Lucie Kralickova


Last Name

Kralickova

First Name

Lucie

ORCID

0000-0001-8803-0164

Organisational unit

09595 - Snijder, Berend (ehemalig) / Snijder, Berend (former)

Filters

2023 - 20254
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Publications 1 - 4 of 4
  • Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications
    Item type: Journal Article
    Malinovska, Liliana; Cappelletti, Valentina; Kohler, Devon; et al. (2023)
    Nature Protocols
    Proteins regulate biological processes by changing their structure or abundance to accomplish a specific function. In response to a perturbation, protein structure may be altered by various molecular events, such as post-translational modifications, protein-protein interactions, aggregation, allostery or binding to other molecules. The ability to probe these structural changes in thousands of proteins simultaneously in cells or tissues can provide valuable information about the functional state of biological processes and pathways. Here, we present an updated protocol for LiP-MS, a proteomics technique combining limited proteolysis with mass spectrometry, to detect protein structural alterations in complex backgrounds and on a proteome-wide scale. In LiP-MS, proteins undergo a brief proteolysis in native conditions followed by complete digestion in denaturing conditions, to generate structurally informative proteolytic fragments that are analyzed by mass spectrometry. We describe advances in the throughput and robustness of the LiP-MS workflow and implementation of data-independent acquisition-based mass spectrometry, which together achieve high reproducibility and sensitivity, even on large sample sizes. We introduce MSstatsLiP, an R package dedicated to the analysis of LiP-MS data for the identification of structurally altered peptides and differentially abundant proteins. The experimental procedures take 3 d, mass spectrometric measurement time and data processing depend on sample number and statistical analysis typically requires similar to 1 d. These improvements expand the adaptability of LiP-MS and enable wide use in functional proteomics and translational applications.
  • Author Correction: Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications
    Item type: Other Journal Item
    Malinovska, Liliana; Cappelletti, Valentina; Kohler, Devon; et al. (2023)
    Nature Protocols
    In the version of this article initially published, the citation at the end of the Fig. 6b caption was incorrect. The correct reference—Murtagh, F., Legendre, P. Ward’s hierarchical agglomerative clustering method: which algorithms implement Ward’s criterion? J. Classif. 31, 274–295 (2014)—has been added and the reference list renumbered. In the second-to-last paragraph of the Introduction, the callout to Fig. 6e originally cited Fig. 7a and has been updated. The text changes have been made to the HTML and PDF versions of the article. Further, the numbered citations to Extended Data figures in the Supplementary Information were incorrect and have been replaced in a revised file online.
  • A transcriptional cilia signature defines an actionable cellular state of colorectal cancer
    Item type: Doctoral Thesis
    Kralickova, Lucie (2025)
    Cancer is a biologically diverse and clinically complex disease, where tumour progression and treatment response are shaped by dynamic processes such as clonal evolution, cellular plasticity, and interactions with the tumour microenvironment. Precision medicine seeks to address this complexity by tailoring treatment to the specific molecular features of each tumour. Genomic profiling in particular has led to important advances by guiding the use of targeted therapies, but its clinical utility is often limited to the subset of patients whose tumours harbour actionable mutations. Transcriptomic, epigenomic, proteomic, and multi-omic approaches aim to expand stratification frameworks, particularly in the context of non-genetic resistance or driver mechanisms, yet these remain largely exploratory or confined to research settings. Like genomics, they typically provide a static snapshot of tumour biology and capture only a subset of its functional complexity. Functional precision medicine (FPM) offers a complementary strategy by directly measuring drug sensitivity in patient-derived tumour cells. Rather than inferring response from molecular features, it captures the aggregate effects of all underlying biological processes, whether known or unknown, genetic or non-genetic, through empirical testing. This enables the identification of treatment vulnerabilities that may not be apparent from molecular profiling and helps address layers of tumour complexity that are poorly understood or difficult to quantify. These functional phenotypes can then be further interrogated through molecular analysis to uncover the biological programmes that drive them. This thesis evaluates pharmacoscopy, a high-content, image-based FPM method that quantifies drug responses at single-cell resolution ex vivo, as a platform for functional profiling in solid tumours and a means of generating clinically and biologically meaningful insight. To evaluate its translational potential, we first assessed the feasibility and scope of pharmacoscopy across solid tumours. A total of 290 samples were profiled across 19 indications, including colorectal cancer (CRC), meningioma, sarcoma, hepatocellular carcinoma, and others. Of these, 251 yielded interpretable drug response profiles, corresponding