A Novel High-Throughput Framework to Quantify Spatio-Temporal Tumor Clonal Dynamics

Bağlamış, Selami; Saha, Jaba; Heijden, Maartje van der; Miedema, Daniël M.; Gent, Démi van; Krawczyk, Przemek M.; Vermeulen, Louis; Sheraton, Vivek M.

doi:10.1007/978-3-031-36024-4_28

Cited by 3 publications

(3 citation statements)

References 19 publications

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“…Nuclear localization signal (NLS) of human c-Myc proto-oncogene (3′ GGACGACGCTTCTCCCAGTTTAACCTG 5′) 57 , 58 or human histone H2B gene sequence (3′ GGTCTCGGTCGCTTCAGACGAGGGCGGGGCTTTTTCCCGAGGTTCTTCCGCCACTGATTCCGCGTCTTCTTTCCGCCGTTCTTCGCGTTCGCGTCGGCGTTCCTCTCGATAAGGTAGATACACATGTTCCAAGACTTCGTCCAGGTGGGACTGTGGCCGTAAAGCAGGTTCCGGTACCCGTAGTACTTAAGCAAACACTTGCTGTAAAAGCTCGCGTAGCGTCCACTCCGAAGGGCGGACCGCGTAATGTTGTTCGCGAGCTGGTAGTGGAGGTCCCTCTAGGTCTGCCGGCACGCGGACGACGACGGACCCCTCAACCGGTTCGTGCGGCACAGGCTCCCATGATTCCGGTAGTGGTTCATGTGGTCGCGATTC 5′) were inserted into LeGO-C2 (27339), LeGO-V2 (27340), and LeGO-Cer2 (27338) (Addgene) vectors for nuclear visualisation, using standard DNA cloning protocols. Cells were transduced with lentiviral gene ontology (LeGO) markers in accordance with previously published works by Weber et al 25 and Heijen et al 18 .…”

Section: Methodsmentioning

confidence: 99%

Using picoliter droplet deposition to track clonal competition in adherent and organoid cancer cell cultures

Baglamis,

Sheraton,

Meijer

et al. 2023

Sci Rep

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Clonal growth and competition underlie processes of key relevance in etiology, progression and therapy response across all cancers. Here, we demonstrate a novel experimental approach, based on multi-color, fluorescent tagging of cell nuclei, in combination with picoliter droplet deposition, to study the clonal dynamics in two- and three-dimensional cell cultures. The method allows for the simultaneous visualization and analysis of multiple clones in individual multi-clonal colonies, providing a powerful tool for studying clonal dynamics and identifying clonal populations with distinct characteristics. Results of our experiments validate the utility of the method in studying clonal dynamics in vitro, and reveal differences in key aspects of clonal behavior of different cancer cell lines in monoculture conditions, as well as in co-cultures with stromal fibroblasts.

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Section: Methodsmentioning

confidence: 99%

Using picoliter droplet deposition to track clonal competition in adherent and organoid cancer cell cultures

Baglamis,

Sheraton,

Meijer

et al. 2023

Sci Rep

Self Cite

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“…The nuclear localization signal (NLS) sequence from the human c-Myc proto-oncogene (3′ GGACGACGCTTCTCCCAGTTTAACCTG 5′) was cloned into LeGO-C2 (#27339, addgene, Watertown, MA, USA), LeGO-V2 (#27340, addgene) and LeGO-Cer2 (#27338, addgene) vectors, encoding mCherry, Venus and Cerulean maker genes, respectively, to enable nuclear visualization [17][18][19]. Standard DNA cloning protocols were employed for the cloning process.…”

Section: Generation Of Nuclear Derivatives Of Lentiviral Gene Ontolog...mentioning

confidence: 99%

High-Content and High-Throughput Clonogenic Survival Assay Using Fluorescence Barcoding

Qian,

Baglamis,

Redeker

et al. 2023

Cancers

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The Clonogenic Survival Assay (CSA) is a fundamental tool employed to assess cell survival and proliferative potential in cancer research. Despite its importance, CSA faces limitations, primarily its time- and labor-intensive nature and its binary output. To overcome these limitations and enhance CSA’s utility, several approaches have been developed, focusing on increasing the throughput. However, achieving both high-content and high-throughput analyses simultaneously has remained a challenge. In this paper, we introduce LeGO-CSA, an extension of the classical CSA that employs the imaging of cell nuclei barcoded with fluorescent lentiviral gene ontology markers, enabling both high-content and high-throughput analysis. To validate our approach, we contrasted it with results from a classical assay and conducted a proof-of-concept screen of small-molecule inhibitors targeting various pathways relevant to cancer treatment. Notably, our results indicate that the classical CSA may underestimate clonogenicity and unveil intriguing aspects of clonal cell growth. We demonstrate the potential of LeGO-CSA to offer a robust approach for assessing cell survival and proliferation with enhanced precision and throughput, with promising implications for accelerating drug discovery and contributing to a more comprehensive understanding of cellular behavior in cancer.

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“…This removes the friction that exists with different data formats and gives space for more efficient and faster data handling, which results in new insights to evolve more rapidly ( Abuimara et al., 2022 ). Large numerical datasets, such as data originating from multiscale simulation studies ( Sheraton et al., 2019 ; Béquignon et al., 2023 ), -omics ( Subramanian et al., 2020 ) or imaging studies ( Bray et al., 2017 ; Baglamis et al., 2023 ), should be properly categorized along with clearly described provenance. Additionally, the origin and composition of the data will have to be described, to enable data reconstructions in such a way that it cannot be misinterpreted.…”

Section: Introductionmentioning

confidence: 99%

FAIR compliant database development for human microbiome data samples

Dorst,

Zeevenhooven,

Wilding

et al. 2024

Front. Cell. Infect. Microbiol.

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IntroductionSharing microbiome data among researchers fosters new innovations and reduces cost for research. Practically, this means that the (meta)data will have to be standardized, transparent and readily available for researchers. The microbiome data and associated metadata will then be described with regards to composition and origin, in order to maximize the possibilities for application in various contexts of research. Here, we propose a set of tools and protocols to develop a real-time FAIR (Findable. Accessible, Interoperable and Reusable) compliant database for the handling and storage of human microbiome and host-associated data.MethodsThe conflicts arising from privacy laws with respect to metadata, possible human genome sequences in the metagenome shotgun data and FAIR implementations are discussed. Alternate pathways for achieving compliance in such conflicts are analyzed. Sample traceable and sensitive microbiome data, such as DNA sequences or geolocalized metadata are identified, and the role of the GDPR (General Data Protection Regulation) data regulations are considered. For the construction of the database, procedures have been realized to make data FAIR compliant, while preserving privacy of the participants providing the data.Results and discussionAn open-source development platform, Supabase, was used to implement the microbiome database. Researchers can deploy this real-time database to access, upload, download and interact with human microbiome data in a FAIR complaint manner. In addition, a large language model (LLM) powered by ChatGPT is developed and deployed to enable knowledge dissemination and non-expert usage of the database.

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A Novel High-Throughput Framework to Quantify Spatio-Temporal Tumor Clonal Dynamics

Cited by 3 publications

References 19 publications

Using picoliter droplet deposition to track clonal competition in adherent and organoid cancer cell cultures

Using picoliter droplet deposition to track clonal competition in adherent and organoid cancer cell cultures

High-Content and High-Throughput Clonogenic Survival Assay Using Fluorescence Barcoding

FAIR compliant database development for human microbiome data samples

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