Isolation and culture of primary rat nucleus pulposus cells (NPCs)
Sprague-Dawley rats (male, three months old) were used in this study. Rat NPCs were obtained as previously described29. Briefly, NP tissues were isolated from rat lumbar disks after sacrifice. The tissues were shredded and digested in 0.25% type II collagenase (Sigma, St. Louis, MO, USA) at 37°C for 15 min. The digested mixture was centrifuged at 300 g for 5 min and suspended in DMEM/F-12 (Gibco, USA) containing 10% fetal bovine serum (FBS; Gibco, USA) at 37°C and 5% CO2. The medium was changed every 2 days, and when the confluence reached 80–90%, the cells were passaged with trypsin-EDTA solution (Gibco, USA). The third passage was used for subsequent experiments.
Experimental design
To explore the effects of oxidative stress on copper sensitivity, NPCs were cultured with nonlethal tert-butyl hydroperoxide (TBHP, 0, 15, 30 µM) (Sigma-Aldrich, Missouri, USA) and/or CuCl2 (0, 2, 4 µM, Sigma-Aldrich, USA) for 24 h. To determine whether SP1 mediated oxidative stress-induced cuproptosis, NPCs were incubated with an SP1 DNA-binding inhibitor, Mithramycin A (MA, 2 µM) (HY-A0122, MedChemExpress, New Jersey, USA), TBHP (30 µM), and CuCl2 (4 µM) for 24 h. To ensure that SP1 mediated cuproptosis by affecting copper transport, after NPCs were treated with MA (2 µM), TBHP (30 µM) or/and CuCl2 (4 µM) for 24 h, Elesclomol (0.1 µM) (HY-12040 MedChemExpress, USA) was administered for another 24 h.
IDD model establishment and injection
Experiments were approved by the Animal Experimentation Committee of the Huazhong University of Science and Technology ([2021] IACUC Number 3077). Male Sprague-Dawley rats (200–300 g) were acquired from the Laboratory Animal Center of the Huazhong University of Science and Technology (Wuhan, China). Rats were randomly divided into four groups: intact, IDD, IDD treated with normal saline (NS), and IDD treated with MA. Rats were anesthetized with 0.6% (w/v) pentobarbital sodium, and coccygeal vertebrae Co5/6 were located via manual palpation and counting, which was confirmed by trial radiography. The rat IDD model was established using a 22-gauge sterile needle puncture at a depth of 5 mm. The needle was rotated 360° and held for 30 s. Surgery was not performed in the intact group. Three days later, 2 µL of NS or MA (100 µg/ml) was injected into the operated NP disks via a 29-gauge Hamilton needle, and the needle was held for 1 min for solution diffusion. The IDD group underwent the same procedure without liquid injection. NS and MA injections were repeated every two weeks. Four weeks after the first dose, the rats were sacrificed, and disks were harvested for further radiography and histological analysis.
MRI Analysis
T2-weighted midsagittal sections of the coccygeal vertebra were obtained using an MRI scanner (Skyra 3.0T, Siemens, Germany). Three radiologists independently participated in the evaluation of disk grading based on the Pfirrmann MRI grade system30. The T2-weighted signal intensity was measured using ImageJ software 1.52i (National Institutes of Health, Bethesda, MD, USA). The relative water content, representing the hydration of disk tissues, was calculated as: relative water content = \(\frac{{D}_{s}}{{D}_{o}}\) (Ds, T2-weighted intensity of disks after surgery; Do, T2-weighted intensity of intact disks).
Histopathological and immunohistochemical evaluation
The rat disk tissues were fixed in paraformaldehyde (4%, w/v). After embedding in paraffin, 4.0 µm sections were cut using a rotary microtome (Thermo Scientific, Massachusetts, USA). Histological evaluation of the slides was performed using hematoxylin and eosin (H&E) and Safranin O-fast green (S&O) staining, following the manufacturer’s protocols. Histological grading was performed independently by three pathologists based on the histological grading scale of Han et al.31.
Immunohistochemical staining, with primary antibodies against SP1 (A14662, Abclonal, China), FDX1 (12592-1-AP, proteintech, Chicago, USA), CTR1 (A0773, Abclonal, China), ATP7A (A8399, Abclonal, China), and ATP7B (A5676, Abclonal, China), were performed to observe the expression levels of these proteins in the tissues. Under high magnification using an optical microscope (Olympus, Tokyo, Japan), five visual fields for each slide were randomly chosen for quantitative analysis and the proportion of positively stained cells was calculated.
The primary antibodies mentioned above were also used for immunofluorescence analysis. After dewaxing and dehydration, the slides were incubated with the corresponding primary antibody working solution overnight at 4°C. Fluorescence-conjugated secondary antibodies (AS0743 and AS074; Abclonal, China) were added to detect fluorescent signals before adding DAPI staining solution (Sigma, USA). An anti-fluorescence quenching sealer (Thermo Fisher Scientific, USA) was used for sealing. A fluorescence microscope (Olympus, Tokyo, Japan) was used to photograph sample fluorescence signals.
