tukey P = 0.01602 and 0.01283); HE/Nissl count comparisons did not establish differences. Median RPNI versus Stump autotomy scores were 1 versus 7 at week 4 and 2 versus 9 at week 8 (Holm-adjusted P = 0.1786 and 0.09524 across six comparisons). RNA-seq and qRT-PCR point estimates had opposite signs for 12/24 candidates. No reversal-associated gene was shared across tissues; external DRG comparisons all had BH q = 0.30. Conclusions RPNI was associated with tissue-specific expression and selected thalamic histological differences. These exploratory findings do not establish global normalization, cross-tissue communication or analgesic efficacy.