New software for automated cilia detection in cells (ACDC)
BackgroundPrimary cilia frequency and length are key metrics in studies of ciliogenesis and ciliopathies. Typically, quantitative cilia analysis is done manually, which is very time-consuming. While some open-source and commercial image analysis software applications can segment input data, they still require the user to optimize many parameters, suffer from user bias, and often lack rigorous performance quality assessment (e.g., false positives and false negatives). Further, optimal parameter combinations vary in detection accuracy depending on cilia reporter, cell type, and imaging modality. A good automated solution would analyze images quickly, robustly, and adaptably—across different experimental data sets—without significantly compromising the accuracy of manual analysis.MethodsTo solve this problem, we developed a new software for automated cilia detection in cells (ACDC). The software operates through four main steps: image importation, pre-processing, detection auto-optimization, and analysis. From a data set, a representative image with manually selected cilia (i.e., Ground Truth) is used for detection auto-optimization based on four parameters: signal-to-noise ratio, length, directional score, and intensity standard deviation. Millions of parameter combinations are automatically evaluated and optimized according to an accuracy ‘F1’ score, based on the amount of false positives and false negatives. Afterwards, the optimized parameter combination is used for automated detection and analysis of the entire data set.ResultsThe ACDC software accurately and adaptably detected nuclei and primary cilia across different cell types (NIH3T3, RPE1), cilia reporters (AcTub, Smo-GFP, Arl13b), and image magnifications (60×, 40×). We found that false-positive and false-negative rates for Arl13b-stained cilia were 1–6%, yielding high F1 scores of 0.96–0.97 (max. = 1.00). The software detected significant differences in mean cilia length between control and cytochalasin D-treated cell populations and could monitor dynamic changes in cilia length from movie recordings. Automated analysis offered up to a 96-fold speed enhancement compared to manual analysis, requiring around 5 s/image, or nearly 18,000 cilia analyzed/hour.ConclusionThe ACDC software is a solution for robust automated analysis of microscopic images of ciliated cells. The software is extremely adaptable, accurate, and offers immense time-savings compared to traditional manual analysis.
- Research Article
- 10.1161/hyp.70.suppl_1.p181
- Sep 1, 2017
- Hypertension
Virtually, every mammalian cell is equipped with an antenna like primary cilium, a cell surface protrusion that is thought to act as a sensory organelle. Many of the rare genetic disorders that cause shorter, absent or disrupted cilia are associated with obesity and cardiovascular dysfunction in humans and rodents, which suggest that cilia length contribute to energy balance and cardiovascular homeostasis. Here, we examined the length of the primary neuronal cilia in the brain nuclei that contribute to metabolic and cardiovascular regulation in high fat diet-induced obese (DIO) mice and DOCA-salt mice. Cilia length was examined by adenylate cyclase 3 (AC3) immunostaining, followed by confocal 3D reconstruction, and quantification by IMARIS imaging analysis software. Analysis of the cilia length and distribution showed reduced frequency of cilia that are over 10 μm in the brain of DIO mice compared to control mice fed normal diet fed mice (17.02±1.36% vs 23.78±1.15%, p=0.032). Interestingly, the most pronounced difference in cilia length was observed in the dorsomedial hypothalamus with the DIO mice displaying significantly shorter cilia (6.90±0.06 μm) relative to controls (7.32±0.14μm in controls, n=5/group p<0.05). Conversely, we found that average neuronal cilia length was elongated in 3-week DOCA-salt treated mice compared to sham group. The number of primary neuronal cilia that are over 10 μm was significantly increased in DOCA-salt mice by 8% (p=0.0114). On the other hand, the number of cilia that are 4-5 μm in length was significantly decreased in DOCA-salt mice compared to sham controls (11.73±1.70% vs 18.73±2.02%, p=0.0385). The supraoptic nucleus was the only nucleus that displayed difference in the length of cilia that are 5-10 μm in length (7.46±0.24 μm vs 6.76±0.15μm, n=5/group, p=0.0509). Our data demonstrate plasticity of neuronal cilia in response to high fat diet and DOCA-salt treatment in defined brain regions. Our results raise the possibility that primary neuronal cilia may function as part of environmental surveillance system in the brain that control energy homeostasis and cardiovascular function. Further analysis of the role of primary neuronal cilia in cardiovascular regulation is underway.
