2.1 Ethics approval and consent to participate
The parents provided written informed consent for genetic studies. The study was approved by the ethics committee of the First Affiliated Hospital of Zhengzhou University (KS-2018-KY-36), and performed according to the principles of the Declaration of Helsinki. We collected peripheral blood samples from the patient and his family members. Genomic DNA was obtained using the TIANamp Genomic DNA Kit (TIANGEN, Beijing, China) according to standard extraction methods.
2.2 Genetic testing
MyGenostics provides a commercially-customized immune sequencing gene panel that can be used to perform sequencing analysis on 270 genes related to immune diseases (table S1). The sequencing data were aligned to the GRCh37/hg19 genome using the Burrows-Wheeler Aligner and variants were annotated using Annovar. Common variants were filtered using maf >0.05 in 1 000 Genomes 41, ExAC (v2.1), and dbSNP build 144. The variant was validated using Sanger sequencing.
2.3 Generation of RNF31 knockout cell lines
293T cells and HeLa cells were purchased from the American Type Culture Collection, and cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum. The wild-type HOIP plasmid was synthesized by GENEWIZ (Suzhou, China), and the full-length c.1882delG mutant HOIP (HOIP-mut) plasmid was obtained by site-directed mutagenesis. Cells were transfected using Neofect DNA transfection reagent (Neofect, Beijing, China) or jetOPTIMUS DNA transfection reagent (Polyplus, Illkirch, France) according to the manufacturer's instructions.
Oligonucleotide sgRNAs (F: caccgttgacaccacgccagtaccg, R: aaaccggtactggcgtggtgtcaac) targeting RNF31 were cloned into the lentiCRISPR-puro-v2 vector. PsPAX2, pMD2.G, lenti-crispr-puro-v2-gRNA, or lenti-puro-v2 plasmids were co-transfected into 293T cells to produce lentiviruses. HeLa cells were infected with lentivirus. The infected cells were then screened with puromycin (Abmole, Housten, TX, USA) at 3 μg /mL. Single-cell clones were tested for RNF31 knockout by Western blot (HOIP antibody, #875227, R&D Systems, Minneapolis, MN, USA), and sanger sequencing was performed to confirm the genomic variant sequence.
2.4 Immunoblotting
Cells were lysed using cell lysis buffer for Western and IP (P0013, Beyotime, Shanghai, China), supplemented with protease inhibitors and phosphatase inhibitors. SDS-PAGE electrophoresis, the proteins were separated by SDS-PAGE electrophoresis and transferred to PVDF membranes in buffer (194 mM glycine, 25 mM Tris, 20% (V/V) methanol). The membranes were incubated with the primary and secondary antibodies. The signal was detected by chemiluminescence (34580, ThermoFisher Scientific, Waltham, MA, USA). Either GAPDH or TUBULIN was used as the internal reference. The intensity of the blots was quantified using ImageJ software.
2.5 Immunoprecipitation
Cells were lysed in Western and IP lysis buffers containing protease inhibitors. The cell lysates were incubated overnight at 4 °C with FLAG antibody (mouse) (M185-3L, MBL, Nagoya, Japan). Then protein G agarose beads were added to the cell lysates and incubated at 4 °C for 2 hours. After washing the agarose beads, the appropriate amount of RIPA lysate and protein loading buffer were added. The immunoprecipitated protein samples were analyzed by immunoblotting using antibodies: FLAG-tag (mouse), MYC-tag (rabbit) (16286-1-AP, Proteintech, Wuhan, China), and HA-tag (rabbit) (M180-3, MBL).
2.6 Ubiquitination experiment
Intracellular total linear ubiquitination level assay by transfecting 293T cells simultaneously with p3×FLAG-CMV-HOIL-1L, p3×FLAG-CMV-SHARPIN, and p3×FLAG-CMV-HOIP, or p3×FLAG-CMV-HOIP-mut, or p3×FLAG-CMV plasmids. Following a 24-hour incubation period, the cells were lysed using protein lysis buffer containing protease and phosphatase inhibitors. The lysates were then subjected to Western blot analysis using LUB9 (MABS451, Millipore) and FLAG antibodies. The signals were detected using an ECL chemiluminescence assay.
2.7 NF-κB–luciferase reporter assays
Hela cells were simultaneously co-transfected with PGL4.32-NFκB-Report, pRL-TK, p3×FLAG-CMV-SHARPIN, p3×FLAG-CMV-HOIL-1L, and p3×FLAG-CMV-HOIP, or p3×FLAG-CMV-HOIP-mut, or p3×FLAG-CMV. After 48 hours, cells were lysed in luciferase cell lysis buffer (Promega, Madison, WI, USA), and the supernatant was collected by centrifugation at 13 000 rpm for 6 minutes. The luciferase activity was measured with the Luciferase Assay System, and the firefly luciferase activity of each lysate was normalized to Renilla luciferase activity.
2.8 Quantitative real-time PCR
Total RNA was extracted from cultured cells using RNAiso (9109, TaKaRa, Dalian, China). Reverse transcription reactions were then conducted using the HiScript II Q RT SuperMix for qPCR kit (R223-01, Vazyme, Nanjing, China). Quantitative PCR assays were performed using the AceQ qPCR SYBR Green Master Mix (Q141-02, Vazyme) kit. Reactions were run on the StepOnePlus™ Real-Time PCR System (4376600, Applied Biosystems, Foster City, CA, USA). ACTB was used as an internal reference for normalization and analyzed using the ΔΔCt method. The primer sequences used were as follows:
ACTB: 5’ ACCGCGAGAAGATGACCCAGAT 3' (F), 5’ GGGATAGCACAGCCTGGATAGCA 3' (R); IL6: 5’ CCCACACAGACAGCCACTCACCT 3' (F), 5’ TGCCTCTTTGCTGCTTTCACACA 3' (R)
2.9 Immunofluorescence assay
Cells were fixed with 4% paraformaldehyde for 30 minutes. Next, the cells were permeabilized by incubating on ice with 5% Triton X-100. The cells were then blocked with 5% (w/v) BSA in PBS for 1 hour and incubated overnight at 4 °C using the primary antibody p65 (10745-1-AP, Proteintech). Then the cells were incubated with Cy3-labeled goat anti-rabbit IgG antibody (GB21303, Servicebio) for 1 hour at room temperature. The nuclei were stained with 4,6-diamino-2-phenyl indole (DAPI) staining solution. Images were acquired using a confocal microscope (Olympus, Tokyo, Japan), and the FV31S-DT was used for image analysis.
2.10 Flow cytometry
Cells were collected and washed with pre-cooled PBS. Then the cells were stained with PI staining solution in binding buffer (E607306, Sangon Biotech, Shanghai, China). The signal was detected on a flow cytometer, Cytoflex (Beckman Coutler, Fullerton, CA, USA), using 488 nm excitation light. Data were analyzed with CytExpert and gated to live and dead cells based on the PI-red fluorescence signal.
2.11 Statistical analysis
All data are presented as mean SD. The data were analyzed using one-way analysis of variance (ANOVA) and two-way ANOVA, followed up by Tukey’s test as required. P values less than 0.05 were considered significant. The P-value settings are: NS, P>0.05; *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001. All statistical analyses were performed using Excel.