Matched primary-metastasis single-nucleus and spatial profiling of leiomyosarcoma identifies antigen-presenting fibroblasts at the tumor-organ interface
- 1Institute of Pathology, LMU Munich, Munich, Germany
Abstract
Leiomyosarcoma is an aggressive soft tissue sarcoma that metastasizes preferentially to lung and liver. Because matched primary and metastatic specimens are rarely available, the cellular changes that accompany metastatic progression remain poorly defined. Here we combined single-nucleus RNA sequencing of archival FFPE tissue from four matched primary-metastasis pairs (two lung, two liver metastases; 48,941 nuclei) with imaging-based spatial transcriptomics of an extended tissue microarray cohort of 21 patients (69 cores, 313,218 cells). Malignant cells, not assignable from transcriptomic references alone, were defined by inferred copy number profiles that were concordant with matched DNA methylation arrays and confirmed the clonal origin of each metastasis. Malignant metaprograms were organ-associated, with a stress- and hypoxia-associated program enriched in lung metastases and a proliferative, matrix-remodeling program enriched in liver metastases. Antigen-presenting cancer-associated fibroblasts (apCAFs) were enriched in metastases relative to matched primaries. This shift was reproduced in the spatial cohort (p = 0.001), where apCAFs formed a discrete band at the tumor-organ interface between malignant cells and adjacent parenchyma, whereas they were sparse and randomly distributed in primary tumors. Spatial transcriptomics further resolved the malignant compartment into three histomolecular phenotypes: (i) smooth-muscle-like with myxoid features, (ii) GPNMB with anaplastic features, and (iii) PDGFRB with vessel-rich stroma, each with a concordant immunohistochemical (-SMA, GPNMB, PDGFRB) and morphological correlate. Together, our data provide a matched primary-metastasis reference for leiomyosarcoma, identify apCAFs as a spatially organized, metastasis-associated stromal population, and delineate histomolecular phenotypes recognizable by routine immunohistochemistry, including a GPNMB phenotype potentially amenable to GPNMB-directed therapies.
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BibTeX
@misc{kuebler2026matched,
title = {{Matched primary-metastasis single-nucleus and spatial profiling of leiomyosarcoma identifies antigen-presenting fibroblasts at the tumor-organ interface}},
author = {A. Kuebler and L. Bergmayr and T. Knoesel and P. Jurmeister and Y. Zhdanovich and L. Berclaz and J. Hendriksen and D. Karaoglu and R. L. Zuber and M. Hoberger and D. Di Gioia and M. Albertsmeier and M. Grube and M. Trepel and C. Mogler and F. Anger and K. Fechner and P. Keyl and S. Froehling and F. Klauschen and L. H. Lindner and A. Burkhard-Meier and A. Mock},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.02.754332},
url = {https://www.biorxiv.org/content/10.64898/2026.10.02.754332v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Matched primary-metastasis single-nucleus and spatial profiling of leiomyosarcoma identifies antigen-presenting fibroblasts at the tumor-organ interface
AU - A. Kuebler
AU - L. Bergmayr
AU - T. Knoesel
AU - P. Jurmeister
AU - Y. Zhdanovich
AU - L. Berclaz
AU - J. Hendriksen
AU - D. Karaoglu
AU - R. L. Zuber
AU - M. Hoberger
AU - D. Di Gioia
AU - M. Albertsmeier
AU - M. Grube
AU - M. Trepel
AU - C. Mogler
AU - F. Anger
AU - K. Fechner
AU - P. Keyl
AU - S. Froehling
AU - F. Klauschen
AU - L. H. Lindner
AU - A. Burkhard-Meier
AU - A. Mock
PY - 2026
DA - 2026/10/02
PB - bioRxiv
DO - 10.64898/2026.10.02.754332
UR - https://www.biorxiv.org/content/10.64898/2026.10.02.754332v1
AB - Leiomyosarcoma is an aggressive soft tissue sarcoma that metastasizes preferentially to lung and liver. Because matched primary and metastatic specimens are rarely available, the cellular changes that accompany metastatic progression remain poorly defined. Here we combined single-nucleus RNA sequencing of archival FFPE tissue from four matched primary-metastasis pairs (two lung, two liver metastases; 48,941 nuclei) with imaging-based spatial transcriptomics of an extended tissue microarray cohort of 21 patients (69 cores, 313,218 cells). Malignant cells, not assignable from transcriptomic references alone, were defined by inferred copy number profiles that were concordant with matched DNA methylation arrays and confirmed the clonal origin of each metastasis. Malignant metaprograms were organ-associated, with a stress- and hypoxia-associated program enriched in lung metastases and a proliferative, matrix-remodeling program enriched in liver metastases. Antigen-presenting cancer-associated fibroblasts (apCAFs) were enriched in metastases relative to matched primaries. This shift was reproduced in the spatial cohort (p = 0.001), where apCAFs formed a discrete band at the tumor-organ interface between malignant cells and adjacent parenchyma, whereas they were sparse and randomly distributed in primary tumors. Spatial transcriptomics further resolved the malignant compartment into three histomolecular phenotypes: (i) smooth-muscle-like with myxoid features, (ii) GPNMB with anaplastic features, and (iii) PDGFRB with vessel-rich stroma, each with a concordant immunohistochemical (-SMA, GPNMB, PDGFRB) and morphological correlate. Together, our data provide a matched primary-metastasis reference for leiomyosarcoma, identify apCAFs as a spatially organized, metastasis-associated stromal population, and delineate histomolecular phenotypes recognizable by routine immunohistochemistry, including a GPNMB phenotype potentially amenable to GPNMB-directed therapies.
ER -