PeakCaller: an automated graphical interface for the quantification of intracellular calcium obtained by high-content screening
Tóm tắt
Intracellular calcium is an important ion involved in the regulation and modulation of many neuronal functions. From regulating cell cycle and proliferation to initiating signaling cascades and regulating presynaptic neurotransmitter release, the concentration and timing of calcium activity governs the function and fate of neurons. Changes in calcium transients can be used in high-throughput screening applications as a basic measure of neuronal maturity, especially in developing or immature neuronal cultures derived from stem cells. Using human induced pluripotent stem cell derived neurons and dissociated mouse cortical neurons combined with the calcium indicator Fluo-4, we demonstrate that PeakCaller reduces type I and type II error in automated peak calling when compared to the oft-used PeakFinder algorithm under both basal and pharmacologically induced conditions. Here we describe PeakCaller, a novel MATLAB script and graphical user interface for the quantification of intracellular calcium transients in neuronal cultures. PeakCaller allows the user to set peak parameters and smoothing algorithms to best fit their data set. This new analysis script will allow for automation of calcium measurements and is a powerful software tool for researchers interested in high-throughput measurements of intracellular calcium.
Tài liệu tham khảo
Sutherland DJ, Goodhill GJ. The interdependent roles of Ca(2+) and cAMP in axon guidance. Dev Neurobiol. 2015;75:402–10.
Rosenberg SS, Spitzer NC. Calcium signaling in neuronal development. Cold Spring Harb Perspect Biol. 2011;3:a004259.
Evans RM, Zamponi GW. Presynaptic Ca2+ channels–integration centers for neuronal signaling pathways. Trends Neurosci. 2006;29:617–24.
Zucker RS. Calcium- and activity-dependent synaptic plasticity. Curr Opin Neurobiol. 1999;9:305–13.
Demuro A, Parker I, Stutzmann GE. Calcium signaling and amyloid toxicity in Alzheimer disease. J Biol Chem. 2010;285:12463–8.
Palmieri L, Papaleo V, Porcelli V, Scarcia P, Gaita L, Sacco R, Hager J, Rousseau F, Curatolo P, Manzi B, Militerni R, Bravaccio C, Trillo S, Schneider C, Melmed R, Elia M, Lenti C, Saccani M, Pascucci T, Puglisi-Allegra S, Reichelt KL, Persico AM. Altered calcium homeostasis in autism-spectrum disorders: evidence from biochemical and genetic studies of the mitochondrial aspartate/glutamate carrier AGC1. Mol Psychiatry. 2010;15:38–52.
Wen Y, Alshikho MJ, Herbert MR. Pathway network analyses for autism reveal multisystem involvement, major overlaps with other diseases and convergence upon MAPK and calcium signaling. PLoS ONE. 2016;11:e0153329.
Nestor MW, Phillips AW, Artimovich E, Nestor JE, Hussman JP, Blatt GJ. Human inducible pluripotent stem cells and autism spectrum disorder: emerging technologies. Autism Res. 2016;9:513–35.
Berridge MJ. Dysregulation of neural calcium signaling in Alzheimer disease, bipolar disorder and schizophrenia. Prion. 2013;7:2–13.
Berridge MJ. Neuronal calcium signaling. Neuron. 1998;21:13–26.
Brini M, Cali T, Ottolini D, Carafoli E. Neuronal calcium signaling: function and dysfunction. Cell Mol Life Sci. 2014;71:2787–814.
Eiraku M, Watanabe K, Matsuo-Takasaki M, Kawada M, Yonemura S, Matsumura M, Wataya T, Nishiyama A, Muguruma K, Sasai Y. Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. Cell Stem Cell. 2008;3:519–32.
Illes S, Theiss S, Hartung HP, Siebler M, Dihné M. Niche-dependent development of functional neuronal networks from embryonic stem cell-derived neural populations. BMC Neurosci. 2009;10:93.
Marchetto MC, Carromeu C, Acab A, Yu D, Yeo GW, Mu Y, Chen G, Gage FH, Muotri AR. A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells. Cell. 2010;143:527–39.
Patel TP, Man K, Firestein BL, Meaney DF. Automated quantification of neuronal networks and single-cell calcium dynamics using calcium imaging. J Neurosci Methods. 2015;243:26–38.
Mackay L, Mikolajewicz N, Komarova SV, Khadra A. Systematic characterization of dynamic parameters of intracellular calcium signals. Front Physiol. 2016;7:525. doi:10.3389/fphys.2016.00525.
Jang MJ, Nam Y. NeuroCa: integrated framework for systematic analysis of spatiotemporal neuronal activity patterns from large-scale optical recording data. Neurophotonics. 2015;2:035003.
Wong LC, Lu B, Tan KW, Fivaz M. Fully-automated image processing software to analyze calcium traces in populations of single cells. Cell Calcium. 2010;48:270–4.
Kaifosh P, Zaremba J, Danielson N, Losonczy A. SIMA: Python software for analysis of dynamic fluorescence imaging data. Front Neuroinform. 2014;27(8):77. doi:10.3389/fninf.2014.00077.
Kaifosh P, Lovett-Barron M, Turi GF, Reardon TR, Losonczy A. Septo-hippocampal GABAergic signaling across multiple modalities in awake mice. Nat Neurosci. 2013;16(9):1182–4. doi:10.1038/nn.3482.
Beaudoin GM 3rd, Lee SH, Singh D, Yuan Y, Ng YG, Reichardt LF, et al. Culturing pyramidal neurons from the early postnatal mouse hippocampus and cortex. Nat Protoc. 2012;7(9):1741–54. doi:10.1038/nprot.2012.099.
Sheskin DJ. Handbook of parametric and nonparametric statistical procedures. Boca Raton: Chapman and Hall; 2011.
Neyman J, Pearson ES, Yule GU. The testing of statistical hypotheses in relation to probabilities a priori. Math Proc Camb Philos Soc. 1933;29:492.
Grienberger C, Konnerth A. Imaging calcium in neurons. Neuron. 2012;73:862–85.
Holliday J, Adams RJ, Sejnowski TJ, Spitzer NC. Calcium-induced release of calcium regulates differentiation of cultured spinal neurons. Neuron. 1991;7:787–96.
Kidd FL, Isaac JT. Glutamate transport blockade has a differential effect on AMPA and NMDA receptor-mediated synaptic transmission in the developing barrel cortex. Neuropharmacology. 2000;39:725–32.
Eisenman LN, Kress G, Zorumski CF, Mennerick S. A spontaneous tonic chloride conductance in solitary glutamatergic hippocampal neurons. Brain Res. 2006;1118:66–74.