miRNA target prediction
Seven target prediction programs—including TargetScan (https://www.targetscan.org/vert_80), miRMap (http://mirmap.ezlab.org), RNA22 (https://cm.jefferson.edu/rna22), miRWalk (http://zmf.umm.uni-heidelberg.de), miRanda (www.microrna.org), microT-CDS (https://dianalab.e-ce.uth.gr/html/dianauniverse/index.php?r=microT_CDS), and miRDB (http://www.mirdb.org)—were applied to screen for miRNAs that potentially bind to the 3′-UTR of CD155 mRNA.
Cell Culture
The human lung cancer cell lines A549, H322, and H23 as well as the human embryonic kidney cell line HEK293T were obtained from American Type Culture Collection (Manassas, VA). The human lung cancer cell line EBC-1 was obtained from RIKEN BioResource Research Center (Ibaraki, Japan). Cells were cultured under 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium for A439 and HEK293T, RPMI 1640 medium for H322 and H23, or Eagle’s minimum essential medium for EBC-1 (Thermo Fisher Scientific), each supplemented with 10% FBS and 1% penicillin-streptomycin (Thermo Fisher Scientific).
Mirna Transfection
Cells were transiently transfected during the exponential growth phase with 50 nM miScript miR-346 mimic (ID:MSY0000773), miScript miR-330-5p mimic (ID:MSY0004693), miScript miR-326 mimic (ID:MSY0000756), miScript miR-423-5p mimic (ID:MSY0004748), miRCURY LNA miR-328-3p mimic (ID:YM00473147), miRCURY LNA miR-6884-5p mimic (ID:YM00472866), miRCURY LNA miR-485-5p mimic (ID:YM00473278), miRCURY LNA miR-1306-5p mimic (ID:YM00473249), miRCURY LNA miR-423-5p mimic (ID:MSY0004748), miRCURY LNA miR-324-5p mimic (ID:YM00473205), mirVana miR-3184-5p mimic (ID:PM18582), or AllStars negative control (ID: SI03650318), all obtained from Qiagen. Transfection was performed for 48 h with the use of the Lipofectamine RNAiMAX or Lipofectamine 3000 reagents (Thermo Fisher Scientific), and the cells were then subjected to experiments.
Construction Of Reporter Plasmids
Complementary DNA corresponding to the full-length 3′-UTR of CD155 mRNA was amplified by PCR from total cDNA of A549 cells with PrimeSTAR GXL DNA Polymerase (Takara) and the primers 5′-TAATTCTAGTTGTTTAAACTAGCGGCCGCCAGCGTCGGGACTGAG-3′ (forward) and 5′-GCATGCCTGCAGGTCGACTCTAGATTTTGCATTATTAAAAGAAGAGTCAAGG-3′ (reverse). Complementary 18- to 22-bp DNA oligonucleotides containing putative miR-346, miR-328-3p, miR-326, or miR-330-5p binding sites of the 3′-UTR of CD155 mRNA, or corresponding mutant sites, were synthesized. The sense and antisense strands were annealed by incubation of 2000 ng of each oligonucleotide in 46 µl of Oligo Annealing Buffer (Promega) first for 3 min at 90°C and then for 1 h at 37°C. The PCR amplicon for the full-length 3′-UTR of CD155 mRNA and the annealed oligonucleotides were separately cloned between the PmeI and XbaI sites of the pmirGLO Dual-Luciferase vector (Promega) with the use of an In-Fusion HD Cloning Kit (Takara). All plasmids used in this study were verified by Sanger sequencing.
Luciferase Reporter Assay
Each reporter plasmid (100 ng) was introduced together with miRNA mimics (50 nM) or a negative control miRNA into HEK293T cells in 96-well plates by transfection for 48 h with the use of Lipofectamine 3000 reagents (Thermo Fisher Scientific). Luciferase activity in cell lysates was then measured with the use of a Dual-Luciferase Assay System (Promega), and firefly luciferase activity was normalized by Renilla luciferase activity.
