Data Source
Raw RNA-seq data for GEO dataset GSE89408 was downloaded from the SRA database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE89408) and quantified to gene-level counts using the ARCHS4 pipeline [17]. GSE89408 dataset, which included 57 early RA samples and 28 normal samples, were selected as the validation sets. Gene counts were downloaded from the ARCHS4 gene expression matrix v5. For more information about ARCHS4, as well as free access to the quantified gene expression matrix, visit the project home page at the following URL: http://amp.pharm.mssm.edu/archs4/download.html.
Data Normalization
Raw counts were normalized to log10-Counts Per Million (logCPM) by dividing each column by the total sum of its counts, multiplying it by 106, followed by the application of a log10-transform.
Volcano plot analysis
Volcano plot was plotted by https://www.bioinformatics.com.cn (last accessed on 10 July 2023), an online platform for data analysis and visualization.
Immune infiltration analysis
The deconvolution method was employed to process marker gene expression values to estimate the proportion of different types of immune cells in the glomerular tissues of both normal and diabetic nephropathy. The CIBERSORT algorithm was used for analysis. These cells comprise 22 different types of immune cells, including M1 and M2 macrophages, plasma cells, static memory CD4 + T cells, γδT cells, and mast cells. For every sample, a boxplot representing the percentage of T cell was created.
Cell culture and huPBMC-AIA model
Human peripheral blood mononuclear cells (HuPBMC) from Charles River (formerly HemaCare). huPBMC was kept at 37°C in a humidified incubator with 5% CO2. Harvested during the exponential growth phase, the cells were resuspended at a density of 10x106 cells/mL in full growth media.
All the animal studies were conducted under protocols approved by the Local Ethical Committee of Harbin Medical University Animal Care and Use. Five-week-old NOG male (Charles River, USA) mice were infused intravenously with 3x106 huPBMC. Peripheral blood was collected, and flow cytometry was used to evaluate the immune cell subpopulations to verify the humanization. The humanized mice were included in the Adjuvant induced arthritis (AIA) induction protocol after achieving sufficient immune blood reconstitution (engraftment efficiency (huCD45 > 25%)).
For the humanized arthritis model, the periarticular space surrounding the ankle was injected with 10 µL of either complete Freund's adjuvant (CFA) 4 mg/mL (Chondrex, Redmond, WA) or PBS. To deplete murine neutrophils, anti-Gr-1 antibody (250µg) (BioXCell, West Lebanon, US) was given intraperitoneally (IP) on days 1 and − 1. Ankle joint processing and arthritis were carried out as previously mentioned [18]. A vernier caliper was used to measure the thickness of the paw.
RNA-seq Analysis and KEGG
Total RNA was extracted from paw of huPBMC-AIA model followed by library preparation according to Illumina standard instruction (VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina®). Agilent 4200 bioanalyzer was employed to evaluate the concentration and size distribution of cDNA library before sequencing with an Illumina novaseq6000. The protocol of high-throughput sequencing was fully according to the manufacturer's instructions (Illumina). The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4). The fragments of genes were counted using stringtie(v1.3.3b) followed by TMM (trimmed mean of M values) normalization. Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q < 0.05) and fold-change > 2 using edgeR software [19]. An online platform (chiplot) was used for the KEGG pathway and Reactome enrichment analyses of DEGs.
Flow Cytometry
Flow cytometric analyses were performed on a flow cytometer CytoFLEX (Beckman Coulter, USA). The peripheral blood, spleen, bone marrow, and paw were processed in the same manner as previously described [18]. Single cell suspensions were stained with a mixture of fluorochrome-conjugated antibodies against human CD45, human CD4, human CD8, human CD278, mouse CD11b, mouse Gr-1, and mouse CD45, after being fixed with the Zombie AquaTM Fixable Viability Kit (BioLegend, San Diego, CA). FlowJo software (Treestar Inc, OR) and online platform (Cytobank, Beckmen, US) was used for the analyses.
Conjugation of Cy7-ICOS mAb
The supplier of the in vivo monoclonal antibody (clone: C398.4A) against human ICOS was BioXCell, located in West Lebanon, USA. The Cy7 NHS ester was supplied by APExBIO. Anti-ICOS mAb was diluted in PBS to 1 mg/mL. Cy7 NHS ester was dissolved in dimethyl sulfoxide to a final concentration of 5 mg/mL before being mixed with anti-ICOS mAb. The ICOS mAb to Cy7 NHS ester molar ratio was 1:10. The mixture was incubated at room temperature for 1 hour. Cy7-ICOS mAb was purified using a Vivaspin2 50 KDa cutoff MWCO spin filter (GE Healthcare, Piscataway, USA). NanoDrop (Thermo Fisher, Waltham, MA, USA) was used to determine the final concentration of Cy7-ICOS mAb.
