Mice and cell lines
6-8-week-old female B6.Cg-Tg(TcraY1,TcrbY1)416Tev/J mice, expressing a rearranged TCR transgene specific for the H2-Db-restricted SV40 large tumor antigen (TAG)206−215 epitope I (SAINNYAQKL), were obtained from The Jackson Laboratory (Bar Harbor, ME, USA) and housed in the Comparative Oncology Shared Resource (COSR) at Roswell Park Comprehensive Cancer Center (RPCCC) (Buffalo, NY, USA). Six-week-old female C.B-Igh-1b-Icr-Tac-Prkdc SCID/Ros (SCID) mice were obtained from the COSR at RPCCC (Buffalo). All animal studies were performed in compliance with the guidelines established by the Institutional Animal Care and Use Committee (IACUC) under approved protocols. The TAG-expressing MOVCAR 5009 ovarian carcinoma cell line, transduced with a retroviral construct encoding the firefly luciferase gene (pWZL-Luc) for in vivo imaging23, was kindly provided by Dr. Denise Connolly (Fox Chase Cancer Center, Philadelphia, PA, USA). MOVCAR 5009 cells were cultured in DMEM (Corning, NY, USA) supplemented with 10% fetal bovine serum (FBS; Corning), 5 µg/ml gentamicin sulfate (Corning), and maintained at 37°C with 5% CO2. The MOVCAR 5009 cell line was authenticated at the American Type Culture Collection (ATCC; Manassas, VA, USA) using short tandem repeat profiling.
Oncolytic vaccinia viruses (OVs)
The OVs used in the study were of the Western Reserve stain with disrupted thymidine kinase (TK) and vaccinia growth factor (VGF) genes for enhanced cancer cell specificity. The generation and characterization of the virus expressing the Fc portion of murine IgG2a (OV-Fc) and CXCR4 antagonist in the context of the Fc portion of murine IgG2a (OV-CXCR4-A) have been described previously17.
In vivo studies
SCID mice (n = 5 per group) were injected i.p. with 5 x 106 MOVCAR 5009 cells and treated i.p. with 5 x 107 PFU of OV-Fc or OV-CXCR4-A 10 days after the tumor challenge, while untreated mice served as control. For the adoptive T cell transfer (ACT), spleens from naïve B6.Cg-Tg(TcraY1, TcrbY1)416Tev/J mice were collected, homogenized, and filtered through a 70 µm cell strainer into ammonium-chloride-potassium (ACK) lysis buffer (Quality Biological, Gaithersburg, MD, USA) to lyse erythrocytes. Cells were washed twice in cold RPMI 1640 media (Corning) and 5 x 106 TCRTAG T cells, separated using Pan T cell isolation kit II (Miltenyi Biotech, Gaithersburg, MD, USA), were injected i.v. to MOVCAR 5009-bearing SCID mice 3 days after oncolytic virotherapy treatment. Tumor growth was monitored by bioluminescence imaging and signals were determined by IVIS Spectrum In Vivo Imaging System (PerkinElmer, Waltham, MA, USA) after i.p. injection of 200 µl D-Luciferin (150 mg/kg body weight; Gold Biotechnology, St. Louis, MO, USA) following the manufacturer’s protocol. The values for average radiance (photons/sec/cm2/sr) in ROIs were determined in the Living Image 4.7.3 Software for IVIS Spectrum.
Immunohistochemistry (IHC)
Immunohistochemical staining was done on the omental tumor sections harvested from MOVCAR 5009-bearing SCID mice 10 days after OV treatments. Briefly, samples were placed in 10% neutral buffered formalin (NBF) for 24 h, dehydrated, and embedded in paraffin. Formalin-fixed paraffin-embedded (FFPE) sections (4 µm thick) were stained using a rat anti-mouse antibody specific for CD31 (clone: SZ31, DAI-310; Dianova, Eching, Germany) at 1:35 dilution for 40 min, followed by incubation with rabbit anti-rat IgG (ab102248; Abcam, Cambridge, UK) for 30 min, and Rabbit EnVision+ (K4003; Agilent Technologies, Santa Clara, CA, USA) for 30 min. Diaminobenzidine (DS9800; Leica Biosystems, Wetzlar, Germany) was applied for 10 min and slides were counterstained with hematoxylin for 8 min. Slides were scanned by the Aperio AT2 Slide scanning system and data were analyzed with the Aperio ImageScope 12.3.3 Software (Leica Biosystems). MVD was evaluated by enumerating the number of CD31+ endothelial clusters within a region of interest and microvessel diameter was measured at the vessel’s largest width as described4, 17.
