Transcriptomics reveals the effects of NTRK1 on endoplasmic reticulum stress response-associated genes in human neuronal cell lines

Background: NTRK1 gene, encoding TrkA, is essential for the nervous system and drives a variety of biological processes, including pain. Given the unsatisfied analgesic effects of some new drugs targeting NTRK1 in clinic, a deeper understanding for the mechanism of NTRK1 in neurons is crucial.

Methods: We assessed the transcriptional responses in SH-SY5Y cells with NTRK1 overexpression using bioinformatics analysis. GO and KEGG analyses were performed, PPI networks were constructed, and the functional modules and top 10 genes were screened. Subsequently, hub genes were validated using RT-qPCR.

Results: A total of 419 DEGs were identified, including 193 upregulated and 226 downregulated genes. GO showed that upregulated genes were mainly enriched in response to endoplasmic reticulum (ER) stress, protein folding in ER, etc., and downregulated genes were highly enriched in a series of cellular parts and cellular processes. KEGG showed DEGs were enriched in protein processing in ER and pathways associated with cell proliferation and migration. The finest module was dramatically enriched in the ER stress response-related biological process. The verified seven hub genes consisted of five upregulated genes (COL1A1, P4HB, HSPA5, THBS1, and XBP1) and two downregulated genes (CCND1 and COL3A1), and almost all were correlated with response to ER stress.

Conclusion: Our data demonstrated that NTRK1 significantly influenced the gene transcription of ER stress response in SH-SY5Y cells. It indicated that ER stress response could contribute to various functions of NTRK1-dependent neurons, and therefore, ER stress response-associated genes need further study for neurological dysfunction implicated in NTRK1.

Endoplasmic reticulum stress; NTRK1; Neurons; RNA sequencing; SH-SY5Y cells; Unfolded protein response.