bims-lypmec 2024-10-06 papers

Issue of 2024‒10‒06
five papers selected by
Satoru Kobayashi, New York Institute of Technology

BMC Biol. 2024 Sep 30. 22(1): 220

OrgaMapper: a robust and easy-to-use workflow for analyzing organelle positioning.

Christopher Schmied, Michael Ebner, Paula Samsó, Rozemarijn Van Der Veen, Volker Haucke, Martin Lehmann.

BACKGROUND: Eukaryotic cells are highly compartmentalized by a variety of organelles that carry out specific cellular processes. The position of these organelles within the cell is elaborately regulated and vital for their function. For instance, the position of lysosomes relative to the nucleus controls their degradative capacity and is altered in pathophysiological conditions. The molecular components orchestrating the precise localization of organelles remain incompletely understood. A confounding factor in these studies is the fact that organelle positioning is surprisingly non-trivial to address e.g., perturbations that affect the localization of organelles often lead to secondary phenotypes such as changes in cell or organelle size. These phenotypes could potentially mask effects or lead to the identification of false positive hits. To uncover and test potential molecular components at scale, accurate and easy-to-use analysis tools are required that allow robust measurements of organelle positioning.RESULTS: Here, we present an analysis workflow for the faithful, robust, and quantitative analysis of organelle positioning phenotypes. Our workflow consists of an easy-to-use Fiji plugin and an R Shiny App. These tools enable users without background in image or data analysis to (1) segment single cells and nuclei and to detect organelles, (2) to measure cell size and the distance between detected organelles and the nucleus, (3) to measure intensities in the organelle channel plus one additional channel, (4) to measure radial intensity profiles of organellar markers, and (5) to plot the results in informative graphs. Using simulated data and immunofluorescent images of cells in which the function of known factors for lysosome positioning has been perturbed, we show that the workflow is robust against common problems for the accurate assessment of organelle positioning such as changes of cell shape and size, organelle size and background.
CONCLUSIONS: OrgaMapper is a versatile, robust, and easy-to-use automated image analysis workflow that can be utilized in microscopy-based hypothesis testing and screens. It effectively allows for the mapping of the intracellular space and enables the discovery of novel regulators of organelle positioning.

Keywords: Data analysis; Fiji; Image analysis; ImageJ; Organelle position; R; Segmentation; Shiny

DOI: https://doi.org/10.1186/s12915-024-02015-8

J Cell Biol. 2024 Dec 02. pii: e202403195. [Epub ahead of print]223(12):

Migratory autolysosome disposal mitigates lysosome damage.

Takami Sho, Ying Li, Haifeng Jiao, Li Yu.

Lysosomes, essential for intracellular degradation and recycling, employ damage-control strategies such as lysophagy and membrane repair mechanisms to maintain functionality and cellular homeostasis. Our study unveils migratory autolysosome disposal (MAD), a response to lysosomal damage where cells expel LAMP1-LC3 positive structures via autolysosome exocytosis, requiring autophagy machinery, SNARE proteins, and cell migration. This mechanism, crucial for mitigating lysosomal damage, underscores the role of cell migration in lysosome damage control and facilitates the release of small extracellular vesicles, highlighting the intricate relationship between cell migration, organelle quality control, and extracellular vesicle release.

DOI: https://doi.org/10.1083/jcb.202403195

Angiogenesis. 2024 Oct 02.

Angiogenesis is limited by LIC1-mediated lysosomal trafficking.

Dymonn Johnson, Sarah Colijn, Jahmiera Richee, Joseph Yano, Margaret Burns, Andrew E Davis, Van N Pham, Amra Saric, Akansha Jain, Ying Yin, Daniel Castranova, Mariana Melani, Misato Fujita, Stephanie Grainger, Juan S Bonifacino, Brant M Weinstein, Amber N Stratman.

Dynein cytoplasmic 1 light intermediate chain 1 (LIC1, DYNC1LI1) is a core subunit of the dynein motor complex. The LIC1 subunit also interacts with various cargo adaptors to regulate Rab-mediated endosomal recycling and lysosomal degradation. Defects in this gene are predicted to alter dynein motor function, Rab binding capabilities, and cytoplasmic cargo trafficking. Here, we have identified a dync1li1 zebrafish mutant, harboring a premature stop codon at the exon 12/13 splice acceptor site, that displays increased angiogenesis. In vitro, LIC1-deficient human endothelial cells display increases in cell surface levels of the pro-angiogenic receptor VEGFR2, SRC phosphorylation, and Rab11-mediated endosomal recycling. In vivo, endothelial-specific expression of constitutively active Rab11a leads to excessive angiogenesis, similar to the dync1li1 mutants. Increased angiogenesis is also evident in zebrafish harboring mutations in rilpl1/2, the adaptor proteins that promote Rab docking to Lic1 to mediate lysosomal targeting. These findings suggest that LIC1 and the Rab-adaptor proteins RILPL1 and 2 restrict angiogenesis by promoting degradation of VEGFR2-containing recycling endosomes. Disruption of LIC1- and RILPL1/2-mediated lysosomal targeting increases Rab11-mediated recycling endosome activity, promoting excessive SRC signaling and angiogenesis.

Keywords: Angiogenesis; Dynein motor; Endosomes; Lic1; Lysosomes; Rilp1/2; Zebrafish

DOI: https://doi.org/10.1007/s10456-024-09951-7

Int J Mol Sci. 2024 Sep 19. pii: 10070. [Epub ahead of print]25(18):

Lysosomal Proteases and Their Inhibitors.

Vito Turk, Veronika Stoka.

The discovery of the lysosome, a major cytoplasmic organelle, represents a breakthrough in the understanding of intracellular protein degradation processes-proteolysis [...].

DOI: https://doi.org/10.3390/ijms251810070

J Clin Med. 2024 Sep 10. pii: 5351. [Epub ahead of print]13(18):

Prevalence of Cardiomyopathy in Patients with Type 1 Diabetes Mellitus.

Oscar Daniel Fabila-de la Cruz, Eduardo Salif Luna-Avila, María Del Pilar Sotelo-González, Andrés D Litardo-Mosquera, Oscar Orihuela, Aldo Ferreira-Hermosillo.

Background: Diabetic cardiac muscle disease or diabetic cardiomyopathy (DbCM) comprises a set of myocardial lesions that are not associated with coronary atherosclerosis or high blood pressure. It is characterized by fibrosis and hypertrophy, which ultimately results in heart failure. Diastolic dysfunction (DD) has been shown to be the first manifestation of diabetic cardiomyopathy. Currently, there are few studies on the prevalence of diabetic cardiomyopathy in adult patients diagnosed with type 1 diabetes mellitus (T1D). Methods: The study included 75 adult participants who underwent an echocardiogram. Data on their comorbidities were collected from their medical records and biochemical parameters were analyzed in blood and urine samples. Results: We found that the prevalence of DbCM in our T1D population was more than one-third (34%), which exceeded the prevalence reported in studies with adolescents and that reported in the population without diabetes. Also, we found that the probability of developing DD after 20 years of T1D diagnosis was 78%. Conclusions: Recommendations need to be issued in relation to diabetic cardiomyopathy to carry out secondary prevention in adult patients with T1D. More multicenter studies, which include a larger population, from different regions of the world need to be performed.

Keywords: cardiovascular diseases; diabetic cardiomyopathy; echocardiography; left ventricular diastolic dysfunction; type 1 diabetes mellitus

DOI: https://doi.org/10.3390/jcm13185351