The multispectral immunofluorescence (mIF) imaging
Sample preparation and staining:
The mIF staining on FFPE omental tumor sections was performed by The Advanced Tissue Imaging Shared Resource (ATISR) at RPCCC using the Opal 6-Plex Detection Kit (NEL821001KT, AKOYA Biosciences, Marlborough, MA, USA) as described68. Briefly, FFPE 4 µm sections were cut and placed on charged slides. Slides were dried at 65°C for 2 h. After drying, the slides were placed on the BOND RXm Research Stainer (Leica Biosystems) and deparaffinized with BOND Dewax solution (AR9222, Lecia Biosystems). The mIF staining process involved serial repetitions of the following for each biomarker: epitope retrieval/stripping with ER1 (citrate buffer pH 6, AR996, Leica Biosystems) or ER2 (Tris-EDTA buffer pH9, AR9640, Leica Biosystems), blocking buffer (AKOYA Biosciences), primary antibody, Opal Polymer HRP secondary antibody (AKOYA Biosciences), Opal Fluorophore (AKOYA Biosciences). Spectral DAPI (AKOYA Biosciences) was applied once slides were removed from the BOND. They were cover-slipped using an aqueous method and Diamond antifade mounting medium (Invitrogen ThermoFisher Scientific, Waltham, MA, USA). The mIF panels consisted of the antibodies as detailed in Supplementary Table 1.
Tissue imaging and analysis:
Slides were imaged on the PhenoImager™ HT (AKOYA Biosciences). Further analysis of the slides was performed using inForm® Software v2.6.0 (AKOYA Biosciences). The whole slides were first scanned in an unmixed view, then representative ROIs were selected for acquisition under the guidance of a pathologist. These ROIs were then rescanned to achieve full spectral unmixing. A representative subset of these unmixed ROIs was then used to train tissue and cell segmentation. Next, a unique algorithm was created using a machine-learning technique, in which the operator selects positive and negative cell examples for each marker. These algorithms were then batch-applied across a greater number of ROIs selected for inclusion in further analysis. The RStudio plugin, phenoptrReports, was used to extract phenotype counts from the resulting data tables.
Spatial Transcriptomics
Sample preparation:
ST analysis was completed on FFPE sections prepared from omental tumors of MOVCAR 5009-bearing SCID mice 10 days after OV treatments using the 10x Genomics Visium platform by the Genomics Shared Resource (GSR) at RPCCC. After tissue mounting on Visium slides, hematoxylin and eosin (H&E) images were captured for downstream data analysis. FFPE blocks were stained with H&E, imaged for pathological review, sectioned at 5 µm, and trimmed to fit in the capture area (6.5 mm x 6.5 mm) of the Visium Spatial slides (10x Genomics, Pleasanton, CA, USA). Each area contains an array of ~ 5000 spots (55 µm in diameter). The tissue areas of interest were identified by a pathologist based on histologically well-organized CD31-expressing tumor vasculature. The RNAs within the tissue were hybridized to the whole transcriptome probe panel and the hybridized probes were captured on the Visium slides. Captured probe products were then extended using the unique molecular identifier (UMI), Spatial Barcode, and partial Read 1, and the obtained cDNA was used for gene expression library construction. Gene expression libraries for each sample were produced with enzymatic fragmentation, end-repair, a-tailing, adapter ligation, and PCR to add Illumina-compatible sequencing adapters. The resulting libraries were evaluated using D1000 Screen Tape on the TapeStation 4200 (Agilent Technologies) and quantitated using the KAPA Biosystems qPCR quantitation kit for Illumina. They were then pooled, denatured, and diluted to 300 pM (picomolar) with 1% PhiX control library added. The resulting pool was then loaded into the appropriate NovaSeq Reagent cartridge followed by sequencing on a NovaSeq6000 according to the manufacturer's protocol (Illumina Inc., San Diego, CA, USA). Once sequencing was completed, tissue images taken after H&E staining on the Visium slide were used to align the gene expression from the spatial barcodes unique to each location in the capture area during data analysis.
10x Genomics Visium data analysis:
For the 10x Genomics Visium analysis, mapping results (binary alignment and map [BAM] files), and quantification matrices were generated using Space Ranger v.1.3.1 software with the mouse mm10 genome and GENCODE annotation database. Then the filtered gene-barcode matrices, which contain barcodes with the UMI counts that passed the cell detection algorithm, were used for further analysis. All downstream analyses were performed using the Seurat single-cell data analysis R package. The normalized and scaled UMI counts were calculated using the SCTransform method. Differentially expressed genes between clusters and samples were identified using the FindMarkers function with the Wilcoxon rank-sum test from Seurat. Pathway analysis was carried out using the fgsea R package with the gene list ranked by average log2 fold change. The Hallmark (H) and the Canonical pathways (CP) of curated gene sets (C2) of the MSigDB pathway database were used in the pathway analysis. Activation/effector and dysfunction scores were calculated using the AddModueScore method from Seurat with selected genes in each functional category.
