Nrf2/UBE3B protects against acute lung injury by inhibiting ferritinophagy through the ubiquitination of NCOA4

doi:10.21203/rs.3.rs-5229445/v1

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Nrf2/UBE3B protects against acute lung injury by inhibiting ferritinophagy through the ubiquitination of NCOA4

https://doi.org/10.21203/rs.3.rs-5229445/v1

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Iron overload and ferroptosis are associated with intestinal ischemia and reperfusion (II/R)-induced acute lung injury (ALI). However, the mechanisms underlying the regulation of iron homeostasis remain unclear. Nrf2 regulates cellular iron homeostasis; however, its impact on ALI pathology and its underlying mechanism of action requires further investigation. Ubiquitin ligase E3B (UBE3B) plays a critical role in the proteasome pathway, which is essential for protein turnover and ubiquitin-mediated signaling. A recent study found that UBE3B plays a role in oxidative stress; however, it remains unknown whether its role is related to Nrf2. Furthermore, the exact role of UBE3B in ALI and its underlying mechanism remain largely uncharacterized. In the present study, immunohistochemical analysis of UBE3B expression in type II alveolar epithelial cells (AECII) was conducted and its expression was found to be increased in II/R-ALI. Western blot analysis indicated that UBE3B hyperactivation may alleviate oxidative stress, thereby protecting against ALI. Moreover, UBE3B was involved in iron metabolism dysfunction and ferroptosis. UBE3B deficiency enhanced the process of nuclear receptor coactivator 4 (NCOA4)-mediated ferritinophagy and increased ferrous ion content, whereas overexpression of UBE3B reversed the harmful effects of Nrf2 knockdown on AECⅡ, which may promote AECⅡ ferroptosis. This study highlights the role of the Nrf2/UBE3B/NCOA4 axis in AECⅡ ferroptosis and II/R-ALI pathogenesis, suggesting that Nrf2 activation may be a promising strategy for ALI treatment.

Nrf2

acute lung injury

ferroptosis

NCOA4

ferritinophagy

UBE3B

Ischemia-reperfusion (IR^*)Ferritinophagy, the selective autophagy of ferritin mediated by nuclear receptor coactivator 4 (NCOA4), involves NCOA4 recognizing ferritin and delivering it to the autophagosome. Within autophagosomes, ferritin is degraded, releasing iron into lysosomes (Feng et al., 2024). Notably, excessive iron levels can trigger cell death (Dong et al., 2021). Previous studies revealed that inhibiting ferroptosis in a ferritinophagy-mediated manner could alleviate sepsis-induced ALI (Zhang et al., 2022, Dong et al., 2023). Therefore, the pursuit of targeted ferroptosis has emerged as a potential therapeutic strategy for these diseases. However, the regulatory mechanisms underlying iron metabolism in AECⅡ cells under pathological conditions require further investigation. Nuclear factor E2-related factor 2 (Nrf2) is a key regulator of oxidative homeostasis, activated in response to increased oxidative stress. Nrf2 binds to the antioxidant response element (ARE) in the nucleus, promoting the transcription and translation of antioxidant and anti-inflammatory proteins, thereby providing cellular protection (Loboda et al., 2016, Gañán-Gómez et al., 2013, Fan et al., 2017). These proteins regulate vital cellular defense mechanisms and offer protection against damage to the brain (Zhai et al., 2013), liver (Kudoh et al., 2014), and heart (Shen et al., 2019), as well as against II/R (Zhao et al., 2010, Dong et al., 2020).

UBE3B is a calmodulin-regulated, mitochondria-associated E3 ubiquitin ligase (Braganza et al., 2017). Knockdown of Ube3b in mice results in reduced viability, recapitulation of key aspects of human disorders, such as reduced weight and brain size, and downregulation of cholesterol synthesis. Previous research has shown that the probable Caenorhabditis elegans ortholog of UBE3B, oxi-1, functions in the ubiquitin/proteasome system in vivo and plays a key role in oxidative stress-related diseases (Basel-Vanagaite et al., 2012). This highlights the diverse effects of UBE3B deficiency and underscores the physiological importance of ubiquitination in neuronal development and function in mammals. However, it is unknown whether its antioxidant effect interacts with Nrf2 and whether it has a critical role in ferroptosis.

The aim of this study was to investigate whether Nrf2 silencing during ischemia induces ferritinophagy via UBE3B and NCOA4 modulation. In this study, we examined ferroptosis and ferritinophagy in an in vitro II/R-ALI model. Moreover, we evaluated whether UBE3B restrained ferritinophagy, normally observed in II/R-ALI, by regulating NCOA4. Our study revealed potential therapeutic targets for managing II/R-ALI.

