Biology subjects

Bulanova, D.

Publications and source records attributed to Bulanova, D..

6 recordsLinked to original sources

bioRxiv2025

Generation of an in vitro 3D multicellular culture model of ovarian high-grade serous carcinoma

The development of translational ovarian cancer models to investigate and overcome treatment resistance accounting for the impact of the tumor microenvironment is critical. Here, we present a protocol to establish a multicellular culture model that retains both genetic complexity and the microenvironment of patient tumors, is amenable for molecular and phenotypic analyses, and high throughput drug testing. We describe steps for culturing and characterizing stromal cells derived from cryopreserved and fresh samples and detail procedures for combining them with organoids. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/686515v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@792c12org.highwire.dtl.DTLVardef@13c6680org.highwire.dtl.DTLVardef@6d73adorg.highwire.dtl.DTLVardef@1c56834_HPS_FORMAT_FIGEXP M_FIG C_FIG Before you beginThis protocol describes the in vitro generation of a complex 3D multicellular model (MC), mimicking relevant cellular and extracellular matrix (ECM) interactions in metastatic ovarian high-grade serous carcinoma (HGSC). First, cultures of stromal cells (cancer-associated fibroblasts (CAF), mesothelial cells and adipocytes) are generated. CAF and mesothelial cell cultures are established from fresh tumor tissues and/or from cryopreserved tissue digest and ascites fluid. Next, the identity of the stromal cells is evaluated using relevant markers, and the validated cultures are expanded and cryopreserved. Adipocytes are isolated from fresh tumor tissues and cultured in suspension for a short period before 3D embedding. Finally, previously established patient-derived cancer organoids1 are combined with relevant components of the tumor microenvironment (TME)2, including Type I collagen (main ECM protein in omental metastases) and stromal cells (Figure 1). The resulting MC model, which is viable for at least 14 days, can be used in various downstream applications. Here, we provide detailed protocols for two of them: high throughput drug sensitivity testing and single-cell RNA sequencing (scRNA-seq). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/686515v1_fig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@13c3a1dorg.highwire.dtl.DTLVardef@10b56f6org.highwire.dtl.DTLVardef@17a6e8forg.highwire.dtl.DTLVardef@f09b27_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Overview of the samples and culture conditions used to establish stromal cell cultures, and their integration with patient-derived organoids to generate the MC model. C_FIG

cancer biology↗

bioRxiv2023

Synthetic lethal interaction between WEE1 and PKMYT1 is a target for multiple low dose treatment of high-grade serous ovarian carcinoma

Ovarian cancer is driven by genetic alterations that necessitate protective DNA damage and replication stress responses through cell cycle control and genome maintenance. This creates specific vulnerabilities that may be exploited therapeutically. WEE1 kinase is a key cell cycle control kinase, and it has emerged as a promising cancer therapy target. However, adverse effects have limited its clinical progress, especially, when tested in combination with chemotherapies. A strong genetic interaction between WEE1 and PKMYT1 led us to hypothesize that a multiple low dose approach utilising joint WEE1 and PKMYT1 inhibition would allow exploitation of the synthetic lethality. In the present study, we found that the combination of WEE1 and PKMYT1 inhibition exhibited synergistic effects in eradicating ovarian cancer cells and ovarian organoid models at a low dose. The WEE1 and PKMYT1 inhibition synergistically promoted activation of CDK1 by decreasing the phosphorylation levels of T14 and Y15 residues. Furthermore, the combined treatment exacerbated DNA replication stress and replication catastrophe, leading to increase of the genomic instability and inflammatory STAT1 signalling activation. Finally, the multiple low dosing was well tolerated in mice. These findings suggest a new multiple low dose approach to harness the potency of WEE1 inhibition through the synthetic lethal interaction with PKMYT1 that may contribute to the development of new treatments for ovarian cancer.

cancer biology↗

bioRxiv2022

A synthetic lethal dependency on casein kinase 2 in response to replication-perturbing drugs in RB1-deficient ovarian and breast cancer cells

