Weighted gene co-expression network analysis reveals specific modules and hub genes related to neuropathic pain in dorsal root ganglions

Abstract

Neuropathic pain is a common, debilitating clinical issue. Here, the weighted gene co-expression network analysis (WGCNA) was used to identify the specific modules and hub genes that are related to neuropathic pain. The microarray dataset of a neuropathic rat model induced by tibial nerve transection (TNT), including dorsal root ganglion (DRG) tissues from TNT model (n=7) and sham (n=8) rats, was downloaded from the ArrayExpress database (E-MTAB-2260). The co-expression network modules were identified by the WGCNA package. The protein–protein interaction (PPI) network was constructed, and the node with highest level of connectivity in the network were identified as the hub gene. A total of 1739 genes and seven modules were identified. The most significant module was the brown module, which contained 215 genes that were primarily associated with the biological process (BP) of the defense response and molecular function of calcium ion binding. Furthermore, C–C motif chemokine ligand 2 (Ccl2), Fos and tissue inhibitor of metalloproteinase 1 (Timp1) which were identified as the hub genes in the PPI network and two subnetworks separately. The in vivo studies validated that mRNA and protein levels of Ccl2, Fos and Timp1 were up-regulated in DRG and spinal cord tissues after TNT. The present study offers novel insights into the molecular mechanisms of neuropathic pain in the context of peripheral nerve injury.

Analysis of Crucial Genes and Pathways Associated with Spared Nerve Injury-Induced Neuropathic Pain

“…Knight et al revealed that Timp1 played a crucial role in pathological pain states associated with inflammation [45]. Moreover, Timp1 is upregulated in DRG and spinal cord tissues after tibial nerve transection, and it may be related to neuropathic pain following peripheral nerve injury [46]. A recent microarray analysis also showed that hub genes like C3 and Timp1 are closely related to SNI-induced neuropathic pain development, providing the theoretical basis for treatment of this disease [14].…”

Inhibition of ferroptosis‐like cell death attenuates neuropathic pain reactions induced by peripheral nerve injury in rats

“…Western blotting was conducted according to previously reported protocols (Cheng et al., 2019), using the following antibodies: rabbit anti‐glutathione peroxidase 4 (GPX4, 1:2000, ab125066, Abcam); rabbit anti‐acyl‐CoA synthetase long‐chain family member 4 (ACSL4, 1:2000, ab155282, Abcam), rabbit anti‐transferrin receptor (TFR, 1:1,000, NB200‐585, Novus), rabbit anti‐ferroportin 1 (FPN1, 1:1,000, NBP1‐21502, Novus) and rabbit anti‐glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH, 1:5,000; YM3215, ImmunoWay Biotechnology). Images were acquired by a Tanon 5,500 imaging system (Tanon), and the optical density of the bands was scanned and quantitatively analysed by the ImagePro Plus 6.0 (National Institutes of Health).…”

Ferrostatin-1 Attenuates Mechanical Hypersensitivity in Rats with Streptozotocin-Induced Diabetes by Inhibiting Spinal Ferroptosis

“…We performed western blot analyses in line with previously reported protocols (Cheng et al, 2019) with the following primary rabbit antibodies against ACSL4 (1:2000, ab155282; Abcam, Cambridge, United Kingdom), GPX4 (1:2000, ab125066; Abcam), transferrin receptor (TFR; 1:1000, NB200-585; Novus, CA, USA), ferroportin 1 (FPN1; 1:1000, NBP1-21502; Novus), and β-actin (1:2000; 4970; Cell Signaling Technology, NY, USA). Images were obtained using the Tanon 5500 chemiluminescent imaging system (Tanon, Shanghai, China) and analyzed using Image J version 1.52 (National Institutes of Health, Bethesda, Maryland, USA).…”