2.1. Materials

Dulbecco’s modified Eagle’s medium (DMEM), fetal bovine serum (FBS), penicillin, and streptomycin sulfate were sourced from Gibco Life Technologies Co. (Grand Island, NY). The Cell Counting Kit-8 (CCK-8) and ROS Assay Kit - Photo-oxidation Resistant DCFH-DA were obtained from Dojindo Laboratories (Kumamoto, Japan). Glutathione (GSH) Content Assay Kit was obtained from Cayman Chemical Company (United States). Phosphate-buffered saline (PBS) Buffer Premixed Powder (1X) and 10X Tris-Glycine SDS-PAGE Running Buffer were supplied by Sangon Biotech (Shanghai) Co., Ltd (Kudoh et al.). LipoFiter Transfection Reagent Kit were sourced from Hanbio Technology (Shanghai) Co., Ltd. (Shanghai, China). Hoechst, Malondialdehyde (MDA) Content Assay Kit, and 4’,6-Diamidino-2-phenylindole (DAPI) were sourced from Beyotime Institute of Biotechnology (Shanghai, China). HRP Goat Anti-Rabbit IgG (H + L) (AS014), Anti-Nrf2 rabbit (A21508), Anti-NCOA4 rabbit (A5695), Anti-β-actin rabbit mAb (High Dilution) (AC026), HA-Tag rabbit mAb (AE105), DDDDK-Tag rabbit mAb (AE092), Anti-Ferritin Heavy Chain rabbit mAb (A19544), and Anti-LC3B rabbit mAb (A19665) were procured from ABclonal Technology Co. (Shanghai, China). The plasmid was acquired from Genomeditech Co., Ltd. (Kudoh et al.). Prussian Blue Iron Stain Kit was sourced from Beijing Solarbio Science & Technology Co., Ltd (Kudoh et al.). The PrimeScript™ RT-PCR Kit was obtained from Takara Biomedical Technology (Beijing) Co., Ltd. The 2x SYBR Green qPCR Master Mix (Low ROX) was obtained from Selleck.cn (Kudoh et al.).

2.2. Isolation of primary alveolar epithelial cells type Ⅱ

Pregnant C57BL/6J mice at embryonic day 19 (E19) were used for the extraction of primary cells. Under sterile conditions, the uterus was dissected to retrieve the fetal mice. Placing the fetal mice in a laminar flow hood, a horizontal incision was made across the chest of each fetal mouse. The lungs were removed and placed in pre-cooled PBS solution. Care was taken to remove non-lung tissues, such as residual tracheal and connective tissues, as much as possible. The lung tissues were washed three times with PBS, cut into approximately 1 mm3 tissue fragments using ophthalmic scissors, washed once with trypsin solution, and then digested at 37°C for a duration of 20 minutes. To halt the digestion, mix the trypsin with an equal volume of medium with FBS. The mixture was subsequently passed through a 200-mesh sieve. and centrifuged at 1500 revolutions per minute for 5 minutes at low temperature. The liquid above the sediment was removed, and the pellet was retained. The pellet was incubated with 0.1% collagenase I at 37°C for 20 minutes. After digestion, an equal amount of DMEM containing 10% FBS was introduced, with centrifugation for 5 minutes at 1000 rpm. The cell was collected and plated into a culture bottle, which was incubated at 37°C with 5% CO2 for 45 minutes. The liquid above the sediment was then aspirated and transferred to another culture bottle. This same step was repeated for 3 times. Finally, the liquid above the sediment was aspirated, and then centrifuged the cells at 800 rpm for a duration of 5 minutes. After discarding the supernatant, the cell was suspended in a culture medium. and seeded into a culture bottle. After incubating for 24 hours, the medium was exchanged to remove unattached cells, and the culture was continued. The growth and morphology of the cells were examined under an inverted microscope.

2.3. Cell culture

The MLE12 cells, obtained from the Cell Bank of the Chinese Academy of Sciences (Shanghai, China), were maintained in a conventional cell culture incubator at 37°C with 5% CO2 and maintained humidity. The cells were maintained in DMEM with 10% FBS and 1% penicillin-streptomycin.

2.4. Oxygen-glucose deprivation and reoxygenation (OGD/R) model

For the OGD/R model induction, cells underwent an initial phase of 8 hours of glucose deprivation, followed by 12 hours of reoxygenation. During the deprivation phase, cells were cultured in a glucose-free medium inside an anaerobic chamber with an atmosphere of 95% N2 and 5% CO2 for 8 hours. Following this, the cells were transitioned to a high-glucose medium and grown in a conventional cell culture incubator for an additional 12 hours to reoxygenate.

2.5. Cell viability assessment

Within a 96-well plate, MLE12 cells were cultured at 1 × 104 cells/well. Once the cells had fully adhered, they were subjected to various treatments. Subsequently, the cells underwent 8 hours of oxygen-glucose deprivation (OGD) followed by 12 hours of reoxygenation to establish the OGD/R model. Upon completion of the model establishment, each well received 10 µL of CCK-8 solution and 90 µL of medium. Following this, the cells were kept for 4 hours in the dark before their optical density (OD) at 450 nm was mrasured by a microplate reader.

2.6. Animals

Twenty-four C57BL/6J mice (6–8 weeks) were acquired from the Animal Center of Shanghai Jiao Tong University School of Medical Sciences. They were kept under regulated environmental conditions, and a 12-hour light/dark cycle, with a temperature of 21 ± 2°C. All experimental procedures were performed following the guidelines stipulated by the National Institutes of Health (NIH) and took permission from the Animal Research Ethics Committee at Shanghai Jiao Tong University (ethical approval number A2023114).