- Research Article
4
- 10.1021/acschembio.4c00186
- Aug 6, 2024
- ACS chemical biology
Primary cilia are membrane-covered microtubule-based structures that protrude from the cell surface and are critical for cell signaling and homeostasis during human development and adulthood. Dysregulation of cilia formation, length, and function can lead to a spectrum of human diseases and syndromes known as ciliopathies. Although some genetic and chemical screens have been performed to define important factors that modulate cilia biogenesis and length control, there are currently no clinical treatments that restore cilia length in patients. We report that the microtubule-targeting agent MI-181(mitotic inhibitor-181) is a potent modulator of cilia length and biogenesis. Treatment of retinal pigment epithelial-1 cells with MI-181 induced an increase in the average size of cilia and in the percent ciliated cells under nonstarved conditions. Importantly, MI-181 was effective at rescuing cilia length and ciliation defects in cells that had been treated with the intraflagellar transport inhibitor Ciliobrevin D or the O-GlcNAc transferase inhibitor OSMI-1. Most importantly, MI-181 induced an increase in cilia length and restored ciliation in cells with compromised shortened cilia at low nanomolar concentrations and did not show an inhibitory response at high concentrations. Therefore, MI-181 represents a lead molecule for developing drugs targeting ciliopathies characterized by shortened cilia.
- Research Article
83
- 10.1007/s00018-011-0744-0
- Jun 14, 2011
- Cellular and Molecular Life Sciences
The primary cilium is an important sensory organelle present in most mammalian cells. Our current studies aim at examining intracellular molecules that regulate cilia length and/or cilia function in vitro and ex vivo. For the first time, we show that intracellular cAMP and cAMP-dependent protein kinase (PKA) regulate both cilia length and function in vascular endothelial cells. Although calcium-dependent protein kinase modulates cilia length, it does not play a significant role in cilia function. Cilia length regulation also involves mitogen-activated protein kinase (MAPK), protein phosphatase-1 (PP-1), and cofilin. Furthermore, cofilin regulates cilia length through actin rearrangement. Overall, our study suggests that the molecular interactions between cilia function and length can be independent of one another. Although PKA regulates both cilia length and function, changes in cilia length by MAPK, PP-1, or cofilin do not have a direct correlation to changes in cilia function. We propose that cilia length and function are regulated by distinct, yet complex intertwined signaling pathways.
- Research Article
131
- 10.1016/j.yexcr.2009.06.028
- Jul 2, 2009
- Experimental cell research
Adenylate cyclase regulates elongation of mammalian primary cilia
- Research Article
49
- 10.1016/j.cellsig.2016.02.018
- Mar 2, 2016
- Cellular Signalling
Modulation of primary cilia length by melanin-concentrating hormone receptor 1
- Research Article
18
- 10.1016/j.ultrasmedbio.2018.12.012
- Feb 20, 2019
- Ultrasound in Medicine & Biology
Non-invasive Low-Intensity Pulsed Ultrasound Modulates Primary Cilia of Rat Hippocampal Neurons
- Abstract
2
- 10.1016/s0924-977x(09)70266-4
- Sep 1, 2009
- European Neuropsychopharmacology
S.19.02 Preclinical and clinical pharmacology of H3-receptor inverse agonists
- Research Article
- 10.1096/fasebj.2019.33.1_supplement.850.11
- Apr 1, 2019
- The FASEB Journal
Fluid intake is tightly related to blood pressure control through balance between electrolytes and water in the body. Virtually, every mammalian cell is equipped with a primary cilium, a cell surface protrusion that is thought to act as a sensory organelle. However, the contribution of primary neuronal cilia to cardiovascular regulation and fluid homeostasis has not been addressed. We hypothesized that primary neuronal cilia contribute to the control of fluid intake and blood pressure. For this, we first examined the length of primary neuronal cilia in the brain nuclei that contribute to osmolarity and cardiovascular regulation in 3‐week DOCA‐salt treated mice vs sham controls (n=5/group). Cilia length was examined by immunostaining a ciliary protein, adenylate cyclase 3 (AC3), followed by confocal 3D reconstruction, and quantification by IMARIS imaging analysis software. We found changes in cilia length in a number of brain nuclei of DOCA‐salt mice. The supraoptic nucleus (SON), a key brain nucleus in the regulation of osmolarity and fluid homeostasis, displayed the most significant changes in cilia length (average primary cilia: 7.46±□□□□□m in DOCA‐salt mice vs 6.76±□□□□□m in sham, p=0.0509). Moreover, the number of primary cilia that are over 10□□m was significantly increased in the SON of DOCA‐salt mice by 8% (p=0.0114). On the other hand, the number of cilia that are 4–5□□m in length was significantly decreased in the SON of DOCA‐salt mice (11.73±1.70%) compared to sham controls (18.73±2.02%, p=0.0385). Next, we assessed the relevance of SON cilia by targeting the ift88 gene which encodes a protein necessary for the formation of cilia. For this, we performed targeted stereotaxic injection of AAV‐Cre into the SON of IFT88flox/flox mice. We found that disruption of SON ift88 (AAV‐Cre group had a 38% ift88 expression level relative to AAV‐GFP control group) caused impairment in water intake in response to 24h water deprivation (30min water intake: 0.78±0.06 ml in AAV‐Cre vs 1.07±0.08 ml in AAV‐GFP, p=0.0129) without affecting total daily water and food consumption. Moreover, ift88 deletion in SON increased systolic blood pressure (133.7±1.71 mmHg vs 115.8±2.33 in AAV‐GFP, p=0.0008) without altering heart rate. Our data demonstrate the importance of primary cilia in the SON in the regulation of water intake and blood pressure. We speculate that primary neuronal cilia may function as part of environmental surveillance system in the brain that ensures cardiovascular homeostasis.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
