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PXD052075-1

PXD052075 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleLoss of Kmt2c or Kmt2d drives brain metastasis via KDM6A-dependent upregulation of MMP3
DescriptionHistone lysine methyltransferases KMT2C and KMT2D are among the most commonly mutated genes in the highly metastatic TNBC subtype of breast cancer. However, it is not known if mutations of either of these genes similarly effect epigenomic and transcriptomic landscape or if a specific downstream target might influence metastases. Here, we generated heterogenous Kmt2c or Kmt2d KO murine TNBC cell lines side-by-side and performed in vivo metastases assay in syngeneic immunocompetent mice. Deficiency for either Kmt2c or Kmt2d, both, induced brain metastases from formerly non-metastatic cells. scRNAseq showed activation of pro-inflammatory pathways but conversely also increase of immune checkpoint blocking genes. Interestingly, histone mass spectrometry revealed changes of H3K27 but not the main substrate H3K4. However, ChIPseq for both, H3K4 and H3K27 modifications showed significant changes compared to wildtype cells. Strikingly, genome occupancy of H3K27me3 was reduced while H3K27 demethylase KDM6A was enriched on genomes of KO cells. Integration with gene expression data revealed significant correlations with histone and KDM6A ChIPseq, identifying them as a main driver of Kmt2c or Kmt2d KO-specific gene regulation. Although our datasets revealed more unique than shared signatures, we found Mmp3 being a common target upon Kmt2c or Kmt2d KO. Indeed, downregulation of Mmp3 reversed induction of Kmt2c and Kmt2d KO-dependent brain metastases. Finally, we found that Kdm6a knockdown reduces Mmp3 levels, again, leading to reduction of brain metastases of Kmt2c or Kmt2d KO cells.
HostingRepositoryMassIVE
AnnounceDate2024-05-07
AnnouncementXMLSubmission_2024-05-07_06:56:49.146.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMalvina
SpeciesList scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationListunknown modification
InstrumentQ Exactive Plus
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-05-07 06:42:58ID requested
12024-05-07 06:56:49announced
Publication List
no publication
Keyword List
submitter keyword: global chromatin profiling
Contact List
Kornelia Polyak
contact affiliationHarvard Medical School
contact emailKornelia_Polyak@dfci.harvard.edu
lab head
Malvina
contact affiliationPapanastasiou
contact emailmalpap@broadinstitute.org
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location
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