2.7. Intestinal ischemia/reperfusion (II/R) mouse model

Prior to the experiment, animals underwent a 24-hour fasting period with access to water. The mice were anesthetized intraperitoneally with sodium pentobarbital at a dosage of 50 mg/kg and underwent a midline incision. To induce intestinal ischemia, The superior mesenteric artery was temporarily occluded using non-invasive vascular clips for a duration of 45 minutes followed by a 180-minute reperfusion period. Sham control mice underwent identical procedures without vascular occlusion. After 3 hours of reperfusion, the animals were euthanize, and tissue samples were promptly frozen at -80°C.

2.8. Malondialdehyde (MDA) assay(Rui et al., 2021)

Homogenize or lyse the tissues or cells using PBS or lysis buffer. For tissues, the weight of the tissue should constitute 10% of the volume of the homogenization or lysis buffer; for cells, use 0.1 ml of lysis or homogenization buffer per one million cells. After homogenization or lysis, centrifuge at 10,000g to 12,000g for 10 minutes at 4ºC and collect the supernatant. Dilute the appropriate amount of the standard with distilled water to concentrations of 1, 2, 5, 10, 20, and 50µM. In a centrifuge tube or another suitable container, add 0.1 ml of the homogenization buffer, lysis buffer, or PBS as a blank control, 0.1 ml of the standards above different concentrations to create the standard curve, and 0.1 ml of the sample for measurement. Then, add 0.2 ml of the MDA detection working solution. Mix well and heat at 100ºC or in a boiling water bath for 15 minutes. Cool the samples to room temperature in a water bath, then centrifuge at 1000g for 10 minutes. Transfer 200 µl of the supernatant to a 96-well plate, and measure the absorbance at 532 nm using a microplate reader. Calculate the MDA content in the sample solution.

2.9. GSH assay(Wu et al., 2023)

The GSH levels were measured using a GSH assay kit (Cayman Chemical, Catalog No. 703002, Ann Arbor, MI, USA).

2.10. Iron ion assay

Weigh 0.1 g of fresh tissue and mix 0.9 mL of homogenization reagent. Centrifuge the mixture at 10,000 × g for a duration of 10 minutes, and collect the resulting supernatant. Dilute the sample to a concentration within the linear range of the kit (0.4–50 µmol/L). Prepare standard tubes by transferring 300 µL of different concentrations of the standard solution into corresponding 1.5 mL EP tubes. Similarly, prepare test tubes by transferring 300 µL of the sample into corresponding 1.5 mL tubes. Mix 150 µL of reagent two to each tube, mix thoroughly, and place the mixture in an incubator set at 37°C for a duration of 10 minutes. Centrifuge all tubes at 12,000 × g for 10 minutes. Transfer 300 µL of the supernatant from each tube into the respective wells of a 96-well plate. Their OD were measured at 593 nm in each well by a microplate reader.

2.11. Perls staining

After preheating the paraffin sections, deparaffinize twice in xylene for 5 minutes each time. Gradually rehydrate with ethanol, 3 minutes per grade, and rinse with distilled water for 3 minutes.

Thaw the frozen sections, allow them to equilibrate at 4°C for 10 minutes, and then rinse them with distilled water for 3 minutes. For cell smears, fix with pre-cooled low-grade alcohol for 3 minutes or 4% tissue cell fixative for 20 minutes, followed by two washes with 70% ethanol for 1 minute each, and two rinses with distilled water for 2 minutes each. Prepare Perls staining working solution before use, add it to cover the sections, stain for a duration of 30 minutes, and rinse with distilled water for 10 minutes. For nuclear fast red staining, stain for 5–10 minutes, rinse quickly with tap water for 2–3 seconds. Dip in 75%, 85%, 95% ethanol for 3–5 seconds each, and twice in 100% ethanol, each time for 1 minute. Clear with xylene or environmentally friendly tissue deparaffinization solution twice, each time for 1–2 minutes. Seal with neutral gum.

2.12. Lung injury score

The mice lung tissues underwent fixation in 10% formalin, and embedding in paraffin and sectioning into 5 µm slices. Thereafter, the slices were stained with hematoxylin and eosin (HE) and examined using a Nikon-Ni-U light microscope equipped with an Optronics DEI-470 digital camera. To evaluate acute lung injury (ALI), a five-point scoring system (0–4) was utilized based on several parameters: The scoring criteria included assessment of alveolar and interstitial edema, intra-alveolar inflammatory cell infiltration, alveolar hemorrhage, and atelectasis, which were graded as follows:

Grade 0: Normal morphology, with < 15% tissue occupancy and > 85% alveolar space occupancy.

Grade 1: Mild injury, with 15–25% tissue occupancy and 75–85% alveolar space occupancy.

Grade 2: Moderate injury, with 25–50% tissue occupancy and 50–75% alveolar space occupancy.

Grade 3: Severe injury, with 50–75% tissue occupancy and 25–50% alveolar space occupancy.

Grade 4: Very severe injury, with 75–100% tissue occupancy and 0–25% alveolar space occupancy.

