Exploring LncRNAs’ Roles In Regulating The Pseudo-Synaptic Structure In Gliomas In Humans And Mice

Research purposes:Gliomas account for 32%of primary tumors in central nervous system,and 81%of malignant tumors in central nervous system are gliomas.The incidence of malignant glioma is about 5 to 8 cases per million people,although the incidence is not very high,gliomas are highly invasive.According to statistics,among all kinds of tumors,the 5-year mortality rate of gliomas is second only to pancreatic cancer and lung cancer,ranked the third.In 2019,three research groups published papers at the same time in the Nature journal,revealing that in human gliomas,tumor cells can imitate normal glial cells and neurons to form pseudo-synaptic structures,which is called neuron-glioma-synapse(NGS).They proposed that this synaptic structure is an important factor for the strong invasiveness of gliomas.Most neurons in human and mouse brain are orthologous(they are evolutionarily old),but many glial cells are not,they rose recently and have different origins.In particular,humans have more types and numbers of glial cells.Based on these,we speculate that neuronglioma-synapse may have species-specific differences.Given that long non-coding RNA(lncRNA)plays important roles in tumor development and metastasis,that a large number of long non-coding RNAs expressed in the human brain are primate-specific,and that mouse transplantation models of human gliomas are often difficult to grow(some gliomas are unique to humans),we speculate that long non-coding RNA and their species specificity may greatly influence gliomas in humans and mice,and specifically,the neuron-glioma-synapse.Based on these findings and analyses,in this study we wish to reveal whether this pseudo-synaptic structure would be common in human and mouse gliomas,and whether it is regulated by long non-coding RNA,especially those species-specific ones.Research method:Single-cell sequencing technologies have been widely used to capture the transcriptome in a large number of cells.These techniques have made it possible to analyze interactions between different cells.In this study,5 batches of human glioma single-cell RNA sequencing(scRNA-seq)data and 2 batches of mouse glioma scRNA-seq data were downloaded from the GEO website.To obtain malignant cells,first we filtered out T cells,macrophages,and oligodendrocytes based on characteristic gene expression in different cells.Because malignant cells have abnormal gene copy numbers,we then calculated the copy number variation of each cell and,by which,selected cells with copy number anomalies.Finally,we clustered all remaining cells;as malignant cells would gather together,we filtered out small clusters with unclear cell types.After collecting malignant cells,cells with pseudo-synaptic signals were identified according to the pseudo-synaptic specific gene set.Genes with differential expression in the cell population with pseudo-synaptic signals and in the cell population without pseudo-synaptic signals were analyzed.From differentially expressed genes long non-coding RNA were identified.Using LongTarget,a software package for predicting the targets of long non-coding RNAs,potential epigenetic(dys)regulation between long non-coding RNAs and protein-coding genes was analyzed,and using SCENIC,a software package for analyzing transcription factors,potential transcriptional regulators of pseudo-synaptic specific genes were analyzed.Research results:This study generates the following findings.(a)Genes relating to the pseudo-synapse structure are expressed almost only in malignant cells,and different pseudo-synapse-related genes show distinct expression features.Some genes are expressed widely in malignant cells in all types of gliomas,some genes are barely expressed in gliomas,and the expression of some genes is tumor-specific.(b)Long non-coding RNAs are involved in the formation of pseudo-synapses.Some long noncoding RNAs may regulate the growth of pseudo-synapses in all types of gliomas,and some long non-coding RNAs may only regulate pseudo-synapses in specific types of gliomas.(c)The regulation of pseudo-synapse-related genes by long non-coding RNAs shows differences between tumors.A long non-coding RNA may regulate the same or different pseudo-synapse-related genes in different gliomas.(d)Different long noncoding RNAs are involved in the regulation of gliomas in humans and in mice.Most pseudo-synaptic-related genes in humans are not expressed in mice.