Animal models are essential for studying nociception, yet differences in cellular and transcriptional architecture complicate translation to human pain biology. To address this gap, we developed a cross-species single-cell transcriptomic integration pipeline to build a comprehensive tongue atlas from mouse, rat, marmoset, and human datasets. Tongue tissue from naïve C57BL/6 mice and common marmosets was collected and processed for scRNA-seq using 10x Genomics platforms. Human datasets were obtained from the Tabula Sapiens Consortium, and rat datasets from NCBI GEO. A unified human gene space was constructed using species-specific ortholog mapping strategies — Ensembl-derived tables for mouse and rat, and NCBI Gene E-utilities for marmoset — yielding ~17,000 mapped genes. Species-aware batch correction was applied using Harmony with conservative parameterization to preserve biological divergence. The final atlas comprises 135,736 cells spanning 7 major cell types. To systematically quantify cross-species conservation, we implemented a multi-step pipeline using FindConservedMarkers (log2FC > 0.6, Bonferroni P < 0.05 across all species), identifying 1,342 conserved genes from 4,026 candidates. Normalized rank-based standard deviation analysis classified 51.8% of conserved genes as stable, including 206 highly stable genes. Epithelial cells showed the strongest transcriptional conservation (Pearson r = 0.83–0.86), while Schwann cells exhibited the highest variability. Validation against canonical markers confirmed conservation in 17 of 24 genes. This atlas and accompanying pipeline provide a scalable computational framework for comparative and translational studies of pain-relevant biology.

Co-authors: Jaclyn Merlo, Sergey Shein, Zhao Lai, Yidong Chen, Shivani Ruparel