2.13. Co-immunoprecipitation (CO-IP) assay

Tissue sample preparation: Rinse the tissue with PBS, add pre-chilled RIPA buffer (mild RIPA, 1000 µL/100 mg tissue, supplemented with 10 µL protease inhibitor/1000 µL RIPA), and keep on ice for 10 minutes. Take two sterilized steel beads and grind the tissue. Centrifuge at 4°C, 12000 rpm for a duration of 15 minutes, and retrieve the liquid. Determine protein concentration using the BCA method. For total protein, take 500 ul and add 10 µL of Nrf2 antibody; take 300 µL and add IgG antibody. Incubate overnight at 4°C with slow inverting. The remaining protein is combined with loading buffer and heated to 100°C, boiling for 15 minutes. Pre-wash Protein A beads: Resuspend Protein A + G magnetic beads by gently pipetting, transfer an appropriate amount into a clean centrifuge tube and adjust to a final volume of approximately 0.5 ml with 1X TBST. Gently resuspend Protein A + G magnetic beads by pipetting. Put the tube on a magnetic rack for 10 seconds to allow the beads to adhere to the magnet, then gently discard the supernatant. Perform this washing step two additional times. Next, perform magnetic separation using the Protein A + G magnetic beads: discard the supernatant, add the sample, resuspend the beads, and allow the mixture to incubate for 30 minutes on a rocking mixer. Add 500 µL of 1X TBST, gently resuspend Protein A + G magnetic beads by pipetting, place on a magnetic stand for 10 seconds, discard the liquid above, and repeat washing three times. For every 10–20 µL of the original magnetic bead volume, mix 10 µL 2X SDS-PAGE loading buffer. Heat the mixture at 100°C for 5 minutes, then place it on a magnetic stand for 10 seconds to separate the beads and collect the supernatant. Analyze by Western Blotting to confirm the binding proteins.

2.14. Western blot

Proteins were blended with SDS-PAGE loading buffer and heated at 95°C for about 15 minutes. The proteins underwent electrophoresis on a 10% SDS-PAGE gel and transferred onto a polyvinylidene fluoride (PVDF) membrane. In succession, the membrane was immersed in TBST solution with 10% skimmed milk for 1.5 hours, subsequent to 3 washes with TBST. Primary antibodies against Nrf2 (Rabbit, 1:500), NCOA4 (Rabbit, 1:1000), UBE3B (Rabbit, 1:1000), FTH1 (Rabbit, 1:1000), LC3 (Rabbit, 1:1000), and β-actin (Rabbit, 1:100000) were then incubated with the membrane overnight at 4°C. On the subsequent day, the protein bands were rinsed 3 times with TBST before being exposed to secondary antibodies (HRP-goat anti-rabbit, 1:5000) for 1 hour. Hereinafter 3 washes with TBST, bands were detected with an enhanced ECL chemiluminescent substrate kit and quantified by the Bio-Rad multicolor fluorescence and chemiluminescence imager.

2.15. Immunofluorescence assay

Cryosections of the lungs were prepared and treated with 0.3% Triton-100 for 15 minutes to permeabilize them, followed by a 2-hour incubation with 3% BSA. And the sections were exposed separately to primary antibodies targeting NCOA4, UBE3B, FTH1, and LC3, and incubated overnight at 4°C. With overnight exposure, the sections were rinsed with five washes of PBS. To visualize the target proteins, the sections underwent incubation with fluorescently labeled secondary antibodies for 1 hour. Subsequently, three washes with PBS were performed. Finally, the sections were counterstained with DAPI to observe cell nuclei and captured by a confocal laser scanning microscope (Carl Zeiss LSM710, Germany).

2.16. Plasmid transfection

To initiate plasmid transfection, cells were seeded in a 6-well plate the previous day at about 1 × 10⁶ cells/well. The cells grew until they reached about 70% confluence the following day. Before the transfection procedure described below, the culture medium was changed to 2 mL of fresh culture medium containing serum. In a sterile and clean centrifuge tube, 125 µL of serum-free DMEM culture medium (devoid of antibiotics) was added for each well slated for transfection. Subsequently, 2 µg of plasmid DNA was introduced into each tube, and gentle pipetting facilitated thorough mixing. Following this, 4 µL of LipoFiter transfection reagent was added, and the mixture was gently swirled to ensure homogeneity. Whether dealing with adherent or suspended cells, the 125 µL Lipo8000™ transfection reagent-DNA concoction was evenly dispensed into each well of the six-well plate, with careful swirling to guarantee uniform distribution. The cells were then allowed to incubate for approximately 72 hours before sample collection.

