van IJzendoorn, D. G. P. | Search bioRxiv

bioRxiv2024

TissueMap: A Web-Based Multiplexed Image Viewer

Datasets generated by spatial biology techniques such as multiplex immunofluorescence staining or spatial transcriptomics profiling of histologic sections carry a tremendous wealth of information. Several commercial platforms exist that can simultaneously acquire 1-1000 distinct marker signals (e.g., MIBI, CODEX, Orion, Nanostring CosMX SMI, Vizgen). However, due to the large size of these datasets, their viewing and sharing are slow, laborious, and require extensive computational resources. To overcome this, we developed TissueViewer, a web-based viewer designed to deliver high-resolution images over the internet with low bandwidth requirements and at high speed.

bioinformatics↗

bioRxiv2022

Interactions in CSF1-driven Tenosynovial Giant Cell Tumors

The majority of cells in Tenosynovial Giant Cell Tumor (TGCT) are macrophages responding to CSF1 that is overproduced by a small number of neoplastic cells with a chromosomal translocation involving the CSF1 gene. Treatment with inhibitors of the CSF1 pathway has been clinically effective. An autocrine loop was postulated where the neoplastic cells are stimulated through the CSF1 receptor (CSF1R) expressed on their surface. Here we show that the neoplastic cells themselves do not express CSF1R and therefore may be unaffected by current therapies. We identified a new marker for synoviocytes, GFPT2, that highlights the tumor cells in TCGT and is associated with activation of the YAP1/TAZ pathway. The neoplastic cells in TGCT are highly similar non-neoplastic synoviocytes. Finally, we provide molecular support for the osteoclast-like features of the giant cells in TGCT that correlate with the destructive effects of TGCT on bone.

cancer biology↗