A. K. Coley1, M. J. Raabe2, C. Lu2, A. Pankaj2, B. Patel2, I. Bhan3, C. R. Ferrone1, M. Aryee4, D. T. Ting2, J. W. Franses2 1Massachusetts General Hospital, Department Of Surgery, Boston, MA, USA 2Massachusetts General Hospital, Cancer Center, Boston, MA, USA 3Massachusetts General Hospital, Division Of Gastroenterology, Boston, MA, USA 4Dana Farber Cancer Insititute, Department Of Data Science, Boston, MA, USA
Introduction:
Hepatocellular carcinoma (HCC) tumorigenesis, progression, and recurrence is influenced by complex interactions between cancer cells, immune cells, and endothelial cells in the tumor microenvironment. Spatial transcriptomic techniques allow for in situ analysis of the complex cell-cell interactions in tumors within their usual spatial context. LIN28B is an RNA binding protein that plays critical roles in embryogenesis and oncogenesis via binding of the let-7 family of tumor suppressor microRNAs and other mRNA targets. LIN28B overexpression has been implicated in several cancer types as a driver of tumor development and metastasis. In HCC, high LIN28B expression is associated with the formation of poorly-differentiated tumors and worse overall clinical prognosis. In this study, we aimed to evaluate the impact of LIN28B expression on tumor-vessel interactions in HCC.
Methods:
We utilized the NanoString GeoMX Digital Spatial Profiler to profile the expression of ~1800 genes in formalin-fixed, paraffin embedded histological sections from 41 patients with HCC who underwent definitive treatment with surgical resection or liver transplantation. A total of 203 paired microscopic tumor (arginase positive) and vessel (CD31 positive) areas of interest (AOIs) were generated. Gene-specific oligonucleotide tags from each AOI were captured, sequenced on the Illumina NextSeq 500, and expression profiles were analyzed using custom computational pipelines. On sequential FFPE sections from the same patients, LIN28B IHC was performed and its expression was quantified using Halo digital image analysis software. Tumor AOIs and vessel AOIs derived from patients with high versus low LIN28B IHC expression were compared using differential expression analysis.
Results:
Differential expression analysis of tumor AOI and vessel AOI genes from LIN28B-high samples versus LIN28B-low samples led to the identification of multiple genes and pathways in both tissue compartments correlating with LIN28B cancer cell expression. Gene set enrichment analysis (GSEA) identified multiple enriched pathways.
Conclusion:
Spatial transcriptomic profiling enabled precise separation of linked, microscopic tumor and vessel subregions in LIN28B-high and LIN28B-low tumors that were defined by distinct gene sets. By preserving spatial relationships, spatial transcriptomic profiling can provide a rich understanding of cell-cell interactions in the tumor microenvironment that can generate novel, testable hypotheses for novel therapeutic targets and biomarkers in the HCC tumor microenvironment.