Okeke, U. | Search bioRxiv

bioRxiv2026

Adaptive immunity is dispensable for salamander appendage regeneration

Complex multi-tissue regeneration capacity varies across vertebrates. Mammals are amongst the least regenerative species, while salamanders can regenerate complex tissues such as limbs and tails throughout life. Previous studies have shown that innate and adaptive immune cells are present during salamander limb regeneration. While innate immune cells have been shown to promote limb regeneration, it is unknown whether adaptive immunity is responsive to amputation or plays a role in appendage regeneration. Here we show that during limb regeneration in axolotls, the immune response is characterized by a coordinated immunoregulatory signature including the downregulation of antigen presentation, cytokine secretion, and T cell activation. We corroborate this transcriptomic data in vivo using skin allografts in newts and define the blastema as an immunosuppressed niche. To test the role of adaptive immune cells in regeneration, we generated Recombination activating gene 1 deficient (Rag1-/-) newts. Rag1-/- newts lack antigen receptor recombination and show a marked reduction of adaptive immune cells. We find that Rag1-/- newts do not reject allografts, confirming their functional immunodeficiency. Finally, we demonstrate that both larval and adult newts regenerate appendages in the absence of adaptive immunity. Our work demonstrates that the adaptive arm of the immune system is not required for appendage regeneration and establishes an important model for novel experimental approaches in comparative immunology and regenerative biology.

immunology↗

bioRxiv2025

Computational Analysis of Silent Mutation Effects on SARS-CoV-2 RNA-Host RNA-Binding Protein Interactome

Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/677528v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@131df69org.highwire.dtl.DTLVardef@1429b6corg.highwire.dtl.DTLVardef@1ea0eacorg.highwire.dtl.DTLVardef@1696837_HPS_FORMAT_FIGEXP M_FIG C_FIG AbstractRNA-Binding proteins (RBPs) play critical roles in host-virus interaction. They facilitate the regulation of viral RNA (vRNA) turnover by recognizing and forming complexes with the vRNA structure via specific RNA motifs-RNA binding domain interaction. However, due to consistent evolving nature of viruses, silent mutations in the viral genome can impact RBP-vRNA binding thereby altering the RNA processing. While efforts have been made in characterizing other forms of mutations leading to changes in amino acids sequence in SARS-CoV-2 variants, details on how silent mutations impact RBP-vRNA interaction remain limited. Here, we use extensive in silico mutagenesis to introduce silent mutations in the SARS-CoV-2 genome to generate four different synthetic variants and map the interaction of the variants and the wild-type with a catalogue of human RBPs. Our result shows variation in accumulation and reduction of the RBPs binding motifs in the variants compared to the virus reference sequence on a global scale and at the UTRs. The majority of the RBPs with AU-rich binding motifs are reduced in the variants, while RBPs with mostly GC-rich motifs accumulate more binding positions, suggesting that a single change from U/A to G/C and vice versa can impact RBP- viral interactions. Furthermore, we use structural analysis to show the interaction of the vRNA with PUF60 and KHDRBS3 proteins, two RBPs that have not been previously implicated in SARS-CoV- 2 interactome. Our findings show that loss to the conserved poly(U) in PUF60 binding motifs in some of the variants affects its interaction with the protein at the 5' end, which may disrupt the function of the protein as an anti-viral RNA regulator. We also predicted the key residues in KHDRBS3 interacting with its binding motif in the wild-type at the 3' end, while noting that the vRNA structural changes in the variants may contribute to the loss of this interaction. Overall, our predictions contribute to the insights into virus evolution and pathogenicity of potential new variants due to the impact of synonymous changes in the nucleotide sequences on protein-RNA interaction.

bioinformatics↗