AdipoQ—a simple, open-source software to quantify adipocyte morphology and function in tissues and in vitro

Sieckmann, Katharina; Winnerling, Nora; Huebecker, Mylene; Leyendecker, Philipp; Ribeiro, Dalila; Gnad, Thorsten; Pfeifer, Alexander; Wachten, Dagmar; Hansen, Jan N.

doi:10.1091/mbc.e21-11-0592

Cited by 9 publications

(10 citation statements)

References 40 publications

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“…Afterward, cells were fixed, labeled, and images were acquired using the Zeiss Celldiscoverer 7 (20× objective, 0.5× magnification changer, resolution 0.9 µm/px, 6 images acquired per well, z‐stack acquired consisting of 7 planes with an inter‐plane distance of 3 µm). Images were quantified in ImageJ using the freely accessible ImageJ plugins ExtractSharpestPlane_JNH (available through GitHub at and archived on zenodo (https://doi.org/10.5281/zenodo.5646492), and AdipoQ Preparator and AdipoQ Analyzer (available on GitHub at https://github.com/hansenjn/AdipoQ) (Sieckmann et al , 2022) to automatize the workflow. Briefly, the sharpest plane of the z‐stack was determined by the highest pixel variance.…”

Section: Methodsmentioning

confidence: 99%

A cAMP signalosome in primary cilia drives gene expression and kidney cyst formation

et al. 2022

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The primary cilium constitutes an organelle that orchestrates signal transduction independently from the cell body. Dysregulation of this intricate molecular architecture leads to severe human diseases, commonly referred to as ciliopathies. However, the molecular underpinnings how ciliary signaling orchestrates a specific cellular output remain elusive. By combining spatially resolved optogenetics with RNA sequencing and imaging, we reveal a novel cAMP signalosome that is functionally distinct from the cytoplasm. We identify the genes and pathways targeted by the ciliary cAMP signalosome and shed light on the underlying mechanisms and downstream signaling. We reveal that chronic stimulation of the ciliary cAMP signalosome transforms kidney epithelia from tubules into cysts. Counteracting this chronic cAMP elevation in the cilium by small molecules targeting activation of phosphodiesterase‐4 long isoforms inhibits cyst growth. Thereby, we identify a novel concept of how the primary cilium controls cellular functions and maintains tissue integrity in a specific and spatially distinct manner and reveal novel molecular components that might be involved in the development of one of the most common genetic diseases, polycystic kidney disease.

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Section: Methodsmentioning

confidence: 99%

A cAMP signalosome in primary cilia drives gene expression and kidney cyst formation

et al. 2022

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“…In comparison with other freely available adipocyte quantification tools like Adiposoft (24), AdipoCount (21), and AdipoQ (27), ATAT introduces novel features. While Adiposoft, AdipoCount, and AdipoQ offer automated quantification of adipocyte number and cross-sectional areas in histological sections of WAT, only AdipoQ assesses the intensity of surrounding pixels adjacent to individual adipocytes.…”

Section: Discussionmentioning

confidence: 99%

Adipose Tissue Analysis Toolkit (ATAT) for Automated Analysis of Adipocyte Size and Extracellular Matrix in White Adipose Tissue

Robino,

Plekhanov,

Zhu

et al. 2023

Preprint

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ObjectiveThe pathological expansion of white adipose tissue (WAT) in obesity involves adipocyte hypertrophy accompanied by expansion of collagen-rich pericellular extracellular matrix (ECM) and the development of crown-like structures (CLS). Traditionally, WAT morphology is assessed through immunohistochemical analysis of WAT sections. However, manual analysis of large histological sections is time-consuming, and available digital tools for analyzing adipocyte size and pericellular ECM are limited. To address this gap, we developed the Adipose Tissue Analysis Toolkit (ATAT), an ImageJ plugin facilitating analysis of adipocyte size, WAT ECM and CLS.Methods and ResultsATAT utilizes local and image-level differentials in pixel intensity to independently threshold background, distinguishing adipocyte-free tissue without user input. It accurately captures adipocytes in histological sections stained with common dyes and automates the analysis of adipocyte cross-sectional area, total-field, and localized region-of-interest ECM. ATAT allows fully automated batch analysis of histological images using default or user-defined adipocyte detection parameters.ConclusionsATAT provides several advantages over existing WAT image analysis tools, enabling high-throughput analyses of adipocyte-specific parameters and facilitating the assessment of ECM changes associated with WAT remodeling due to weight changes and other pathophysiological alterations that affect WAT function.Study Importance QuestionsWhat is already known about this subject?The manual analysis of large WAT histological sections is very time-consuming, while digital tools for the analysis of WAT are limited.What are the new findings in your manuscript?-ATAT enables fully automated analysis of batches of histological images using either default or user-defined adipocyte detection parameters-ATAT allows high-throughput analyses of adipocyte-specific parameters and pericellular extracellular matrix-ATAT enables the assessment of fibrotic changes associated with WAT remodeling and crown-like structuresHow might your results change the direction of research or the focus of clinical practice?-ATAT is designed to work with histological sections and digital images obtained using a slide scanner or a microscope.-This tool will help basic and clinical researchers to conduct automated analyses of adipose tissue histological sections.

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“…Currently, there is the possibility of analyzing, in an automated way, the adipocytes in culture after cytochemistry and immunofluorescent staining, which facilitates and complements the analyses previously discussed [ 93 , 111 ].…”

Section: Alternative Methods To Animal Testing In Adipogenesismentioning

confidence: 99%

Alternative Methods as Tools for Obesity Research: In Vitro and In Silico Approaches

Pamplona

Zoehler²,

Shigunov³

et al. 2022

Life

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The study of adipogenesis is essential for understanding and treating obesity, a multifactorial problem related to body fat accumulation that leads to several life-threatening diseases, becoming one of the most critical public health problems worldwide. In this review, we propose to provide the highlights of the adipogenesis study based on in vitro differentiation of human mesenchymal stem cells (hMSCs). We list in silico methods, such as molecular docking for identification of molecular targets, and in vitro approaches, from 2D, more straightforward and applied for screening large libraries of substances, to more representative physiological models, such as 3D and bioprinting models. We also describe the development of physiological models based on microfluidic systems applied to investigate adipogenesis in vitro. We intend to identify the main alternative models for adipogenesis evaluation, contributing to the direction of preclinical research in obesity. Future directions indicate the association of in silico and in vitro techniques to bring a clear picture of alternative methods based on adipogenesis as a tool for obesity research.

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AdipoQ—a simple, open-source software to quantify adipocyte morphology and function in tissues and in vitro

Cited by 9 publications

References 40 publications

A cAMP signalosome in primary cilia drives gene expression and kidney cyst formation

A cAMP signalosome in primary cilia drives gene expression and kidney cyst formation

Adipose Tissue Analysis Toolkit (ATAT) for Automated Analysis of Adipocyte Size and Extracellular Matrix in White Adipose Tissue

Alternative Methods as Tools for Obesity Research: In Vitro and In Silico Approaches

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