2.17. Quantitative real-time PCR assay

Cells or tissues were treated with TRIzol to extract RNA. The isolated RNA was subsequently converted in reverse to generate cDNA by using the PrimeScript™ RT-PCR Kit. Subsequent qPCR was conducted with 2x SYBR Green qPCR Master Mix. The primer sequences for each target are as follows:

Mouse_actin, beta (β-actin)

Forward primer: GCTCACCATTCACCATCTTGTCTTG

Reverse primer: TCCTGCTTGCTGATCCACATCTG

Mouse_Nrf2

Forward primer: TTGCCACCGCCAGGACTACA

Reverse primer: AACTTGTACCGCCTCGTCTGGA

Mouse_nuclear receptor coactivator 4 (Ncoa4)

Forward Primer: GCCAGAGCAGAAGTCAGCATCC

Reverse Primer: GCCAGTCCTGTGGGTTGGTACT

Mouse_ferritin heavy polypeptide 1 (FTH1)

Forward primer: CCATCAACCGCCAGATCAACCT

Reverse primer: GCAAAGTTCTTCAGAGCCACATCAT

Mouse_microtubule-associated protein 1 light chain 3 beta

Forward primer: CAAGCCTTCTTCCTCCTGGTGA

Reverse primer: TTGCTGTCCCGAATGTCTCCTG

2.18. Transmission electron microscopy (TEM)

The mice lung tissues were preserved in 0.05 M sodium cacodylate buffer with 2.5% glutaraldehyde at pH 7.2 at 25°C for a duration of 2 hours. Following this, they were dealt with 2% OsO4 in 0.1 M sodium cacodylate buffer for an additional 2 hours, followed by immersion in 1% aqueous uranyl acetate for a period of 18 hours. With the dehydration in ethanol, the samples were preserved in resin, sectioned using copper grids, and stained with lead citrate and uranyl acetate. Visualization was carried out by a transmission electron microscope (FEI Company, Oregon).

2.19. Statistical Analysis

The mean values with their standard deviations (SD) are presented. Statistical analyses were carried out by using Prism software (version 9.0.0), employing one-way analysis of variance (ANOVA) for between-group comparisons. Statistical significance was shown as follows: * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

3.1. II/R causes ferroptosis and ferritinophagy in mouse lung tissue

Iron plays a key role in ferroptosis initiation and can promote the generation of reactive oxygen species (ROS) through the Fenton reaction. Thus, we determined iron levels in the lung tissues of an II/R-ALI model to evaluate the role of ferroptosis. Iron levels in II/R mice were significantly higher than those in sham mice (Fig. 1a–b). We then assessed ferroptotic markers. Lipid peroxidation represents a critical characteristic of ferroptosis, culminating in the production of malondialdehyde (MDA) as its final product. As shown in Fig. 1c, MDA levels increased significantly, whereas glutathione (GSH) levels decreased (Fig. 1d), both of which are characteristic of ferroptosis. Furthermore, using TEM, we demonstrated that AECⅡ from II/R mice exhibited characteristics more typical of ferroptosis than those of sham mice, including decreased mitochondrial size and reduced cristae size (Fig. 1e). Utilizing hematoxylin and eosin (HE) staining (Fig. 1f–g), we further demonstrated that II/R resulted in significant damage to lung tissue (p < 0.05). NCOA4 mediated ferritinophagy has been demonstrated to play a critical role in regulating the intracellular Fe²⁺ balance, and emerging evidence has shown that NCOA4 can regulate ferroptosis (Wang et al., 2024, Jiang et al., 2024a, Wang et al., 2023b, Shi et al., 2023). The present study investigated whether NCOA4 is involved in II/R and whether ferroptosis induced by II/R is regulated by ferritinophagy. FTH1 and LC3 showed increased co-localization after II/R (Fig. 1h). The mRNA levels of NCOA4 and LC3II were observed to be higher in the II/R group than in the control group (Fig. 1i). Western blotting showed that NCOA4 and LC3Ⅱ protein levels were significantly elevated, whereas levels of FTH1 (a critical protein of ferritinophagy) were markedly diminished in the II/R model compared with those in the sham mice. Notably, we found that the Nrf2 and UBE3B expression levels were increased significantly following II/R (Fig. 1j–k). Collectively, these data indicated that II/R-ALI mice demonstrated enhanced ferroptosis and ferritinophagy. Nevertheless, the relationship between the two and the role of Nrf2-related pathways in this process requires further exploration.

3.2. Nrf2 knockout accelerates ferroptosis and ferritinophagy and aggravates II/R-ALI

To investigate the role of Nrf2 in regulating ferritinophagy in the context of II/R-ALI, we studied Nrf2 conditional knockout (CKO) mice. Nrf2 plays a crucial role in modulating antioxidant stress and ferroptosis. Ferritinophagy increases the cytosolic catalytic Fe(Ⅱ) levels, resulting in ferroptosis (Jiang et al., 2024b). We observed iron deposition using Perls’ staining. Compared to sham mice, the lung tissue of Nrf2 CKO mice showed more severe iron deposition (Fig. 2a). The lung tissues of Nrf2 CKO mice exhibited higher iron content (Fig. 2b). Meanwhile, our results revealed pronounced suppression of GSH in the II/R model, which was particularly notable in Nrf2 CKO mice (Fig. 2c) and found elevated MDA levels in the II/R model, which was particularly pronounced in Nrf2 CKO mice (Fig. 2d). The pathology of II/R-ALI was more severe in Nrf2 CKO II/R mice than in WT mice (Fig. 2e–f), indicating that Nrf2 provides protection against ALI, consistent with other studies (Zou et al., 2024). Likewise, our TEM observations demonstrated that the mitochondria were smaller in size, the cristae were either reduced or absent, and the outer membrane was torn in Nrf2 CKO II/R mice compared to that in WT mice (Fig. 2g). This suggests accelerated iron accumulation and ferroptosis in the absence of Nrf2.