- Supplementary Content
61
- 10.3389/fcell.2021.661350
- May 19, 2021
- Frontiers in Cell and Developmental Biology
Primary cilia are small, antenna-like organelles that detect and transduce chemical and mechanical cues in the extracellular environment, regulating cell behavior and, in turn, tissue development and homeostasis. Primary cilia are assembled via intraflagellar transport (IFT), which traffics protein cargo bidirectionally along a microtubular axoneme. Ranging from 1 to 10 μm long, these organelles typically reach a characteristic length dependent on cell type, likely for optimum fulfillment of their specific roles. The importance of an optimal cilia length is underscored by the findings that perturbation of cilia length can be observed in a number of cilia-related diseases. Thus, elucidating mechanisms of cilia length regulation is important for understanding the pathobiology of ciliary diseases. Since cilia assembly/disassembly regulate cilia length, we review the roles of IFT in processes that affect cilia assembly/disassembly, including ciliary transport of structural and membrane proteins, ectocytosis, and tubulin posttranslational modification. Additionally, since the environment of a cell influences cilia length, we also review the various stimuli encountered by renal epithelia in healthy and diseased states that alter cilia length and IFT.
- Research Article
175
- 10.1091/mbc.e10-03-0269
- Jan 26, 2011
- Molecular Biology of the Cell
The primary cilium is an evolutionarily conserved dynamic organelle important for regulating numerous signaling pathways, and, as such, mutations disrupting ciliogenesis result in a variety of developmental abnormalities and postnatal disorders. The length of the cilium is regulated by the cell through largely unknown mechanisms. Normal cilia length is important, as either shortened or elongated cilia have been associated with disease and developmental defects. Here we explore the importance of cytoskeletal dynamics in regulating cilia length. Using pharmacological approaches in different cell types, we demonstrate that actin depolymerization or stabilization and protein kinase A activation result in a rapid elongation of the primary cilium. The effects of pharmacological agents on cilia length are associated with a subsequent increase in soluble tubulin levels and can be impaired by depletion of soluble tubulin with taxol. In addition, subtle nocodazole treatment was able to induce ciliogenesis under conditions in which cilia are not normally formed and also increases cilia length on cells that have already established cilia. Together these data indicate that cilia length can be regulated through changes in either the actin or microtubule network and implicate a possible role for soluble tubulin levels in cilia length control.
- Research Article
18
- 10.1523/eneuro.0360-22.2023
- Mar 1, 2023
- eNeuro
Primary cilia are cellular appendages critical for diverse types of Signaling. They are found on most cell types, including cells throughout the CNS. Cilia preferentially localize certain G-protein-coupled receptors (GPCRs) and are critical for mediating the signaling of these receptors. Several of these neuronal GPCRs have recognized roles in feeding behavior and energy homeostasis. Cell and model systems, such as Caenorhabditis elegans and Chlamydomonas, have implicated both dynamic GPCR cilia localization and cilia length and shape changes as key for signaling. It is unclear whether mammalian ciliary GPCRs use similar mechanisms in vivo and under what conditions these processes may occur. Here, we assess two neuronal cilia GPCRs, melanin-concentrating hormone receptor 1 (MCHR1) and neuropeptide-Y receptor 2 (NPY2R), as mammalian model ciliary receptors in the mouse brain. We test the hypothesis that dynamic localization to cilia occurs under physiological conditions associated with these GPCR functions. Both receptors are involved in feeding behaviors, and MCHR1 is also associated with sleep and reward. Cilia were analyzed with a computer-assisted approach allowing for unbiased and high-throughput analysis. We measured cilia frequency, length, and receptor occupancy. We observed changes in ciliary length, receptor occupancy, and cilia frequency under different conditions for one receptor but not another and in specific brain regions. These data suggest that dynamic cilia localization of GPCRs depends on properties of individual receptors and cells where they are expressed. A better understanding of subcellular localization dynamics of ciliary GPCRs could reveal unknown molecular mechanisms regulating behaviors like feeding.
