Cell lines, mice, and reagents
Mouse CRC cell line MC38 was purchased from BMCR (http://www.cellresource.cn/). Cells were cultivated in RPMI-1640 enriched using 10% FBS, 10mg/mL penicillin-streptomycin, and 0.1 mmol/L nonessential amino acids (all materials from Gibco) at 37°C and 5% CO2. Six- to 8-week-old female C57BL/6 mice were acquired through SPF (Beijing) Biotechnology Co., Ltd. Food and water were available to all mice at all times under pathogen-free conditions. Anti-mouse SIRPα antibody (clone P84), anti-mouse CD8 antibody (clone YTS 169.4), anti-mouse PD-1 antibody (clone 29F.1A12), and isotype controls were acquired through Bio X Cell.
In Vivo Tumor Growth Experiments
Cellometer Mini Cell Counter (Nexcelom Biosience, Lawrence, MA) was used to count the cells after they had been cultured for less than two weeks. Female C57BL/6 mice aged 6 to 8 weeks were administrated through subcutaneous injection of 1 × 106 MC38 cells at the right flank. Approximately 100 mm3 of tumor volume was reached after 8–9 days, after which treatments were assigned (n = 10–12 per group). On day 8 or 9, the C57BL/6 mice were treated with either anti-SIRPα antibody (200mg per mouse) by intraperitoneal injection (i.p.), anti-PD-1 antibody (200mg per mouse) by i.p., HRT of 12 Gy, or the combination. The HRT was delivered by 6 MV X-rays with an output dose rate of 500 MU/min, from a Varian 600CD (Varian Medical Systems, Palo Alto, CA) linear accelerator, prepared with a 120 leaf Millennium multileaf collimator (MLC). Both the gantry and collimation angles were 0 degree. Five separated radiation fields with the field size of 2 cm × 2 cm at the isocenter plane were formed using the MLC, so that 5 mice at most could be irradiated simultaneously. To ensure an adequate dose of radiotherapy, the tumor of each mouse was placed within 1 cm × 1 cm of the center of each radiation field, with the rest of the body placed as far outside the radiation field as possible. The mice were placed at the isocenter plane, on a 20 cm thickness solid water phantom, and a 1.5cm thickness build-up was placed above the mice. Every two to three days, tumor diameters were recorded, and sizes were determined utilizing following formula: V = L × W2 × 0.5, where L and W represent the tumor's long and short diameters, respectively. Tumor growth delays tests were conducted twice for verification. Mice were killed when they exhibited symptoms of illness or developed subcutaneous tumors that were approximately 1,500 mm3 in size. On days 0, 3, and 6 following radiation exposure, every mouse was injected i.p. with 200 mg of anti-CD8 antibody or rat IgG2b isotype control for the CD8+ T-cell depletion tests.
Flow Cytometry
Single cell suspensions of tumors were prepared, and flow cytometry was carried out as mentioned earlier [19, 20]. Cells were stained with the following antibodies obtained from BioLegend: CD16/32 (clone 93, catalog No. 103132), Zombie UV™ Fixable Viability Kit (catalog No. 100752), CD45-PerCP/Cy5.5 (clone 30-F11, catalog No. 103132), CD45-APC/Cy7 (clone 30-F11, catalog No. 103116), CD11b-FITC (clone M1/70, catalog No. 101206), SIRPα-PE (clone BM8, catalog No. 123122), Gr-1-PerCP/Cy5.5 (clone RB6-8C5, catalog No. 108428), F4/80-AF647 (clone N418, catalog No. 117318) ,CD11c-PE/Cy7 (clone N418, catalog No. 117318), I-A/I-E-AF700 (clone M5/114.15.2, catalog No. 107622), CD86-BV421 (clone GL-1, catalog No. 105032), CD206-BV605 (clone C068C2, catalog No. 141721), CD8a-AF700 (clone 53 − 6.7, catalog No. 100730), CD8-BV510 (clone 53 − 6.7, catalog No. 100752), TNF-α-BV421 (clone MP6-XT22, catalog No. 506328), IFN-γ-PE (clone XMG1.2, catalog No. 505808), CD39-PE/Cy7 (clone Duha59, catalog No. 143806), Tim-3-APC/Fire™ 750 (clone RMT3-23, catalog No. 119738), PD-1-BV605 (clone 29F.1A12, catalog No. 135220). The next antibodies were obtained through eBioscience: Mouse Regulatory T Cell Staining Kit #2 (clone FJK-16s, catalog No. 88-8118-40). FlowJo program (Tree Star Inc.) was utilized to examine the findings that were acquired through a BD LSRFortessa Flow Cytometer.