To elucidate the Nrf2 regulation of ferritinophagy-associated proteins, we assessed their expression in Nrf2 CKO mice. Thus, Nrf2 levels were significantly elevated in the II/R model compared to those in the sham mice. NCOA4 and LC3Ⅱ protein levels were further increased in Nrf2 CKO mice, whereas FTH1 levels were reduced in the II/R model and further lower in Nrf2 CKO mice (Fig. 2h–i). Additionally, UBE3B levels, which were high in the II/R model, were significantly reduced in Nrf2 CKO mice, indicating that they may be regulated by Nrf2. Taken together, these results indicate that Nrf2 CKO mice lose their ability to modulate ferritinophagy following II/R. Based on these data, we can deduce that Nrf2 negatively regulates cellular ferritinophagy and ferroptosis in II/R-ALI cells. However, the specific regulatory mechanisms require further investigation.

3.3. Nrf2 deficiency reduces UBE3B expression and accelerates ferritinophagy, while overexpression of UBE3B alleviates cell damage via modulation of NCOA4 in AECII

We used AECII cells to further investigate the signaling pathways involved in the Nrf2 regulation of ferritinophagy. These cells were derived from the lung tissue of Nrf2 KO mice. We demonstrated that Fe accumulated in AECII cells after oxygen glucose deprivation/re-oxygenation (OGD/R) induction, but not in non-induced AECII cells. Moreover, its levels significantly increased in the Nrf2^−/− group (Fig. 3a). Next, we evaluated the levels of oxidative stress markers, such as CCK8, GSH, and MDA. Cell viability and GSH percentage were further reduced, whereas the percentage of MDA levels increased (Fig. 3a–d). In line with our in vivo studies, Nrf2/UBE3B expression was markedly increased following OGD/R induction in AECII cells, while NCOA4 and LC3II protein levels were further increased in the shNrf2 group. Additionally, FTH1 levels were low in the OGD/R group and even lower in the shNrf2 group (Fig. 3e–f).

However, UBE3B overexpression reversed the changes caused by Nrf2 deficiency. We simultaneously transfected Nrf2^−/− and OEUBE3B lentiviruses into AEC and performed OGD/R modeling. Nrf2^−/− increased NCOA4 and LC3II, while overexpression of UBE3B reduced this effect and increased the expression of the FTH1 protein (Fig. 3g–h). In addition, we determined the iron content in the Nrf2^−/−+UBE3B group relative to that in the Nrf2^−/− control group. Iron levels were significantly increased in the Nrf2^−/− group, which was reversed by UBE3B overexpression (Fig. 3i). Our results showed that cell viability and GSH levels increased, and MDA levels decreased in OGD/R OEUBE3B cells as compared to OGD/R Nrf2^−/− cells (Fig. 3i–l). UBE3B overexpression significantly reversed the above changes caused by Nrf2 deficiency, indicating that UBE3B overexpression could inhibit NCOA4-mediated ferritinophagy, thereby alleviating ferroptosis.

3.4. UBE3B deficiency promotes NCOA4-mediated ferritinophagy and aggravates cell injury

To further delineate the UBE3B-mediated regulation of ferritinophagy, AECⅡ cells were infected with UBE3B-shRNA lentivirus. UBE3B deficiency significantly aggravated ferritinophagy, indicating that NCOA4 and LC3Ⅱ expression (Fig. 4a-b), cell death (Fig. 4c), oxidative stress (Fig. 4d-e), and iron content (Fig. 4f) were further aggravated by shUBE3B OGD/R. These data indicate that the anti-ferritinophagy role of UBE3B may be produced by modulating NCOA4 levels after OGD/R induction.

3.5. UBE3B binds to NCOA4 and induces ubiquitination degradation, thereby regulating ferritinophagy

We further investigated the potential mechanism by which UBE3B mediates NCOA4 protein expression in AECII. Ubiquitin E3 ligases have been well established to play a crucial role in selecting specific substrates for ubiquitination reactions, operating through the interaction between ubiquitin E3 ligases and substrates (Toma-Fukai and Shimizu, 2021). Therefore, we performed co-immunoprecipitation (CO-IP) with an Nrf2 antibody; the immunoblotting results showed an interaction between NCOA4 and UBE3B (Fig. 5a) and was colocalized in cells (Fig. 5b). To determine the region of UBE3B that recognizes NCOA4, we cloned and expressed four fragments spanning the UBE3B open reading frame, as shown in Fig. 5c. Endogenous NCOA4 was combined with fragments 1 and 2 (Fig. 5d). Additionally, shRNA-mediated depletion of UBE3B significantly increased the half-life of NCOA4 (Fig. 5e), further supporting the hypothesis that UBE3B-mediated ubiquitination and degradation of NCOA4 suppress ferritinophagy.

