{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Tomohiko Ikehara"],"organism":["Homo sapiens"],"software":["bcl2fastq v2.20","10x Space Ranger 2.1.1"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15756"],"description":["Post-transplant hepatocellular carcinoma (HCC) recurrence is a devastating disease with an abysmal prognosis and no established treatment or prevention options. We performed spatial analysis to profile the tumor immune microenvironment in primary HCC at liver transplantation and in recurrent HCC at re-hepatectomy and elucidate the molecular mechanisms that drive recurrence under immunosuppression. This analysis offers potential for developing new therapeutic strategies against post-transplant HCC recurrence. Paired FFPE samples from primary and recurrent sites were collected from patients who underwent re-hepatectomy for HCC recurrence after liver transplantation due to HCC. The Visium CytAssist Spatial Gene and Protein Expression for FFPE, 11 mm (10x Genomics) was utilized to perform Visium experiments on FFPE tissue from the primary tumor and the recurrent tumor (comprising tumor and non-tumor regions)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Human liver tumor samples were collected during surgical resection (primary and recurrent lesions). Sections (5 µm) were mounted onto 10x Genomics Visium slides (11 mm) using CytAssist, H&E stained, imaged, and stored at −80 °C. De-identified metadata (age, sex) were retained.","Library Construction - Visium gene expression (GEX) libraries and Feature Barcode antibody-derived tag (ADT) libraries were prepared with 10x Genomics kits following the manufacturer’s protocols. Libraries were quantified (Qubit) and quality-checked (Bioanalyzer/Tapestation) before pooling.","Sequencing - Pooled libraries were sequenced on an Illumina NovaSeq 6000 with paired-end reads using standard Visium run parameters for GEX and ADT. Base calls were converted to FASTQ with bcl2fastq/DRAGEN, and per-lane sample demultiplexing was performed.","Nucleic Acid Extraction - No bulk extraction was performed. Poly-A RNA was captured in situ according to the 10x Genomics Visium manufacturer’s instructions. For protein, oligo-conjugated antibodies were applied following the CytAssist Spatial Protein procedure, and excess reagents were removed by the recommended washes."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw FASTQ were processed with Space Ranger v2.x (10x Genomics, GRCh38 reference). Alignment and counting per spot were performed with default Visium pipeline. GEX: UMI counts were generated; low-quality spots and genes were filtered. ADT: Feature Barcode counts were generated; background correction and CLR/log-normalization applied. Processed matrices (.tsv/.mtx) were exported; downstream QC/integration in R/Seurat v5.","Sequence Alignment - FASTQ files were processed with 10x Genomics Space Ranger using a GRCh38 reference; spots were registered to tissue images and count matrices were generated. Downstream analyses were performed in R (Seurat), with batch correction by Harmony when applicable."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["spatial transcriptomics by high-throughput sequencing"],"species":["Homo sapiens"],"pubmed_title":["Mechanisms of Post-Transplant Hepatocellular Carcinoma Recurrence Under Tacrolimus-Induced Immunosuppression"],"pubmed_authors":["Tomohiko Ikehara"],"additional_accession":[]},"is_claimable":false,"name":"Spatial transcriptomics and proteomics of post-transplant HCC recurrence using 10x Visium CytAssist","description":"Post-transplant hepatocellular carcinoma (HCC) recurrence is a devastating disease with an abysmal prognosis and no established treatment or prevention options. We performed spatial analysis to profile the tumor immune microenvironment in primary HCC at liver transplantation and in recurrent HCC at re-hepatectomy and elucidate the molecular mechanisms that drive recurrence under immunosuppression. This analysis offers potential for developing new therapeutic strategies against post-transplant HCC recurrence. Paired FFPE samples from primary and recurrent sites were collected from patients who underwent re-hepatectomy for HCC recurrence after liver transplantation due to HCC. The Visium CytAssist Spatial Gene and Protein Expression for FFPE, 11 mm (10x Genomics) was utilized to perform Visium experiments on FFPE tissue from the primary tumor and the recurrent tumor (comprising tumor and non-tumor regions).","dates":{"release":"2026-04-01T00:00:00Z","modification":"2026-04-02T01:05:02.765Z","creation":"2025-10-16T12:01:10.927Z"},"accession":"E-MTAB-15756","cross_references":{"ENA":["ERP182302"],"EFO":["EFO_0002944","EFO_0004170","EFO_0030005","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}