Clinical Samples And Immunohistochemical Staining
A total of 94 CRC patients (86 had adjacent normal tissues) had paraffin tissue slices (HColA180Su21) acquired through Shanghai Outdo Biotech (National Human Genetic Resources Sharing Service Platform with code No. 2005DKA21300, Shanghai, China). CRC samples and controls were stained using immunohistochemical staining (IHC) in accordance with the recommended practices (Cell Signaling Technology). In brief, the slides were first incubated with primary antibodies: anti-SIRPα (1:500 dilution, Abcam, ab53721) or anti-CD47 (1:10000 dilution, Abcam, ab218810), followed by goat anti-rabbit secondary antibodies conjugated with horseradish peroxidase. A 2-Solution DAB Kit (Invitrogen) was used to visualize antibody binding. Independent scoring of the IHC results was performed by two expert pathologists who were blinded to the trial information. In the event of inconsistent scoring, the pathologists consulted with each other and re-reviewed the slides. Each tissue specimen was evaluated using a traditional H score for indicators, by the sum of relative intensity (0: negative; 1: weak; 2: moderate; 3: strong) of specific staining multiplied by the percentage of positive cells. Supplementary table 2 shows the clinical features of the patients (from whom tissues were obtained). For survival analyses, patient OS were categorized based on the median value of the scoring results and were denoted as Kaplan–Meier plots and examined for significance utilizing log-rank tests.
Multiplexed Immunofluorescence Staining
To evaluate the density of the CD8+ and CD86+ cell composition of the TME and their relative spatial positioning in tumors, the PANO 4-plex IHC kit (catalog No. 10079100100, Panovue) was utilized for multiplex staining of tissue that was formalin-fixed and then embedded in paraffin. Following sequential application of CD8 (catalog No. 98941, CST) and CD86 (catalog No. 19589, CST) antibodies, horseradish peroxidase-conjugated secondary antibodies were incubated and tyramide signal amplification was performed. Following each tyramide signal amplification operation, the slides were microwave-heated. The DAPI stain was applied after all antigens were labeled. Multispectral images from the stained slides were acquired at 10× and 40× magnification using Zeiss Axio Imager Z2 multispectral microscope within the same exposure time. Each slide was scanned in five random areas without necrosis or damage.
Bioinformatic Analysis
We compared SIRPα and CD47 mRNA expressions of colon cancer and normal tissues by submitting a query to TNM plot [21] with selection of Gene chip data. As well, we obtained RNA-seq data from the Cancer Genome Atlas (TCGA) and the GTEx (Genotype-Tissue Expression) database using the GEPIA2 [22] tool, set to a P-value cutoff = 0.01, log2FC (fold change) cutoff = 1, and "matched TCGA normal and GTEx data".
To analyze the correlation between SIRPα and exhausted T cell signature, RNA-seq data were obtained from the TCGA dataset using the GEPIA2 [22] tool. The T-cell-exhaustion signature gene set included HAVCE2, TIGIT, LAG3, PDCD1, CXCL13, LAYN, and CD39.
Public single-cell melanoma dataset GSE120575 was utilized to examine the connection between SIRPα expression and ICB resistance. The scRNA-seq analysis was carried out employing Seurat (V4.0.4). For quality control, the data was filtered to incorporate only genes that were expressed in a minimum of 5 cells and cells that expressed a minimum of 200 genes, with a maximum of 8000 genes and a minimum of 40,000 unique molecular identifier (UMI) counts and less than 15% of mitochondrial gene expression. Harmony (V0.1.0) was performed for removing the batch effects. The monocyte/macrophage cell type was defined through the expression of following marker genes: FCN1, VCAN, CD14, CD33, and CSF3R, as described in the original article [23].
Statistical analysis
All findings were recovered from more than two separate experiments. Data were analyzed utilizing Prism 8.0 software (GraphPad Software). Results are denoted as the mean ± standard error of the mean (SEM) for all figure panels unless otherwise indicated. The P values were evaluated employing the independent Student t-test, paired Student t-test, Wilcoxon test, or the Pearson correlation test. Log-rank univariate analysis and Cox regression multivariate analysis were used to identify factors related to prognosis. Survival curves were displayed utilizing the Kaplan–Meier method and compared utilizing a log-rank test. Statistical significance was set to be a P-value ≤ 0.05 in 2-tailed tests.