to a technical success rate of 87%. The method proved effective on surgical resections, fluid samples, and core nee- dle biopsies, demonstrating adaptability across specimen types and clinical contexts. In CRC, ex vivo profiling yielded results in 92% of cases overall, including 95% of surgical resections and 86% of core biopsies. In contrast, rates were lower in sarcoma, where fewer than half of the core biopsies (6 of 13) produced usable data. These differences likely reflect a combination of technical, logistical, and tumour-intrinsic factors such as cellularity and tissue architecture. Taken together, these results support the feasibility of pharmacoscopy for functional profiling across a broad range of solid tumours, while highlighting the importance of sample quality and tumour context. The resulting drug response profiles revealed a wide spectrum of ex vivo sensitivities, including to agents not routinely used in the respective indications. In CRC, where chemotherapy remains the mainstay of treatment, many tumours showed selective vulnerability to non-standard targeted therapies. Top-hitting compounds included the tyrosine kinase inhibitor dasatinib, all tested proteasome inhibitors (bortezomib, carfilzomib, ixazomib), and histone deacetylase inhibitors (belinostat, panobinostat), none of which are currently used in standard CRC treatment. In meningioma, where systemic therapies are not formally established, we observed common sensitivities to cisplatin, cobimetinib, ixazomib, and bortezomib. Even in rare or latestage tumours, where treatment options are often lacking or exhausted, pharmacoscopy was still able to identify distinct ex vivo drug sensitivities, highlighting its potential utility in clinically challenging settings. To explore the biological processes underlying the functional phenotypes identified through pharmacoscopy, we integrated ex vivo drug response profiles with transcriptomic data in CRC. This analysis led to the identification of a transcriptional programmeenriched for cilia-associated genes in malignant epithelial cells, which we termed the IBDS non-canonical cilia (IBDS NCC) signature. Rather than reflecting full reactivation of canonical ciliogenesis, the programme involves selective activation of a restricted subset of cilia-related genes. IBDS NCC expression was associated with heightened ex vivo sensitivity to multiple targeted therapies, including the FGFR inhibitor erdafitinib. Transcriptional network analysis and siRNA-mediated perturbation implicated the ciliogenesis regulators RFX2 and RFX3 as upstream modulators of this drugsensitive state. Clinically, elevated IBDS NCC expression correlated with poor prognosis and disease progression in an independent cohort, and was most pronounced in CMS2 and CMS4 subtypes—molecular phenotypes associated with WNT pathway activation and poor clinical outcomes, respectively. Staining for acetylated α-tubulin, a general marker of ciliary structures, showed a trend towards higher expression in drug-sensitive tumours, both ex vivo and in situ, although the association was modest and did not reach statistical significance in all settings. This lends further support to a directional relationship with the transcriptomic signature, while also underscoring the need for more specific protein-level markers to define the non-canonical cilia phenotype captured by IBDS NCC. These results support the IBDS NCC programme as a distinct, therapeutically vulnerable tumour state and illustrate how functional and molecular integration can uncover clinically actionable tumour states. Together, this thesis supports pharmacoscopy as a technically feasible and biologically informative platform for functional profiling in solid tumours. The work demonstrates its ability to recover drug sensitivities from real-world clinical specimens, to identify therapeutic opportunities beyond standard-of-care, and to uncover mechanistically and clinically relevant tumour states. While prospective validation is required to assess clinical utility, this thesis contributes to the conceptual and methodological foundation for the integration of functional profiling into precision oncology.
  • Alpha-synuclein interacts with regulators of ATP homeostasis in mitochondria
    Item type: Journal Article
    Serdiuk, Tetiana; Fleischmann, Yanick; Ghosh, Dhiman; et al. (2025)
    Nature Communications
    Mitochondrial dysfunction and accumulation of α-synuclein aggregates are hallmarks of the neurodegenerative Parkinsons disease and may be interconnected. To investigate the interplay between α-synuclein and brain mitochondria at near atomic structural level, we apply NMR and identify α-synuclein protein interactors using limited proteolysis-coupled mass spectrometry (LiP-MS). Several of the proteins identified are related to ATP synthesis and homeostasis and include subunits of ATP synthase and the adenylate kinase AK2. Furthermore, our data suggest that α-synuclein interacts with the Parkinsons disease-related protein DJ1. NMR analysis demonstrates that both AK2 and DJ1 bind to the C-terminus and other segments of α-synuclein. Using a functional assay for AK2, we show that monomeric α-synuclein has an activating effect, whereas C-terminally truncated α-synuclein and α-synuclein in an amyloid fibrillar state have no significant effect on AK2 activity. Our results suggest that α-synuclein modulates ATP homeostasis in a manner dependent on its conformation and its C-terminal acidic segment.
Publications 1 - 4 of 4