Rod photoreceptors have a dual dependency on both aerobic glycolysis and OXPHOS and diverge metabolically from other retinal neurons
Data files
Sep 15, 2026 version files 13.43 GB
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Figure_1.zip
145.71 MB
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Figure_2.zip
2.65 GB
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Figure_3.zip
1.15 GB
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Figure_4.zip
1.18 GB
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Figure_5.zip
2 GB
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Figure_6.zip
450.16 MB
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README.md
6.33 KB
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Supp._Fig._2.zip
983.87 MB
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Supp._Fig._3.zip
245.34 MB
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Supp._Fig._4.zip
709.98 MB
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Supp._Fig._5.zip
1.74 GB
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Supp._Fig._6.zip
262.66 MB
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Supp._Fig._7.zip
1.67 GB
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Supp._Fig._8.zip
250.59 MB
Abstract
The retina metabolizes glucose into lactate, a hallmark of aerobic glycolysis known as the Warburg effect. Although evidence points to rod photoreceptors as the primary source of aerobic glycolysis, a comparison of the energy metabolism in different retinal neurons has yet to be performed. We combined two-photon fluorescence lifetime imaging of biosensors with pharmacological protocols to analyze metabolic dynamics in healthy and diseased rod photoreceptors and RBPMS-positive ganglion and calretinin-positive amacrine cells. Our data reveal distinct metabolic profiles among retinal neurons, identify rods as the drivers of aerobic glycolysis, demonstrate that inner retinal neurons rely on oxidative phosphorylation, show that rods need both glycolysis and oxidative phosphorylation to maintain ATP levels, and suggest that rods can metabolize lactate. A mutation causing retinitis pigmentosa increases lactate production in rods but changes the energy metabolism only subtly otherwise. Our results improve the understanding of retinal physiology and are relevant for pathologies involving imbalanced energy metabolism.
Dataset DOI: 10.5061/dryad.gxd25482w
Description of the data and file structure
The data was collected to investigate the metabolic difference between rod photoreceptors and inner retinal neurons. Therefore, mice recieved intravitreal or subretinal inejctions containing adeno-associated viruses encoding different metabolic biosensors. Those sensors were visualized using two-photon (Ca2+ data) and two-photon fluorescence lifetime imaging microscopy (ATP, lactate, NADH/NAD+). The imaging protocols for rod photoreceptors were repeated in a mouse model of retinitis pigmentosa (RhoP23H/+) to investigate changes in photoreceptor metabolism during degeneration.
These datasets include imaging data (.tiff and ome.tiff.) as well as folders containing the ROIs used for analysis and excel sheets with the settings needed to run the analysis. The data is split based on the figure panels in the manuscript. Within the folders the data is either structured based on protocol and/or cell class. Within each figure folder is a .txt file containing information about how to run the analysis.
Files and variables
File: Figure_1.zip
Description: Dataset contains imaging data of GCaMP6s expressed in wildtype rod photoreceptors. Photoreceptors segments (PS) region of interest was used for analysis.
File: Figure_4.zip
Description: Dataset contains FLIM imaging data of the lactate sensor LiLac expressed in rods and inner retina neurons of wildtype mice.
File: Figure_5.zip
Description: Dataset contains FLIM imaging data of the ATP sensor ATeam1.03 in rods of RhoP23H/+ mice.
File: Figure_6.zip
Description: Dataset contains FLIM imaging data of the lactate sensor LiLac expressed in rods of RhoP23H/+ mice.
File: Figure_3.zip
Description: Dataset contains FLIM imaging data of the ATP sensor ATeam1.03 in rods and inner retina neurons of wildtype mice to investigate the different contribution of OXPHOS and glycolysis to ATP production in these cell classes.
File: Supp._Fig._2.zip
Description: Dataset contains FLIM imaging data of the ATP sensor ATeam1.03 in rods of wildtype mice to investigate the fluorescence lifetime stability of the sensor and ATP recovery using different protocols.
File: Supp._Fig._3.zip
Description: Dataset contains imaging data of GCaMP6s expressed in wildtype rod photoreceptors during the glucose-lactate-glucose exchange protocol. Photoreceptors segments (PS) region of interest was used for analysis.
File: Supp._Fig._4.zip
Description: Dataset contains FLIM imaging data of the ATP sensor ATeam1.03 in rods of wildtype mice during glutamine supplementation.
File: Figure_2.zip
Description: Dataset contains FLIM imaging data of the ATP sensor ATeam1.03 in rods and inner retina neurons of wildtype mice.
File: Supp._Fig._5.zip
Description: Dataset contains FLIM imaging data of the ATP sensor ATeam1.03 in inner retina neurons of wildtype mice to investigate alternative fuels for ATP production instead of glucose.
File: Supp._Fig._6.zip
Description: Dataset contains FLIM imaging data of the NADH/NAD+ sensor Perodx in rods of wildtype mice to measure baseline redox ratio in the different cell classes.
File: Supp._Fig._7.zip
Description: Dataset contains FLIM imaging data of the lactate sensor LiLac expressed in rods of wildtype mice using different protocols to block MCTs.
File: Supp._Fig._8.zip
Description: Dataset contains imaging data of GCaMP6s expressed in RhoP23H/+ rod photoreceptors. Photoreceptors segments (PS) region of interest was used for analysis.
File: dffanalysis-master.zip
Description: Contains the code to analyse the Ca2+ data as well as documentation explaining on how to execute the code
File: flimanalysis-main.zip
Description: Contains the code to analyze FLIM data. FLIMpreprocess to extract ROI data for rod photoreceptors and FLIM analysis to calculate the lifetime of rod photoreceptors (using ROI data) and inner retinal neurons. It also contains documentation on how to execute the code.
Code/software
Viewing of the data
To view the images ImageJ can be used and the Bio Formats plugin is needed to view the FLIM data.
Ca2+ data - DFF analysis
DFFAnalysis is program to calculate ΔF/F out of a series of images (Ca2+ data). Within the DFF analysis folder is a PDF (DFFAnalysisDoc) explaining how to run the analysis
The information for the excel file can be found in the excel sheet filestoprocess or options in each single folder. Also the ROIs which were used for analysis are included in the different folders.
FLIM analysis - FLIM analysis main
The FLIM analysis main folder contains the code to run the FLIM analysis. Within the folder is a PDF document (flimanalysis) in the doc folder explaining how to execute the analysis and which packages are needed. In each folder of each experiment are excel files containing the settings which were used to run the analysis as well as the ROI information for rod photoreceptors.
Software and code needed to run analysis
To run the codes for the analysis the following Software/Code is needed:
Ca2+ data: The DffAnalysis needs to be run in Matlab (MathWorks, R2018b). The traces (ΔF/F) were calculated from the PS ROI using the first frame of each image as baseline.
FLIM data rod photoreceptors: To analyse the lifetime of all rod photoreceptor data the regions of interest (ROI) needs to be extracted first using the code FLIMpreprocess code (MathWorks, R2018b). Afterwards the resulting ROI data will be used to calculate the lifetime using FLIManalysis (MathWorks, R2020a). To run the different analysis, each folder containing one experiment also contains an excel sheet with the specifics needed to run the analysis.
FLIM data inner retina neurons: The lifetime is calculated using FLIManalysis (MathWorks, R2020a). To run the analyis, each folder containing one experiment also contains an excel sheet with the specifics needed to run the analysis.
