Ubiquitin Carboxyl‐Terminal Esterase L1 (UCHL1) and its Associated Gene Network as Potential Regulators of the Glioma Cancer Stem Cell Niche

Abstract

IntroductionCancer cells with stem‐like properties (CSCs) have been identified in gliomas and have been proposed as the basis for the plasticity and survival of these malignant tumors. These CSCs are able to regenerate themselves, to differentiate into the cells forming the bulk of the tumor, and to communicate with their microenvironment to increase angiogenesis or to recruit inflammatory cells that sustain tumor growth and survival. Ubiquitin Carboxyl‐Terminal Esterase L1 (UCHL1) is a deubiquitinase highly expressed in the nervous system and in some cancers. Recent studies have demonstrated that UCHL1 can affect invasion, epithelial‐mesenchymal transition, chemosensitivity, and cell cycle among other functions. Previous work from our group suggested a potential role of UCHL1 in high‐grade pediatric glioma invasion and self‐renewal. To gain some insight in the UCHL1‐associated pathways, we conducted transcriptomic and bioinformatics analyses using a lentiviral knockdown (KD) system (Addgene) in human SJ‐GBM2 glioma cells obtained from the Children's Oncology Group.MethodsTwo different shRNA constructs targeting UCHL1 coding region were used. SJ‐GBM2 cells infected with shTurboGFP vector were used as control. RNAseq (Illumina), Gene Ontology (DAVID), and Ingenuity Pathway Analysis (Qiagen) were conducted to identify UCHL1‐associated gene networks.ResultsTranscriptome comparisons of UCHL1 knockdowns in SJ‐GBM2 glioma cells versus vector control identified 306 differentially expressed genes (at least 2‐fold change; p <0.05). Within the list of top differentially expressed genes, in the UCHL1 KDs we found downregulation of the Wnt targets POSTN, SP7, and DLL1, of the transporter ABCA4, of the homeobox gene DLX4, and of some genes recently linked to cancer progression ACTA2, AQ4, GRAP2, and ALK. Gene Ontology (GO) analysis of these 306 genes revealed significant enrichment in “signal peptides”, “extracellular matrix“, and “secreted proteins” GO Terms. “Angiogenesis and blood vessel development”, “neuron differentiation/development”, cell adhesion”, and “cell migration” also showed significant enrichment. Top canonical pathways identified by Ingenuity Pathway Analysis included “Clathrin‐mediated Endocytosis Signaling” (p = 5.14×10‐4), “Virus Entry via Endocytic Pathways” (p = 6.15×10‐4), and “High Mobility Group‐Box 1 (HMGB1) Signaling” (p = 6.15×10‐4). While FGF2, IL1B, TNF and PDGFB were predicted as top upstream regulators (p < 2×10–16) of the UCHL1 KD‐associated transcriptome.ConclusionsGiven the relevance of the cancer microenvironment in sustaining the CSC niche, studying UCHL1 as a potential mediator of the interactions between glioma cancer cells and the tissue microenvironment may lead to novel therapeutic targets for this childhood malignancy.Support or Funding InformationFunding for this work was provided in part by the Greehey Cancer Research Institute Permanent Health Fund Permanent Endowments – Higher Education (Children's Cancer Research) at the University of Texas Health Science Center at San Antonio, the Greehey Graduate Fellowship in Children's Health (Greehey Family), the Shelby Rae Tengg Foundation, and the University of the Incarnate Word Faculty Development Funds. TD was a student in the UIWRSO Summer Fellowship Training Program.