Western blot analysis
The culture medium was removed, and the cells were washed with PBS and lysed in lysis buffer (Beyotime, China) supplemented with the protease inhibitor phenylmethanesulfonylfluoride (PMSF, Beyotime) and phosphatase inhibitor cocktail I (Sigma, USA). The cell lysates were sonicated and centrifuged at 13,000 g for 15 min at 4°C. A BCA protein assay kit (Boster, China) was used to determine protein concentration, and the supernatants were denatured with SDS-PAGE denaturation buffer (Servicebio, China). 10 micrograms of protein were loaded into 10% or 15% SDS-PAGE gels, then transferred onto polyvinylidene fluoride (PVDF) membranes and blocked. The antibodies used were SP1 (A14662, Abclonal), FDX1 (12592-1-AP, Proteintech), CTR1 (A0773, Abclonal), ATP7A (A8399, Abclonal), ATP7B (A5676, Abclonal), and GAPDH (10494-1-AP, Proteintech). Membranes were immunoblotted overnight at 4°C. and were then incubated with secondary antibodies for 1 h at room temperature. Finally, the protein bands were visualized using enhanced chemiluminescence following the manufacturer’s instructions (Amersham Biosciences, Piscataway, NJ, USA). Data were processed using ImageJ and GraphPad Prism 8.
Flow cytometry of PI
The culture medium was removed, and the cells were washed with PBS. After digestion, cells were centrifuged at 300 g for 5 min, and then harvested for suspension with 100 µl of 1x binding buffer with addition of 2 µl propidium iodide (PI) (HYC2019, HYCEZMBIO, Wuhan, China). Cells were incubated in the dark at room temperature for 10 min and detected by flow cytometry (BD LSRII, Becton Dickinson) within 30 min. The proportion of PI + cells was calculated as the rate of cell death.
siRNA transfection
CTR1 and FDX1 siRNAs were purchased from GenePharma Co., Ltd. (Suzhou, China). Rat NPCs were transfected with CTR1 or FDX1 siRNAs (10 nM) using Lipofectamine 3000 (Thermo Fisher Scientific), according to the manufacturer’s instructions. The culture medium was then replaced with DMEM/F-12 medium after 24 h transfection, and incubated for a further 48 h for later experiments. The siRNA sequences used are listed in Supplementary Table 1.
Real-time PCR
Total RNA was harvested using the RNA-easy™ Isolation Reagent (Vazyme Biotech Co., Ltd., Nanjing, China), following the manufacturer’s instructions. NanoDrop 2000 analysis software was used to calculate the concentration of the extracted RNA. A reverse transcription kit (Vazyme Biotech Co., Ltd., Nanjing, China) was used for cDNA synthesis. The cycle threshold (CT) was determined using the SYBR PrimeScript RT-PCR Kit (Vazyme Biotech Co., Ltd, Nanjing, China) on a Step One Plus Real-Time PCR system (Bio-Rad, Hercules, CA, USA). The results were quantified using the 2 -△△CT method, with GAPDH levels used for normalization. The primer sequences used are listed in Supplementary Table 2.
Chip-qpcr
An Enzymatic Chromatin IP Kit (9003, CST, USA) was used to extract chromatin and DNA according to the manufacturer's protocol. A ChIP-grade anti-SP1 antibody (1 ug/6 ug chromatin, ab231778, Abcam, USA) was used to precipitate chromatin bound to SP1. Subsequent qPCR followed the above procedure, and the result was expressed as a percentage of the input. Primers were designed using SP1-related ChIP-seq datasets from the Cistrome Data Browser. Primers were designed in the promoter proximal region with the highest ChIP-seq peaks (Supplementary Table 3).
Preprocessing of bulk Transcriptome data
The bulk RNA-seq dataset consists of three control and six degenerative NP tissues obtained from the GEO database (https://www.ncbi.nlm.nih.gov/geo; accession number: GSE176205). We applied Salmon ver1.9.0 based on the Galaxy platform (https://usegalaxy.org/) in quasi-mapping mode with the Human Transcript sequences reference file from Genecode (https://www.gencodegenes.org/human/) to quantify the FASTA files of the GSE176205 dataset.
RNA-seq data analysis
All analyses were performed using R (ver 4.2.1) and Rstudio (https://posit.co/ver 2022.12.0 + 353). We aggregated Salmon-quant transcript level expression data at the gene level and imported the results into DESeq2 with Tximport (ver. 1.24.0). Differential analysis was performed using DESeq2 (ver 1.36.0)32. The GSVA package (version 1.44.5) was used to calculate the ssGSEA score as the cutoff value.
Single-cell RNA-seq data analysis
R packet Seurat ver4.2.0 was used to analyze the scRNA-seq data33. After creating Seurat objects from GSE165722, we filtered out cells with less than 200 genes and more than 10% mitochondrial genes. Then, the gene expression of each cell was standardized using the SCTransform method, and the standardized samples were integrated using the CCA algorithm. After the best dimension was determined by the PCA method, the integrated Seurat object was reduced and visualized by t-distributed stochastic neighbor embedding (t-SNE)34. Based on the Human Primary Cell Atlas (HPCA), SingleR was used to automatically annotate the reduced-dimensional dataset35. The “FeaturePlot()” command was used to map the expression of a single gene in different cell populations.
Statistical analysis
Each experiment was performed independently with at least three biological replicates. All data are presented as the mean ± standard deviation (SD), and t-tests were conducted to analyze differences between the two groups. Multiple datasets were analyzed using one-way repeated-measures analysis of variance (ANOVA). Non-parametric data (Pfirrmann grade and histological score) were analyzed using the Kruskal-Wallis H test. Statistical charts were created using GraphPad Prism 8. p < 0.05 was considered statistically significant.