Data from: ApoA-I protects pancreatic β-cells from cholesterol-induced mitochondrial damage and restores their ability to secrete insulin
Data files
Nov 14, 2025 version files 972.25 MB
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APOA1_KRBH_point5.raw
972.12 MB
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Rat_specific_database_search_20220803_F002928_output.csv
69.34 KB
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Rat_specific_database_search_20220803_F002928_output.pdf
67.45 KB
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README.md
1.22 KB
Abstract
BACKGROUND: High cholesterol levels in pancreatic β-cells cause oxidative stress and decrease insulin secretion. β-cells can internalize apo (apolipoprotein) A-I, which increases insulin secretion. This study asks whether internalization of apoA-I improves β-cell insulin secretion by reducing oxidative stress.
METHODS: Ins-1E cells were cholesterol-loaded by incubation with cholesterol-methyl-β-cyclodextrin. Insulin secretion in the presence of 2.8 or 25 mmol/L glucose was quantified by radioimmunoassay. Internalization of fluorescently labeled apoA-I by β-cells was monitored by flow cytometry. The effects of apoA-I internalization on β-cell gene expression were evaluated by RNA sequencing. ApoA-I-binding partners on the β-cell surface were identified by mass spectrometry. Mitochondrial oxidative stress was quantified in β-cells and isolated islets with MitoSOX and confocal microscopy.
RESULTS: An F 1 -ATPase β-subunit on the β-cell surface was identified as the main apoA-I-binding partner. β-cell internalization of apoA-I was time-, concentration-, temperature-, cholesterol-, and F 1 -ATPase β-subunit-dependent. β-cells with internalized apoA-I (apoA-I + cells) had higher cholesterol and cell surface F 1 -ATPase β-subunit levels than β-cells without internalized apoA-I (apoA-I − cells). The internalized apoA-I colocalized with mitochondria and was associated with reduced oxidative stress and increased insulin secretion. The IF 1 (ATPase inhibitory factor 1) attenuated apoA-I internalization and increased oxidative stress in Ins-1E β-cells and isolated mouse islets. Differentially expressed genes in apoA-I + and apoA-I − Ins-1E cells were related to protein synthesis, the unfolded protein response, insulin secretion, and mitochondrial function.
CONCLUSIONS: These results establish that β-cells are functionally heterogeneous, and apoA-I restores insulin secretion in β-cells with elevated cholesterol levels by improving mitochondrial redox balance.
https://doi.org/10.5061/dryad.83bk3j9vd
The deposited data contains two files. The raw file can be viewed using Xcalibur ThermoScientific software and contains the MSMS profile of the sample. OpenChrom (www.openchrome.net) can be used to view *.raw files. This file is named APOA1_KRBH_point5.raw.
The PDF and CSV are the search result file obtained using the Mascot algorithm. These files are named:
Rat_specific_database_search_20220803_F002928_output.pdf Rat_specific_database_search_20220803_F002928_output.csv.
Mascot Daemon was used to search a rat-specific database downloaded from Swiss-Prot on 1st Feb, 2021 and specific taxonomy of Rat was applied. The following parameters were used:
• Semi-tryptic
• MS/MS ion search
• Peptide mass tolerance 5ppm
• Fragment mass tolerance 0.05Da
• 2 missed cleavages
• Target FDR of 1%
• Modifications for C, M, STY
Software
- Microsoft Word environment/other tabular data software
- ThermoScientific Xcalibur software environment
Identification of the F1-ATPase β-subunit on the Ins-1E cell surface
Tosylactivated Dynabeads (Thermo Fisher Scientific) were used to identify apoA-I binding partners on the Ins-1E cell surface. Briefly, apoA-I (100 µg) was dissolved in borate buffer (0.1 M, pH 9.5) containing ammonium sulphate (1.2 M) and incubated at 37 °C overnight with Dynabeads (5 mg, 165 µL). The beads with bound apoA-I were collected using a magnet and coupling efficiency was determined by measuring the concentration of unbound apoA-I in the supernatant. The beads with bound apoA-I were resuspended in PBS (pH 7.4, 250 µL) with 0.1% (w/v) BSA and incubated for 5 min at room temperature on a rotary shaker. The beads were collected and resuspended in PBS (250 µL) with 0.5 % (w/v) BSA, then incubated for a further 1 h at 37 °C to reduce non-specific binding. The beads were collected again and resuspended in PBS (pH 7.4, 250 µL) without BSA.
Ins-1E cells were seeded in a 12-well plate, washed with KRBH buffer, then maintained at 4 °C for 1 h with KRBH with 0.1% (w/v) BSA (200 µL) and Dynabeads (50 µL) with bound apoA-I. The supernatant was discarded, and the cells were washed gently with ice-cold PBS, then harvested with PBS containing EDTA-Na2 (2 mM) and collected into an Eppendorf tube. The Dynabeads and the bound cells were collected with a magnet. The supernatant was removed and the beads were washed with PBS (pH 7.4) and 0.1% (v/v) Tween20, then washed with PBS (pH 7.4). Non-specifically bound proteins were removed from the Dynabeads by incubation overnight at room temperature with trypsin at protein to enzyme ratio of 100:1. The beads were then collected using a magnet, the supernatant was discarded and the beads were washed (x3) with PBS. ApoA-I binding partners on the beads were eluted with 0.15% (v/v) trifluoro acetic acid, concentrated using C18 stage tips as previously described and analysed by LC–MS/MS.
Mass Spectrometry
The eluted peptides were reconstituted in 0.1% (v/v) formic acid (10 μL) and resolved by nano-LC using an Ultimate 3000 HPLC and an autosampler (Dionex, Amsterdam, The Netherlands). Briefly, the sample (0.5 µL), was loaded onto a micro C18 pre-column (300 μm×5 mm, Dionex) with H2O:CH3CN (98:2) in 0.1% (v/v) trifluoro acetic acid at a flow rate of 10 μL/min. After washing, the pre-column was switched (Valco 10 port valve, Dionex) into line with a fritless nanocolumn (75 μm×22 cm) containing reverse phase C18 media (particle size: 1.9 μm, pore size: 120 Å, Dr. Maisch HPLC GmbH). Peptides were eluted using a linear gradient of H2O:CH3CN (98:2 to 64:36) in 0.1% (v/v) formic acid at a flow rate of 250 nL/min over 90 min. The QExactive (Thermo Electron, Bremen, Germany) mass spectrometer was run in DDA mode where 2000 V was applied to a low-volume union and the column (45 °C) was positioned 0.5 cm from the heated capillary (275 °C). A survey scan 350–1750 m/z was acquired in the Orbitrap (resolution 70,000 at 200 m/z) with an accumulation target of 106 ions, lock mass enabled and up to the 10 most abundant ions (AGC target set to 105, minimum AGC target set to 1.5×104) with charge states ≥ +2 and ≤ +6 sequentially isolated and fragmented.
Protein dataset-peak lists were generated from raw files using Mascot Daemon v2.5.1 (Matrix Science, London, UK, www.matrixscience.com). All MS/MS spectra were searched against the Uniprot database (Feb 2021) of 563,972 sequences for protein identification with the following criteria: (1) taxon, Rat; (2) allowed 1 missed cleavages; (3) variable modifications, oxidation (M), phosphorylation (S,T,Y), Carbomidomethyl (C); (4) peptide tolerance, ±5 ppm; (5) fragment tolerance, ±0.5 Da; (6) peptide charge +2 and +3; and (7) enzyme specificity, semi-tryptic. A decoy database search was also performed. Only proteins that had a significance threshold of p<0.007 (<1% FDR) were recorded.
