Data for: Preliminary study based on methylation and transcriptome gene sequencing of lncRNAs and immune infiltration in hypopharyngeal carcinoma

Background: Hypopharyngeal squamous cell cancer (HSCC) is one of the most
malignant tumors of the head and neck. It is not easy to detect in the
early stage due to its hidden location; thus, lymph node metastasis is
highly likely at diagnosis, leading to a poor prognosis. It is believed
that epigenetic modification is related to cancer invasion and metastasis.
However, the role of m6A-related lncRNA in the tumor microenvironment
(TME) of HSCC remains unclear. Methods: The whole transcriptome and
methylation sequencing of 5 pairs of HSCC tissues and adjacent tissues
were performed to identify the methylation and transcriptome profiles of
lncRNAs. The biological significance of lncRNAs differentially expressing
the m6A peak was analyzed by Gene Ontology and Kyoto Encyclopedia of Genes
and Genomes. By constructing an m6A lncRNA-microRNA network, the mechanism
of m6A lncRNAs in HSCC was analyzed. The relative expression levels of
selected lncRNAs were examined by quantitative polymerase chain reaction.
The CIBERSORT algorithm was used to evaluate the relative proportion of
immune cell infiltration in HSCC and paracancerous tissues. Results: Based
on an in-depth analysis of the sequencing results, 14413 differentially
expressed lncRNAs were revealed, including 7329 up-regulated and 7084
down-regulated lncRNAs. Additionally, 4542 up-methylated and 2253
down-methylated lncRNAs were detected. We demonstrated methylation
patterns and gene expression profiles of lncRNAs of HSCC transcriptome. In
the intersection analysis of lncRNAs and methylated lncRNAs, 51 lncRNAs
with up-regulated transcriptome and methylation and 40 lncRNAs with
down-regulated transcriptome and methylation were screened, and
significantly differentiated lncRNAs were further studied. In the immune
cell infiltration analysis, B cell memory was significantly elevated in
cancer tissue, while γδT cell amount was significantly decreased.
Conclusion: m6A modification of lncRNAs might be involved in HSCC
pathogenesis. Infiltration of immune cells in HSCC might provide a new
direction for its treatment. This study provides new insights for
exploring the possible HSCC pathogenesis and searching for new potential
therapeutic targets.