The temporal architecture of the seminiferous epithelial cycle revealed by spatial transcriptomics

Spermatogenesis features the seminiferous epithelial cycle, a periodic progression of germ-cell differentiation along the seminiferous tubules. Using seqFISH+ spatial transcriptomics, we profiled 2,653 genes in 867,062 mouse testis cells, revealing tubule-level transcriptional patterns that recapitulate the cycle and enable high-resolution temporal mapping of cells. Unlike other somatic cells, Sertoli cells exhibit a cyclic transcriptional profile synchronized with spermatogenesis. This cyclicity persists in germ-cell-depleted testes (busulfan and W/W^v), although with gene-specific dephasing and reduced amplitude, supporting an intrinsic Sertoli cyclic program. We identify retinoic acid (RA) as a permissive signal: germ-cell-depleted Sertoli cells cycle RA enzymes, while inhibiting RA synthesis via WIN 18,446 arrests them mid-cycle. Ligand-receptor analysis reveals bidirectional germ-Sertoli signaling. Notably, Wnt inhibition with LGK974 partially recapitulates germ-cell-depletion dephasing and amplitude changes. These findings support an integrative model where an intrinsic Sertoli program maintains baseline periodicity, while germ-cell signals refine the cycle to coordinate spermatogenesis.