A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids

Sockell, Alexandra; Wong, Wing; Longwell, Scott; Vu, Thy; Karlsson, Kasper; Mokhtari, Daniel; Schaepe, Julia; Lo, Yuan-Hung; Cornelius, Vincent; Kuo, Calvin; Van Valen, David; Curtis, Christina; Fordyce, Polly M.

doi:10.1016/j.cels.2023.08.002

Cited by 3 publications

(5 citation statements)

References 90 publications

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“…Noteworthy, the devised complementary engineered artificial niches present a methodological approach to quantify the functional behavior of blasts derived from patients, assessing the polarity across different stages of AML, with potential implications for future prognostic evaluations, as well as identification of the exact contribution of the loss of blast polarity to the progression of leukemia. They also constitute a convenient platform to parallelize genomic or chemical screens combined with automated image analysis 45 in order to reveal the molecular mechanism underlying the defective polarization of leukemic cells and identify chemical strategies to revert it.…”

Section: Discussionmentioning

confidence: 99%

AML patient blasts exhibit polarization defect upon interaction with bone marrow stromal cells

Saadallah,

Vianay,

Bonnemay

et al. 2024

Preprint

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Hematopoietic stem and progenitor cells (HSPCs) establish specific interactions with bone marrow stromal cells, leading to their polarization. Given the role of cell polarity in protection against tumorigenesis and the importance of the niche in hematological disorders such as acute myeloid leukemias (AMLs), we investigated the polarization capacities of leukemic blasts from patients. Using engineered micro-niches and centrosome position with respect to the contact site with stromal cells as a proxy for cell polarization, we showed that AML cell lines and primary cells from AML patient blasts were unable to polarize in contact with healthy stromal cells. In return, exposure to AML patient-derived stromal cells compromised the polarization of healthy adult HSPCs and AML blasts from patients. Using live cell imaging in engineered “bone-marrow-on-a-chip”, we further revealed that stromal cells from a leukemic niche increased the migration speed and distance of healthy HSPCs and AML blast as compared to their behavior in contact with healthy stromal cells. The results collectively demonstrated the respective influences of intrinsic AML blast transformation and extrinsic contact with AML stromal cells on the defective polarization of AML blast. They suggested that leukemic progression is associated with cell polarization defects and proposed new methodological approaches to investigate this relationship in AML progression.

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Section: Discussionmentioning

confidence: 99%

AML patient blasts exhibit polarization defect upon interaction with bone marrow stromal cells

Saadallah,

Vianay,

Bonnemay

et al. 2024

Preprint

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“…Organoids are hetero-cellular biomimetic tissue models that have become a powerful experimental tool transforming basic science and translational research [ 126 ]. While the traditional low-throughput methods provide valuable biological insights, high-throughput methods are needed to fully exploit the potential of organoids as ex vivo models.…”

Section: Novel Applications Of Morphological Profiling In Drug Discoverymentioning

confidence: 99%

“…While the traditional low-throughput methods provide valuable biological insights, high-throughput methods are needed to fully exploit the potential of organoids as ex vivo models. Modeling the development of disease with organoids that can recapitulate tissue structure, pathology, phenotypes, and differentiation has revolutionized the study of various human diseases including cancer [ 126 , 127 ]. In a recent study, Silva et al.…”

Section: Novel Applications Of Morphological Profiling In Drug Discoverymentioning

confidence: 99%

“…These can cause limitations in understanding the phenotypic heterogeneity, while most of the methods do not employ integrated analytical pipelines into the overall workflow [ 135–139 ] or the ability to selectively retrieve organoids for downstream investigations. Overcoming some of these issues, Forsyth and a team of researchers [ 126 ] have built an open-source microwell-based platform for high-throughput quantification using image-based parameters. The method utilizes an organoid-optimized deep-learning model that can be integrated with existing culturing protocols and micro-well platforms to investigate phenotypic features across different tissues.…”

Section: Novel Applications Of Morphological Profiling In Drug Discoverymentioning

confidence: 99%

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Morphological profiling for drug discovery in the era of deep learning

Tang,

Ratnayake,

Seabra

et al. 2024

Briefings in Bioinformatics

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Morphological profiling is a valuable tool in phenotypic drug discovery. The advent of high-throughput automated imaging has enabled the capturing of a wide range of morphological features of cells or organisms in response to perturbations at the single-cell resolution. Concurrently, significant advances in machine learning and deep learning, especially in computer vision, have led to substantial improvements in analyzing large-scale high-content images at high throughput. These efforts have facilitated understanding of compound mechanism of action, drug repurposing, characterization of cell morphodynamics under perturbation, and ultimately contributing to the development of novel therapeutics. In this review, we provide a comprehensive overview of the recent advances in the field of morphological profiling. We summarize the image profiling analysis workflow, survey a broad spectrum of analysis strategies encompassing feature engineering– and deep learning–based approaches, and introduce publicly available benchmark datasets. We place a particular emphasis on the application of deep learning in this pipeline, covering cell segmentation, image representation learning, and multimodal learning. Additionally, we illuminate the application of morphological profiling in phenotypic drug discovery and highlight potential challenges and opportunities in this field.

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“…Such platforms include microwell arrays, microphysiological systems (or organs-on-a-chip), and 3D bioprinting. Microwell arrays are screening platforms that emerge from high-density cell aggregates, generally of a composition defined by Poisson statistics, and arranged spatially for straightforward imaging [23][24][25] . Microwells can improve organoid homogeneity but are generally limited in the eventual size and geometry of the resulting tissue.…”

Section: Introductionmentioning

confidence: 99%

MAGIC matrices: freeform bioprinting materials to support complex and reproducible organoid morphogenesis

Graham,

Khoo,

Srivastava

et al. 2024

Preprint

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Organoids are powerful models of tissue physiology, yet their applications remain limited due to a lack of complex tissue morphology and high organoid-to-organoid structural variability. To address these limitations we developed a soft, composite yield-stress extracellular matrix that supports freeform 3D bioprinting of cell slurries at tissue-like densities. Combined with a custom piezoelectric printhead, this platform allows more reproducible and complex morphogenesis from uniform and spatially organized organoid “seeds.” At 4 °C the material exhibits reversible yield-stress behavior to support long printing times without compromising cell viability. When transferred to cell culture at 37 °C, the material cross-links and exhibits similar viscoelasticity and plasticity to basement membrane extracts such as Matrigel. We use this setup for high-throughput generation of intestinal and salivary gland organoid arrays that are morphologically indistinguishable from those grown in pure Matrigel, but exhibit dramatically improved homogeneity in organoid size, shape, maturation time, and budding efficiency. The reproducibility of organoid structure afforded by this approach increases the sensitivity of assays by orders of magnitude, requiring less input material and reducing analysis times. The flexibility of this approach additionally enabled the fabrication of perfusable intestinal organoid tubes. Combined, these advances lay the foundation for the efficient design of complex tissue morphologies in both space and time.

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A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids

Cited by 3 publications

References 90 publications

AML patient blasts exhibit polarization defect upon interaction with bone marrow stromal cells

AML patient blasts exhibit polarization defect upon interaction with bone marrow stromal cells

Morphological profiling for drug discovery in the era of deep learning

MAGIC matrices: freeform bioprinting materials to support complex and reproducible organoid morphogenesis

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