Ferroptosis is an iron-dependent form of cell death that involves oxidative processes. It includes the Fenton reaction wherein ferrous iron reacts with hydrogen peroxide to produce ferric iron and ROS. If not promptly neutralized, ROS can harm lipid membranes, ultimately leading to cell death (Stockwell et al., 2017). NCOA4 binds to FTH1 within the autophagosome, facilitating the transfer of ferritin to the lysosome for degradation. This process releases free iron, which serves as a crucial source of intracellular ferrous ions (Wang et al., 2023a). Inhibition of ferritinophagy prevents ferroptosis; several studies have revealed that ferritinophagy-mediated ferroptosis promotes ischemia/reperfusion organ injury (Jin et al., 2023, Li et al., 2021). Therefore, we hypothesized that II/R or OGD/R may play a critical role in promoting ferroptosis and ferritinophagy. To test this hypothesis, we assessed the levels of oxidative stress markers, such as GSH, MDA, and Fe²⁺. We also evaluated the expression of ferritinophagy-related proteins, including NCOA4, FTH1, and LC3Ⅱ. According to our findings, the GSH percentage was dramatically reduced, while the MDA percentage and Fe²⁺ levels were markedly elevated. Additionally, evaluation of the ferritinophagy-related proteins NCOA4, FTH1, and LC3Ⅱ indicated that both ferroptosis and ferritinophagy were notably elevated in the II/R and OGD/R groups compared to controls. At the same time, we observed that the co-localization of FTH1 and LC3 increased significantly in type Ⅱ alveolar epithelial cells of II/R mice. Therefore, the epithelium undergoes ferritinophagy during II/R.

NCOA4-mediated ferritinophagy plays a crucial role in regulating intracellular Fe²⁺ balance, and emerging evidence has shown that NCOA4 can regulate ferroptosis (Ma et al., 2024). In cells, NCOA4 binds to FTH1 and LC3Ⅱ in the lysosome, facilitating the release of ferrous iron and enhancing the Fenton reaction to promote ferritinophagy, thereby triggering ferroptosis (Lee et al., 2022, Man et al., 2022, Masaldan et al., 2018). Nrf2 is a pivotal transcription factor of oxidative stress that stimulates downstream pathways that regulate ferroptosis by modulating GSH, iron and lipid metabolism, and mitochondrial function (Abdalkader et al., 2018). Previous studies have shown that Nrf2 regulates NCOA4-mediated ferritinophagy (Ma et al., 2024, Anandhan et al., 2023). Therefore, Nrf2 affects ferritinophagy-dependent ferroptosis by activating autophagy proteins. However, the precise role of Nrf2 in ferritinophagy associated with II/R-ALI remains to be elucidated. Nrf2 CKO mice exhibited more severe iron deposition, stronger GSH suppression, and higher MDA levels than WT II/R mice (Fig. 2). Additionally, examination of the ferritinophagy-related proteins FTH1 and LC3Ⅱ/LC3I suggested that ferritinophagy was significantly enhanced in Nrf2 CKO mice compared to that in WT mice. Simultaneously, we found that Nrf2 negatively regulates NCOA4. However, the specific regulatory mechanisms of these two remain to be investigated.

Ubiquitin protein ligases form a vast superfamily, comprising more than 600 genes (George et al., 2018). These enzymes transfer ubiquitin molecules onto target proteins that are earmarked for degradation by the ubiquitin-proteasome system. Within this family, ubiquitin ligase E3B belongs to the HECT-type enzyme subgroup (Ambrozkiewicz and Kawabe, 2015). UBE3B is a mitochondria-associated ubiquitin protein ligase (Braganza et al., 2017). According to a recent study, disruption of mouse Ube3b results in decreased viability and mimics important characteristics of human disorders, including reduced weight and brain size, as well as the downregulation of cholesterol synthesis. UBE3B plays a critical role in oxidative stress responses (Basel-Vanagaite et al., 2012). However, it is unknown whether this antioxidant effect is related to Nrf2. In the present study, we identified high levels of UBE3B in an II/R model, suggesting possible UBE3B involvement in the regulation of ferritinophagy and II/R-ALI. UBE3B expression was significantly lower in Nrf2 CKO mice, suggesting that UBE3B is regulated by Nrf2. Braganza et al. found that silencing UBE3B in human cells led to alterations in mitochondrial morphology and physiology, decreased mitochondrial volume, and markedly inhibited cellular proliferation (Braganza et al., 2017). Mitochondrial damage is one of the characteristic signs of ferroptosis. In our study, we found that UBE3B overexpression reversed the damage caused by the loss of Nrf2, including prevention of AECⅡ cellular injury and reduction of Fe accumulation, NCOA4 proteins, and LC3Ⅱ/LC3I ratios, while promoting FTH1 levels (Fig. 3). In contrast, UBE3B inhibition reversed the above-mentioned changes (Fig. 4), demonstrating that UBE3B is regulated by Nrf2 and protects against OGD/R-driven ferritinophagy by regulating NCOA4. Upon conducting a literature search, we discovered that no study has yet reported the ubiquitination of NCOA4 or related ubiquitin E3 ligases. We speculated that UBE3B acts as an E3 ubiquitin ligase during the ubiquitination and degradation of NCOA4, thereby regulating ferritinophagy. We identified UBE3B as a novel protein that promoted the ubiquitination and degradation of NCOA4 (Fig. 5). This suggests that UBE3B interacts with NCOA4 to regulate its expression, thereby mediating ferritinophagy.

