Biology subjects

Rantanen, V.

Publications and source records attributed to Rantanen, V..

3 recordsLinked to original sources

bioRxiv2020

Agile workflow for interactive analysis of mass cytometry data

MotivationSingle-cell proteomics technologies, such as mass cytometry, have enabled characterization of cell-to-cell variation and cell populations at a single cell resolution. These large amounts of data, however, require dedicated, interactive tools for translating the data into knowledge. ResultsWe present a comprehensive, interactive method called Cyto to streamline analysis of large-scale cytometry data. Cyto is a workflow-based open-source solution that automatizes the use of of state-of-the-art single-cell analysis methods with interactive visualization. We show the utility of Cyto by applying it to mass cytometry data from peripheral blood and high-grade serous ovarian cancer (HGSOC) samples. Our results show that Cyto is able to reliably capture the immune cell sub-populations from peripheral blood as well as cellular compositions of unique immune- and cancer cell subpopulations in HGSOC tumor and ascites samples. AvailabilityThe method is available as a Docker container at https://hub.docker.com/r/anduril/cyto and the user guide and source code are available at https://bitbucket.org/anduril-dev/cyto Contactsampsa.hautaniemi@helsinki.fi Supplementary informationSupplementary material is available and FCS files are hosted at flowrepository.org/id/FR-FCM-Z2LW

bioinformatics↗

bioRxiv2019

Epigenetic inhibitors sensitize DLBCL cells to rituximab and doxorubicin

Primary therapy for diffuse large B-cell lymphoma (DLBCL) is an immunochemotherapy regimen comprising rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). While R-CHOP cures 60% of the patients with DLBCL, those who do not respond or relapse have dismal prognosis, and effective treatment strategies are needed. Due to the plastic nature of the epigenome and its fundamental role in regulating cell identity, we hypothesized that reprogramming the epigenome can overcome resistance to R-CHOP. We developed a novel drug screening protocol to identify epigenetic modifiers that sensitize DLBCL cell lines to immunochemotherapy. Of the herein tested 60 epigenetic compounds, we identified several histone deacetylase (HDAC) and histone methyltransferase (HMT) inhibitors that acted synergistically with immunochemotherapy. We show that sensitization through HDAC and HMT inhibitors is achieved by dysregulating homologous recombination, a central DNA repair pathway, as well as by disrupting the cell cycle and affecting the apoptotic pathway. Epigenetic inhibitors are well-tolerated, which together with our findings support their use in combination with immunochemotherapy in patients with primary refractory and relapsed DLBCL.

cancer biology↗

bioRxiv2018

FGFR4 phosphorylates MST1 to confer breast cancer cells resistance to MST1/2-dependent apoptosis

Cancer cells balance with the equilibrium of cell death and growth to expand and metastasize. The activity of mammalian sterile20-like kinases MST1/2 has been linked to apoptosis and tumor suppression via YAP/Hippo pathway dependent and independent mechanisms. With a kinase substrate screen we identified here MST1 and MST2 among the top substrates for fibroblast growth factor receptor 4 (FGFR4). In COS-1 cells, MST1 was phosphorylated at Y433 residue in an FGFR4 kinase activity-dependent manner, as assessed by mass spectrometry. Blockade of this phosphorylation by Y433F mutation induced MST1 activation, as reflected by increased autophosphorylation at T183 in FGFR4 overexpressing MDA-MB-231 cells. Importantly, the specific short-term inhibition or knockdown of FGFR4 also led to MST1/2 activation in conjunction with induction of MST1/2-dependent apoptosis in an endogenous model of HER2+ breast cancer cells. Moreover, FGFR4 knockdown increased the level of active nuclear MST1 coincidentally with cell polarization and membrane-association of YAP in three-dimensional breast cancer cell spheres. Consistently, FGFR4 overexpression correlated with reduced Hippo pathway-mediated, nuclear translocation-inhibiting YAP phosphorylation, and abysmal HER2+ breast carcinoma patient outcome in TCGA cohort. Our results reveal a novel mechanism for FGFR4 oncogenic activity via suppression of the stress-associated MST1/2-dependent apoptosis machinery in the tumor cells with prominent HER/ERBB signaling driven proliferation.

cancer biology↗