- Research Article
7
- 10.3390/cells12111520
- May 31, 2023
- Cells
The primary cilium plays critical roles in the homeostasis and development of neurons. Recent studies demonstrate that cilium length is regulated by the metabolic state of cells, as dictated by processes such as glucose flux and O-GlcNAcylation (OGN). The study of cilium length regulation during neuron development, however, has been an area left largely unexplored. This project aims to elucidate the roles of O-GlcNAc in neuronal development through its regulation of the primary cilium. Here, we present findings suggesting that OGN levels negatively regulate cilium length on differentiated cortical neurons derived from human-induced pluripotent stem cells. In neurons, cilium length increased significantly during maturation (after day 35), while OGN levels began to drop. Long-term perturbation of OGN via drugs, which inhibit or promote its cycling, during neuron development also have varying effects. Diminishing OGN levels increases cilium length until day 25, when neural stem cells expand and undergo early neurogenesis, before causing cell cycle exit defects and multinucleation. Elevating OGN levels induces greater primary cilia assembly but ultimately results in the development of premature neurons, which have higher insulin sensitivity. These results indicate that OGN levels and primary cilium length are jointly critical in proper neuron development and function. Understanding the interplays between these two nutrient sensors, O-GlcNAc and the primary cilium, during neuron development is important in paving connections between dysfunctional nutrient-sensing and early neurological disorders.
- Abstract
4
- 10.1016/j.bpj.2014.11.3074
- Jan 1, 2015
- Biophysical Journal
Primary Cilia Length is Critical to Cellular Mechanotransduction
- Research Article
- 10.1161/hyp.72.suppl_1.p148
- Sep 1, 2018
- Hypertension
Primary cilia are considered sensory hubs housing a variety of mechanosensory proteins, chemosensory receptors, and ion channels to translate extracellular stimuli into an intracellular biochemical signals such as the synthesis and release of nitric oxide (NO). Malformations in cilia structure or defects in cilia function lead to ciliopathies such as Polycystic Kidney Disease (PKD) and hypertension. Muscarinic receptors 1 and 3 play an essential role in regulating cardiovascular function by mediating both dilation and constriction in the vasculature. However, nothing is known about the relationship between primary cilia and muscarinic receptors. Supported by our exciting discovery of the mAChRs in the cilia, we hypothesize that primary cilia in the vascular system play important roles in regulating blood pressure through NO biosynthesis. Our objective is to unravel the mechanism by which cilia dysfunction contribute to hypertension and to introduce cilia as a novel therapeutic target for PKD. To explore the relationship between mAChRs and primary cilia, the effects of muscarinic modulators on cilia length and function in wildtype, and cilia mutant endothelial cells, Pkd1 – / – (dysfunctional cilia) and Tg737 orpk/orpk (cilia-less) were examined. We show that both AChM1R and AChM3R localize to primary endothelial cilia. AChM1R and AChM3R activation lead to a significant increase in cilia length in endothelial cells treated with cdd0102a, an AChM1R and AChM3R agonist (2.84±0.02 vs. 3.47± 0.04 for wildtype, 2.31± 0.03 vs. 2.53± 0.03 for Pkd1 – / – , and 0.024 ± 0.005 vs. 0.3 ± 0.004 for Tg737 orpk/orpk ) compared to control cells. Treatment with pirenzepine, an AChM1R antagonist, led to a significant decrease of cilia length (2.66± 0.02 vs. 2.48± 0.03 in wildtype, and 2.12± 0.02 vs. 1.93± 0.02 in Pkd1 – / – ) compared to control cells. Treatment with cdd0102a also significantly upregulated the expression of AChM1R, AChM3R and phosphorylated eNOS in wildtype and Pkd1 - / - cells. More importantly, cdd0102a treatment rescued NO response in Pkd1 - / - cells in response to fluid shear stress. Our data clearly suggest that modulating cilia sensory function could have a positive influence on nitric oxide generation and blood pressure regulation.
- Research Article
5
- 10.1016/j.yexcr.2023.113671
- Jun 3, 2023
- Experimental Cell Research
Increase in primary cilia number and length upon VDAC1 depletion contributes to attenuated proliferation of cancer cells