This study has some limitations. First, we did not identify other ubiquitin ligases for Nrf2. Hence, it remains unclear whether Nrf2 binds to multiple ubiquitin ligases involved in ferroptosis or ferritinophagy. In addition, we did not identify any potential ubiquitination sites of NCOA4. Future studies should investigate the following aspects: (1) Whether Nrf2 also regulates other ubiquitin ligases and has similar effects, (2) further verification of potential ubiquitination sites of NCOA4, and (3) whether the findings of this study can serve as a reference for developing treatments for other types of acute organ injuries that share similar pathogenesis with ALI.

In conclusion, the findings of the present study demonstrated the presence of ferritinophagy in II/R and OGD/R and revealed that Nrf2 regulates iron homeostasis by enhancing the ubiquitination and degradation of NCOA4 mediated by the ubiquitin E3 ligase UBE3B, thus inhibiting ferritinophagy. In contrast, inhibition of Nrf2 expression led to decreased UBE3B expression, which increased the half-life of NCOA4 and promoted ferritinophagy, thereby enhancing the accumulation of Fe and promoting oxidative stress and ferroptotic cell death. Overall, our study has great therapeutic potential to improve the treatment of II/R-driven ALI.

Acknowledgements

The authors gratefully acknowledge the support from the National Natural Science Foundation of China (82270080, 82172084, 81803002).

Author contributions

YW, HD, YG, HC, and BH conducted experiments and analyzed data. YW, HD, and YG prepared the manuscript. XX, RH, and HJ were involved in the conceptualization, review, and editing of the manuscript. XX and RH obtained and provided funding support. All authors have formally endorsed the final version. ‡These authors contributed equally: Yanjun Wang, Hui Dong, and Yunfan Gu.

Data statement

The authors confirm that the data supporting the findings of this study are available within the article and its supplementary materials.

Funding sources

This work is sponsored by National Natural Science Foundation of China (82270080, 82172084, 81803002).

Institutional Review Board Statement

All experimental procedures were conducted according to the guidelines set forth by the National Institutes of Health (NIH) and were approved by the Animal Research Ethics Committee of Shanghai Jiao Tong University, under ethical approval number A2023114.

Data statement

The authors confirm that the data supporting the findings of this study are available within the article and its supplementary materials.

Declaration of interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. All authors have formally endorsed the final version.

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* Abbreviations : AECII, type II alveolar epithelial cells; ALI, acute lung injury; ARE, antioxidant response element; CCK-8, cell counting kit-8; CKO, conditional knockout; CO-IP, Co-immunoprecipitation; GSH, glutathione; HE, hematoxylin and eosin; II/R, intestinal ischemia-reperfusion; IR, ischemia reperfusion; MDA, malondialdehyde, NCOA4, nuclear receptor coactivator 4; Nrf2, nuclear factor E2-related factor 2; OGD/R, oxygen glucose deprivation/re-oxygenation; ROS, reactive oxygen species; TEM, transmission electron microscopy; UBE3B, ubiquitin ligase E3.

Scheme 1 is available in the Supplementary Files section.

No competing interests reported.

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Graphical abstract Scheme 1. Nrf2 regulates iron homeostasis by enhancing the ubiquitin E3 ligase UBE3B-mediated ubiquitination and degradation of NCOA4, thus inhibiting ferritinophagy.

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Nrf2/UBE3B protects against acute lung injury by inhibiting ferritinophagy through the ubiquitination of NCOA4

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Abstract

Figures

1. Introduction

2. Materials and methods

2.1. Materials

2.2. Isolation of primary alveolar epithelial cells type Ⅱ

2.3. Cell culture

2.4. Oxygen-glucose deprivation and reoxygenation (OGD/R) model

2.5. Cell viability assessment

2.6. Animals

2.7. Intestinal ischemia/reperfusion (II/R) mouse model

2.8. Malondialdehyde (MDA) assay(Rui et al., 2021)

2.9. GSH assay(Wu et al., 2023)

2.10. Iron ion assay

2.11. Perls staining

2.12. Lung injury score

2.13. Co-immunoprecipitation (CO-IP) assay

2.14. Western blot

2.15. Immunofluorescence assay

2.16. Plasmid transfection

2.17. Quantitative real-time PCR assay

2.18. Transmission electron microscopy (TEM)

2.19. Statistical Analysis

3. Results

3.1. II/R causes ferroptosis and ferritinophagy in mouse lung tissue

3.2. Nrf2 knockout accelerates ferroptosis and ferritinophagy and aggravates II/R-ALI

3.4. UBE3B deficiency promotes NCOA4-mediated ferritinophagy and aggravates cell injury

3.5. UBE3B binds to NCOA4 and induces ubiquitination degradation, thereby regulating ferritinophagy

4. Discussion

Declarations

References

Abbreviations

Scheme 1

Additional Declarations

Supplementary Files

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Version 1