Single Cell RNA sequencing
Sample preparation:
The scRNAseq analysis was performed on single-cell suspensions prepared from tumor-draining lymph nodes (tdLNs) of MOVCAR 5009-bearing SCID mice 10 days after oncolytic virotherapy treatments. The lymph nodes were harvested, homogenized, and obtained cells were resuspended in 0.04% BSA (Sigma-Aldrich, Burlington, MA, USA) in phosphate-buffered saline without calcium and magnesium (PBS; Corning), passed through a 70 µm cell strainer (Fisher Scientific, Waltham, MA, USA) to receive single-cell suspension and washed three times in pre-chilled 1% BSA in PBS. Single-cell gene expression libraries were created using the 10x Genomics Chromium Next GEM Single Cell 3’ Kit v.3.1 (10x Genomics). To evaluate the viability and number of cells, as well as the absence of clumps and debris in single-cell suspensions, trypan blue and a Countess FL automated cell counter (Thermo Fisher Scientific) were used. Subsequently, samples from different experimental groups (ACT, OV-Fc/ACT, OV-CXCR4-A/ACT) were loaded separately in equal amounts into the Chromium Controller (10x Genomics), and reverse transcription and cDNA amplification were performed. This full-length amplified cDNA was then used to generate transcriptome libraries by enzymatic fragmentation, end-repair, A-tailing, adapter ligation, and PCR to add Illumina-compatible sequencing adapters. Evaluation of the obtained libraries was achieved on D1000 screen tape using a TapeStation 4200 (Agilent Technologies) and quantitation using the Kapa Biosystems qPCR Quantitation Kit for Illumina. The libraries were denatured, diluted to 300 pM with 1% PhiX control library, loaded into the NovaSeq reagent cartridge, and sequenced on a NovaSeq6000 according to the manufacturer’s protocol (Illumina). The received sequencing data from the 10x Genomics libraries were processed in the Cellranger v.7.0.0 Software (10x Genomics).
scRNAseq analysis:
For the scRNAseq analysis, mapping results (binary alignment and map [BAM] files), and quantification matrices were generated using Cell Ranger v.7.0.0 Software with the mouse mm10 genome and GENCODE annotation database. Then the filtered gene-barcode matrices, which contain barcodes with the UMI counts that passed the cell detection algorithm, were used for further analysis. All downstream analyses were performed using the Seurat single-cell data analysis R package. First, cells with very low or high RNA feature content (< 500 or > 7500 genes detected) or higher mitochondrial RNA content (> 15%) were filtered out from the analysis to remove empty cells and doublets. Then, the normalized and scaled UMI counts were calculated using the SCTransform method. Subsequently, dimension reductions, including principal component analysis (PCA), UMAP, and t-distributed stochastic neighbor embedding (tSNE), were carried out using the highly variable genes. Cell clusters were identified using the shared nearest neighbor (SNN)-based clustering on the first 12 principal components. The cell clusters were annotated by SingleR packages using the ImmGen reference database of the cell dex R package. Differentially expressed genes between clusters and samples were identified using the FindMarkers function with the Wilcoxon rank-sum test from Seurat.
Flow Cytometry
Flow cytometry analysis was performed on single-cell suspensions prepared from the inguinal tumor-draining lymph nodes of MOVCAR 5009-bearing SCID mice 10 days after oncolytic virotherapy treatment. Briefly, cells were incubated with an anti-mouse CD16/CD32 Fc blocking antibody (BD Biosciences, Franklin Lakes, NJ, USA) for 20 min at 4°C followed by extracellular staining with anti-mouse fluorochrome-conjugated antibodies for 30 min at 4°C in the dark. All antibodies were purchased from BD Biosciences or BioLegend (San Diego, CA, USA), as detailed in Supplementary Table 2. For the exclusion of dead cells, Live/Dead Fixable Aqua Stain was used according to the manufacturer’s instructions (Thermo Fisher Scientific). Samples were acquired with the LSR Fortessa flow cytometer (BD Biosciences) and FACSDiva Acquisition Software (BD Biosciences). Data analysis was performed using WinList 3D 9.0.1 (Verity Software House, Topsham, ME, USA).
Statistical analysis
Statistical analyses were performed using GraphPad Prism 10 (GraphPad Software Inc., San Diego, CA, USA) and R Software. Two-way ANOVA with Tukey’s multiple comparisons was used to determine significant differences in tumor growth between groups. The Wilcoxon rank sum test was used for testing differences between samples for mIF, 10x Genomics Visium, and single-cell RNA sequencing data. Fisher exact test was used for testing cell composition between samples. The Pearson correlation between activation/effector score and dysfunction score was tested using the stat cor method from the ggpubr package. Data are presented as mean ± S.D. For the box plots, the line inside the box shows the median, the lower and upper hinges correspond to the first and third quartiles (the 25th and 75th percentiles). The upper whisker extends from the hinge to the largest value no further than 1.5 * IQR from the hinge (where IQR is the inter-quartile range or distance between the first and third quartiles). The lower whisker extends from the hinge to the smallest value at most 1.5 * IQR of the hinge. Data beyond the end of the whiskers, "outlying" points, are plotted individually. The threshold for statistical significance was set to p < 0.05.