Cell uptake study
Dulbecco's medium (IMDM). The 500X concentrate of the Cell stimulation Cocktail (Invitrogen, Carlsbad, USA) was added straight to the culture medium at a rate of 1X (2 uL/mL) to activate T cells. Following 1-hour incubation at 37°C, 2µg of Cy7-ICOS mAb was added after 48 hours of stimulation. Before the binding assay, activated T cells were treated with 100 µg of unconjugated ICOS mAb and incubated for 1 hour at 37°C for the blocking group. A multiscan spectrum (Tecan, Switzerland) and a CytoFLEX flow cytometer were used to analyze the data.
In vivo 4-view Near-infrared fluorescence imaging (NIRF) studies
An OPTICAL IMAGING IN VISIBLE & NIR I (Biospace, California, USA) was applied to collect the NIRF imaging data. On the 3rd day following the induction of arthritis, 50 µg of Cy7-ICOS mAb was administered via the mouse tail vein following anesthesia with 2–3% isoflurane gas. On days 3, 4, 5, 6, and 7, NIRF imaging was performed using the following parameters: Acquisition mode: FLI integration (1000 ms per frame − 5 frames) Fluorophore: Cy7, Excitation = 737 nm, Background = 687 nm, Emission = 797 nm, Filter cut off = 780–815 nm (band pass) nm; Lens: 50mm f/1.2; Aperture = 1.2; Focus = 93.0. Overlaying x-ray images and optical signals is possible with the PhotonIMAGER Optima's X-ray module. Improved optical signal localization and quantification are provided by the 4-View – 3D module (Acquisition mode: FLI integration (1000 ms per frame − 5 frames Fluorophore: Cy7, Excitation = 737 nm, Background = 687 nm, Emission = 797 nm, Filter cut off = 780–815 nm (band pass) nm Lens: 35mm f/1.4; Aperture = 1.4; Focus = 94.0). Region of interest (ROI) of NIRF images was drawn using software (M3 vision, Biospace, California, USA).
Ex Vivo Biodistribution
To validate the ROI data, mice were euthanized after the imaging session on day 7 and subjected to the standard ex vivo biodistribution analysis described above. The following organs were harvested: the heart, liver, lung, spleen, kidney, intestine, right paw (RP), left paw (LP), bone, muscle, skin, and blood. Parameters for acquisition: 50mm f/1.2 lens; 1.2 aperture; 96.0 focus.
Immunofluorescence
Immunofluorescence (IF) staining antibodies: Abcam (Boston, USA) provided the IgG H&L (Alexa Fluor® 488) (ab173003) and IgG H&L (Alexa Fluor® 594) (ab150108). BioLegend provided a purified anti-human CD3 antibody (Clone: OKT3) and an anti-human/mouse/rat CD278 (ICOS) antibody (Clone: C398.4A). After the mice were sacrificed, the ankle joints were fixed with 4% paraformaldehyde and decalcified for 40 days with 10% EDTA. After embedding in paraffin After deparaffinization, antigen retrieval, and BSA blockade, ankle joint sections were stained overnight at 4°C with CD3 or CD278 antibodies. The fluorescent-labeled secondary antibodies were then added and incubated for 1 hour. After staining the nuclei with DAPI (Beyotime, Shanghai, China), the sections were examined under a fluorescent microscope (Nikon, Japan).
Safety Evaluation
During the procedures, the body weight was recorded. Blood was collected three days after the last administration, and serum was separated by centrifugation. Standard kits were used to measure serum levels of ALT, AST, BUN, and Crea. Major organs (heart, liver, spleen, lung, and kidney) were removed, fixed with 4% paraformaldehyde, and stained with hematoxylin and eosin (H&E). A Light microscope (Nikon, Japan) was then used to image the sections.
Statistical Analysis
An online platform for data analysis and visualization, https://www.chiplot.online, was used for data management and analysis. For the statistical analyses, GraphPad Prism 9.0v (GraphPad, CA, USA) software was utilized. Our tests have not been parametric. There were only two groups compared using the Mann-Whitney test. P-values below 0.05 were regarded as statistically significant.