biostudies-arrayexpressYong ZhouMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15762This study aimed to elucidate the mechanism by which exosomes from bone-metastatic Lewis lung carcinoma (BM-LLC) cells promote osteolytic metastasis. We performed RNA-seq on mouse RAW264.7 macrophages (osteoclast precursors) treated with exosomes derived from either non-metastatic (NC-LLC) or bone-metastatic (BM-LLC) Lewis lung carcinoma cells. The goal was to identify differentially expressed genes and key regulatory pathways involved in exosome-induced osteoclast differentiation. Integrated analysis with small RNA sequencing data from the exosomes identified the miR-484-PECAM1 axis as a critical driver of this process. Our findings reveal that BM-LLC exosomes deliver miR-484 to recipient macrophages, repress PECAM1 expression, and subsequently upregulate osteoclastogenic markers (TRAP, CTSK, RANKL) and master transcription factors (NFATc1, c-Fos), thereby reprogramming osteoclastogenesis and driving bone destruction.biostudies-arrayexpressSample Treatment - RAW264.7 cells were treated with 10 μg/mL of exosomes (isolated from NC-LLC or BM-LLC cell culture supernatants) for 72 hours. The culture medium was refreshed every 48 hours.Sample Collection - Total RNA was extracted from RAW264.7 cells after 72 hours of exosome treatment using Trizol reagent (Invitrogen, #15596026).Library Construction - RNA libraries for sequencing were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). Briefly, mRNA was enriched, fragmented, and reverse-transcribed into cDNA. After end repair and adapter ligation, libraries were amplified by PCR. The final library quality was checked using an Agilent Bioanalyzer.Nucleic Acid Extraction - Total RNA was extracted from cells using Trizol reagent (Invitrogen, #15596026) according to the manufacturer's instructions. RNA quality and concentration were assessed using a NanoDrop spectrophotometer.Sequencing - The library was sequenced on an Illumina HiSeq 2500 using a 150 bp paired-end strategy.Growth Protocol - RAW264.7 murine macrophage cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. Cells were maintained at 37°C in a humidified incubator with 5% CO₂.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Raw sequencing reads (FASTQ files) were first assessed for quality using FastQC. Adapter sequences and low-quality bases were trimmed using Trimmomatic. The cleaned reads were then aligned to the mouse reference genome (GRCm38/GRCm39) and transcriptome using HISAT2 (or STAR). The resulting BAM files were used for subsequent quantification.Data Transformation - Raw sequencing reads were aligned to the mouse reference genome (GRCm38) using HISAT2. Gene-level counts were obtained using featureCounts. The raw count matrix was then normalized using the DESeq2 method to generate the normalized expression values provided in the processed data file.UnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 2500RNA-seq of coding RNAMus musculusExosomal miR-484 Drives Osteolytic Metastasis by Repressing PECAM1 to Reprogram OsteoclastogenesisZhongkai Tong1, Xiaoxiao Zhu1, Mengqing Hu2, Cenli Wang3, Xiaofei Liang3, Chunli Wu1,Zhenyan Li3, Lin He3, Jian Li3, Zhenyue Ye1, Zhaoxing Dong1#, Yong Zhou1#Yong ZhoufalseRNA-seq of mouse RAW264.7 macrophages treated with bone-metastatic lung cancer-derived exosomes to investigate osteoclast differentiationThis study aimed to elucidate the mechanism by which exosomes from bone-metastatic Lewis lung carcinoma (BM-LLC) cells promote osteolytic metastasis. We performed RNA-seq on mouse RAW264.7 macrophages (osteoclast precursors) treated with exosomes derived from either non-metastatic (NC-LLC) or bone-metastatic (BM-LLC) Lewis lung carcinoma cells. The goal was to identify differentially expressed genes and key regulatory pathways involved in exosome-induced osteoclast differentiation. Integrated analysis with small RNA sequencing data from the exosomes identified the miR-484-PECAM1 axis as a critical driver of this process. Our findings reveal that BM-LLC exosomes deliver miR-484 to recipient macrophages, repress PECAM1 expression, and subsequently upregulate osteoclastogenic markers (TRAP, CTSK, RANKL) and master transcription factors (NFATc1, c-Fos), thereby reprogramming osteoclastogenesis and driving bone destruction.2025-12-31T00:00:00Z2025-12-31T02:02:53.786Z2025-10-17T13:45:04.869ZE-MTAB-15762ERP182417EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969