Rna Extraction And Rt-qpcr Analysis
Total RNA was isolated from cultured cells with the use of an RNeasy Mini Kit or an miRNeasy Mini Kit (Qiagen). Total RNA from tissue samples was extracted with the use of an AllPrep DNA/RNA FFPE Kit (Qiagen). For analysis of the abundance of CD155 mRNA, total RNA (400 ng) was subjected to reverse transcription (RT) with PrimeScript RT Master Mix (Takara) and the resulting cDNA was subjected to quantitative PCR (qPCR) analysis in triplicate with TB Green Premix Ex Taq II (Takara) in a Thermal Cycler Dice Real Time System (Takara). The qPCR primers (forward and reverse, respectively) were 5′-GGCAACTACACCTGCCTGTT-3′ and 5′-AATCACCTGGCACTCAGACC-3′ for CD155 mRNA and 5′-ACTCAACACGGGAAACCTCA-3′ and 5′-AACCAGACAAATCGCTCCAC-3′ for 18S rRNA (endogenous normalization control). For analysis of mature miRNAs, total RNA (10 ng) was subjected to RT with a miRCURY LNA RT Kit (Qiagen) and the resulting cDNA was subjected to qPCR analysis in triplicate with a miRCURY LNA SYBR Green PCR Kit (Qiagen) in a Thermal Cycler Dice Real Time System (Takara). The small nuclear RNAs U6 and SNORD38B were used as endogenous controls for lung cancer cell lines and tumor samples, respectively (Supplementary Table S1). Relative mRNA or miRNA abundance was determined with SDS software by the 2–ΔΔCt method.
Flow Cytometry
For analysis of CD155 expression at the cell surface, cultured cells were harvested, suspended in ice-cold PBS supplemented with 1% FBS, and incubated for 30 min on ice in the dark with phycoerythrin-conjugated mouse monoclonal antibodies to human CD155 (diluted 1:100; #337610, BioLegend) or an immunoglobulin G1 κ isotype control (diluted 1:100; #400114, BioLegend). The cells were then subjected to flow cytometric analysis with a FACSVerse instrument (BD Biosciences) and Flowjo software (Tree Star). The relative median fluorescence intensity (MFI) ratio was calculated as CD155 MFI divided by isotype-control MFI.
Immunoblot Analysis
Immunoblot analysis
Cultured cells were lysed in RIPA buffer (Thermo Fisher Scientific), the lysates were fractionated by SDS-PAGE, and the separated proteins were transferred to a polyvinylidene difluoride membrane. The membrane was incubated overnight at 4°C with antibodies to CD155 (diluted 1:1000; clone D8A5G, #81254, Cell Signaling Technology), and immune complexes were then detected with horseradish peroxidase–conjugated goat antibodies to rabbit immunoglobulin G (GE Healthcare UK), Pierce Western Blotting Substrate Plus (Thermo Fisher Scientific), and a ChemiDoc Touch MP system (Bio-Rad). β-actin was detected with corresponding primary antibodies (diluted 1:1000; clone 13E5, #4970, Cell Signaling Technology) and horseradish peroxidase–conjugated goat antibodies to rabbit immunoglobulin G (GE Healthcare UK) as a loading control.
Patients And Tissue Samples
Formalin-fixed, paraffin-embedded tissue samples were collected retrospectively from 57 individuals who had undergone surgical resection of lung adenocarcinoma at Kyushu University Hospital between February and December 2020. Diagnosis of the 57 patients was based on the WHO Classification of Lung Tumors. All 57 samples were subjected to immunohistochemistry and RT-qPCR analysis. The characteristics of the patients were obtained from their medical records. This aspect of the study was performed in accordance with the Declaration of Helsinki (as revised in 2013) and was approved by the Ethics Committee of Kyushu University and Kyushu University Hospital (ethics approval ID: 2021 − 289).
Immunohistochemistry
All tumor samples were subjected to immunohistochemical analysis with rabbit monoclonal antibodies to CD155 (clone D8A5G, #81254, Cell Signaling Technology) at a dilution of 1:200. Fixed sections were incubated with the primary antibodies overnight at 4°C, after which immune complexes were detected with the use of a Histofine Simple Stain Max-PO Kit (Nichirei Bioscience) and the peroxidase substrate 3,3′-diaminobenzidine. All staining was evaluated by two investigators including a pathologist, and the tumor proportion score (TPS) for CD155 expression in tumor cells was determined as the percentage of viable tumor cells showing staining at any intensity in a section containing at least 100 viable tumor cells.
Statistical analysis
Differences in miRNA abundance or luciferase reporter activity were assessed with the Student’s t test or Mann-Whitney U test, as appropriate. All statistical analysis was performed with GraphPad Prism 8 (GraphPad Software). A P value of < 0.05 was considered statistically significant.
Data Availability
The data that support the findings of this study are available from the corresponding author, YY, upon reasonable request.