Treatment of patients with high-grade serous ovarian carcinoma (HGSOC) and triple-negative breast cancer (TNBC) includes platinum-based drugs, gemcitabine, and PARP inhibitors. However, resistance to these therapies develops in most cases, highlighting the need for novel therapeutic approaches and biomarkers to guide the optimal treatment choice. Using a CRISPR loss-of-function screen for carboplatin sensitizers in the HGSOC cell line OVCAR8, we identified CSNK2A2, the gene encoding for the alpha () catalytic subunit of casein kinase 2 (CK2). Expanding on this finding, we confirmed that the CK2 inhibitors silmitasertib and SGC-CK2-1 sensitized many, but not all, TNBC and HGSOC cell lines to the drugs that perturb DNA replication, including platinum drugs, gemcitabine, and PARP inhibitors. We identified RB1 tumor suppressor deficiency as a prerequisite context for the CK2 inhibition-mediated sensitization to these therapeutics. In RB1-deficient cells, CK2 inhibition resulted in accumulation of cells in S phase of the cell cycle, associated with micronuclei formation, and accelerated PARP inhibitor-induced aneuploidy and mitotic cell death. Patient HGSOC organoids that lacked RB1 expression displayed an enhanced long-term response to carboplatin and PARP inhibitor niraparib when combined with silmitasertib, suggesting RB1-stratified efficacy in patients. As RB1 deficiency affects up to 25% of HGSOC and 40% of TNBC cases, CK2 inhibition, proven safe from previous clinical exploration with silmitasertib, is a promising approach to overcome resistance to standard therapeutics in large strata of patients.

cancer biology↗

bioRxiv2022

A platform for efficient establishment, expansion and drug response profiling of high-grade serous ovarian cancer organoids

The broad research use of organoids from high-grade serous ovarian carcinoma (HGSC) has been hampered by low culture success rates and limited availability of fresh tumor material. Here we describe a method for generation and long-term expansion of HGSC organoids with efficacy markedly improved over previous reports (55% vs. 23-38%). We established organoids from cryopreserved material, demonstrating the feasibility of using viably biobanked tissue for HGSC organoid derivation. Genomic, histologic and single-cell transcriptomic analyses revealed that organoids recapitulated genetic and phenotypic features of original tumors. Organoid drug responses correlated with clinical treatment outcomes, although in culture conditions-dependent manner and only in organoids maintained in human plasma-like medium (HPLM). Organoids from consenting patients are available to the research community through a public biobank and organoid genomic data explorable through an interactive online tool. Taken together, this resource facilitates the application of HGSC organoids in basic and translational ovarian cancer research.

cancer biology↗

bioRxiv2020

Method to identify physical, chemical and biological factors that trigger Bcl-xL-mediated apoptosis

The evidence that pan-Bcl-2 or Bcl-xL-specific inhibitors prematurely kill virus-infected or RNA/DNA-transfected cells provides rationale for investigating these apoptotic inducers further. Here, we show that Bcl-xL-specific agent A-1155463 prematurely kills cells of different origins and the small roundworms (C. elegans), when combined with DNA-damaging agent 4-nitroquinoline-1-oxide (4NQO). The synergistic effect of 4NQO-A-1155463 combination was p53-dependent, was associated with the release of Bad and Bax from Bcl-xL, which triggered mitochondrial outer membrane permeabilization (MOMP). Combinations of Bcl-xL-specific inhibitors with certain anticancer compounds or physical insults also killed cells. Collectively, our results suggest that biological, chemical and physical factors trigger evolutionary conserved Bcl-xL-mediated apoptotic pathway.

cancer biology↗

bioRxiv2019

Improved detection of differentially represented DNA barcodes for high-throughput lineage phenomics

Cellular DNA barcoding has become a popular approach to study heterogeneity of cell populations and to identify lineages with differential response to cellular stimuli. However, there is a lack of reliable methods for statistical inference of differentially responding lineages. Here, we used mixtures of DNA-barcoded cell pools to generate a realistic benchmark read count dataset for modelling a range of outcomes of lineage-tracing experiments. By accounting for the statistical properties intrinsic to the DNA barcode read count data, we implemented an improved algorithm that provides a significantly higher accuracy at detecting differentially responding lineages, compared to current RNA-seq data analysis algorithms. Building on the reliable statistical methodology, we illustrate how multidimensional phenotypic profiling (or high-throughput lineage phenomics) enables one to deconvolute phenotypically distinct cell subpopulations within a cancer cell line. The mixture control dataset and our analysis results provide a systematic foundation for benchmarking and improving algorithms for lineage-tracing experiments.

bioinformatics↗