Cheung, J. P. Y. | Search bioRxiv

bioRxiv2026

Spatial mitochondrial lineage tracing uncovers a premetastatic niche and microenvironment programmed fate switching in osteosarcoma

Osteosarcoma progression involves complex spatiotemporal dynamics, yet the lineage relationships underlying tumor cell fate decisions remain poorly understood. Here we integrate single cell and spatial transcriptomics and mitochondrial variants-based lineage tracing to map the evolution of a late-stage, non-metastatic osteosarcoma. Single cell pseudotemporal reconstruction of malignant cells reveals a stepwise cascade of transcriptional programs that instructs bifurcation of COL3A1 progenitors into ALPL osteoblastic and THY1 mesenchymal lineages. Critically, we demonstrate that the metastatic THY1 mesenchymal cell fate is not governed by cell-autonomous transcriptional programs alone; this pro-tumorigenic state requires strict spatial licensing via direct co-localization with PLVAP dysfunctional endothelia to form a pro-metastatic niche (THY1_Endo) enriched for PTN/NOTCH signaling. To distinguish clonal ancestry from microenvironmental plasticity, we leveraged spatially resolved somatic mitochondrial variants as endogenous lineage tracers. A spatial autocorrelation filter confirmed significant clonal spatial coherence (Z = 10.07, p {approx} 4x10-{superscript 2}). Phylogenetic reconstruction using a Wright-Fisher drift model coupled with a hidden Markov tree (WF-HMT) revealed a striking directional transition rate from COL3A1 to THY1 tumor cells (724.08) versus the reverse (4.09)--a [~]177-fold asymmetry--whereas the COL3A1 to ALPL transition rate was lower (0.47). Notably, drift-agnostic coarse VAF clustering failed to resolve ALPL versus THY1 bifurcation, underscoring that explicit modeling of stochastic mitochondrial drift is essential for uncovering directional fate locking. We propose a "time-space-lineage" relay model where sequential microenvironmental signals program tumor cell fate and pre-metastatic niche assembly through irreversible clonal commitment. This multi-dimensional framework bridges single-cell states, spatial organization, temporal dynamics, and clonal ancestry --underscoring the power of somatic mitochondrial variants to resolve clonal history and intercept cancer evolution.

bioinformatics↗

bioRxiv2023

Association of an estrogen-sensitive Pax1-Col11a1-Mmp3 signaling axis with adolescent idiopathic scoliosis

Adolescent idiopathic scoliosis (AIS) is a common and progressive spinal deformity in children that exhibits striking sexual dimorphism, with girls at more than five-fold greater risk of severe disease compared to boys. Despite its medical impact, the molecular mechanisms that drive AIS are largely unknown. We previously defined a female-specific AIS genetic risk locus in an enhancer near the PAX1 gene. Here we sought to define the roles of PAX1 and newly-identified AIS-associated genes in the developmental mechanism of AIS. In a genetic study of 10,519 individuals with AIS and 93,238 unaffected controls, significant association was identified with a variant in COL11A1 encoding collagen (1) XI (rs3753841; NM_080629.2_c.4004C>T; p.(Pro1335Leu); P=7.07e-11, OR=1.118). Using CRISPR mutagenesis we generated Pax1 knockout mice (Pax1-/-). In postnatal spines we found that PAX1 and collagen (1) XI protein both localize within the intervertebral disc (IVD)-vertebral junction region encompassing the growth plate, with less collagen (1) XI detected in Pax1-/- spines compared to wildtype. By genetic targeting we found that wildtype Col11a1 expression in costal chondrocytes suppresses expression of Pax1 and of Mmp3, encoding the matrix metalloproteinase 3 enzyme implicated in matrix remodeling. However, this suppression was abrogated in the presence of the AIS-associated COL11A1P1335L mutant. Further, we found that either knockdown of the estrogen receptor gene Esr2, or tamoxifen treatment, significantly altered Col11a1 and Mmp3 expression in chondrocytes. We propose a new molecular model of AIS pathogenesis wherein genetic variation and estrogen signaling increase disease susceptibility by altering a Pax1-Col11a1-Mmp3 signaling axis in spinal chondrocytes.

genetics↗