Identification of hub genes significantly linked to temporal lobe epilepsy and apoptosis via bioinformatics analysis.

Background: Epilepsy stands as an intricate disorder of the central nervous system, subject to the influence of diverse risk factors and a significant genetic predisposition. Within the pathogenesis of temporal lobe epilepsy (TLE), the apoptosis of neurons and glial cells in the brain assumes pivotal importance. The identification of differentially expressed apoptosis-related genes (DEARGs) emerges as a critical imperative, providing essential guidance for informed treatment decisions. Methods: We obtained datasets related to epilepsy, specifically GSE168375 and GSE186334. Utilizing differential expression analysis, we identified a set of 249 genes exhibiting significant variations. Subsequently, through an intersection with apoptosis-related genes, we pinpointed 16 genes designated as differentially expressed apoptosis-related genes (DEARGs). These DEARGs underwent a comprehensive array of analyses, including enrichment analyses, biomarker selection, disease classification modeling, immune infiltration analysis, prediction of miRNA and transcription factors, and molecular docking analysis. Results: In the epilepsy datasets examined, we successfully identified 16 differentially expressed apoptosis-related genes (DEARGs). Subsequent validation in the external dataset GSE140393 revealed the diagnostic potential of five biomarkers (CD38, FAIM2, IL1B, PAWR, S100A8) with remarkable accuracy, exhibiting an impressive area under curve (AUC) (The overall AUC of the model constructed by the five key genes was 0.916, and the validation set was 0.722). Furthermore, a statistically significant variance (p < 0.05) was observed in T cell CD4 naive and eosinophil cells across different diagnostic groups. Exploring interaction networks uncovered intricate connections, including gene-miRNA interactions (164 interactions involving 148 miRNAs), gene-transcription factor (TF) interactions (22 interactions with 20 TFs), and gene-drug small molecule interactions (15 interactions involving 15 drugs). Notably, IL1B and S100A8 demonstrated interactions with specific drugs. Conclusion: In the realm of TLE, we have successfully pinpointed noteworthy differentially expressed apoptosis-related genes (DEARGs), including CD38, FAIM2, IL1B, PAWR, and S100A8. A comprehensive understanding of the implications associated with these identified genes not only opens avenues for advancing our comprehension of the underlying pathophysiology but also bears considerable potential in guiding the development of innovative diagnostic methodologies and therapeutic interventions for the effective management of epilepsy in the future.

Nemo-like kinase (NLK) gene regulates apoptosis via the p53 signaling pathway in Litopenaeus vannamei under low-temperature stress.

The Nemo-like kinase (NLK) is an important serine/threonine-protein kinase in many signaling pathways. However, its function in crustaceans, such as shrimps, is still poorly understood and needs to be further explored. In the present study, the full-length cDNA of NLK from Litopenaeus vannamei (LvNLK) was cloned. The full-length LvNLK cDNA has 2497 bp, including an open reading frame (ORF) of 1524 bp encoding a protein with 507 amino acids and a predicted molecular mass of 56.1 kDa. Phylogenetic analysis revealed that LvNLK shared high similarities with NLK from other known species. Low-temperature stress markedly upregulated the expression of LvNLK. Its overexpression in hemocytes suppressed the expression of BCL2-associated X (Bax) and tumor protein P53 (p53) in vitro. Meanwhile, the BCL2 apoptosis regulator (Bcl-2), MDM2 proto-oncogene (MDM2), and Yin Yang 1 (YY1) were upregulated. Moreover, LvNLK silencing in vivo increased the susceptibility of shrimps to low-temperature stress. The generation of ROS and the rate of hemocyte apoptosis also increased when LvNLK was silenced. Additionally, qPCR results indicated that LvNLK might participate in apoptosis via the p53 signaling pathway in vitro and in vivo. These results suggested that LvNLK is indispensable for the environmental adaptation of L. vannamei. Our current findings also demonstrated that NLK is evolutionarily conserved in crustaceans and provided insights into the environmental adaptation of invertebrates.

FABP regulates fatty acid metabolism and oxidative response via PPARα/RXR signaling in Litopenaeus vannamei following environmental exposure of clofibric acid.

Clofibric acid (CFA), a drug and personal care product, has been identified as ubiquitous in the aquatic system and surface water, causing pollution to the environment. In this study, after environmental (4 µg/L) levels of CFA challenge, the LvFABP, LvACS gene expressions, total haemocyte count (THC), relative enzymes (SOD1 and GST) activities in Litopenaeus vannamei were observed to decrease. In the meantime LvFATP, LvRXR expression and the level of NEFA were upregulated in L. vannamei body. LvFABP expression in vivo was knocked down by dsRNA-mediated RNA interference (RNAi), which led to significantly decreased levels of PPARα (including LvFATP, LvRXR and LvACS). When exposed to environmental CFA after 4 days, LvFABP knocked down group had a sharp upregulation of LvFATP, LvRXR, LvACS expression, GST activity and NEFA amount, following decreased THC and SOD1 activity. These results suggested that environmental concentration CFA may have some toxicological effect on L. vannamei, following fatty acids metabolism and oxidative stress responses by LvFABP via the PPARα/RXR signaling pathway, including LvFATP, LvRXR and LvACS.

A Litopenaeus vannamei p70S6K gene is involved in the antioxidative and apoptosis under low temperature.

p70S6K is involved in cellular response, such as tumor metastases, the immune response and tissue repair in vertebrates. The role of p70S6K in these physiological processes in crustaceans remains, however, unknown. In this study, the Lvp70S6K was identified, containing a 5' UTR of 294 bp, an ORF of 1494 bp ad a 3' UTR of 211 bp, encoding 497 amino acids with a theoretical molecular weight of 70 kDa and an estimated isoelectric point of (pI) of 5.16. The multiple alignment found that Lvp70S6K was highly homologous with other invertebrates. Lvp70S6K mRNA was detected in all the tested tissues and the Lvp70S6K expression levels was significantly down-regulated and reached the lowest level (0.44-fold, p < 0.01) at 1.5 h after low temperature stress. The subcellular localization of Lvp70S6K could be detected in cytoplasm. ROS production was significantly up-regulation (1.19-fold, p < 0.01), total hemocyte count (THC) was significantly down-regulation (0.22-fold, p < 0.01), apoptosis rate was markedly increased (1.09-fold, p < 0.01), apoptosis-related genes of LvPDCD4 (1.61-fold, p < 0.01) and LvCyt.C (1.23-fold, p < 0.01) were up-regulated, and anti-apoptotic gene of LvBcl-2 (0.69-fold, p < 0.01), LvIAP1 (0.68-fold, p < 0.01) and LvIAP2 (0.45-fold, p < 0.01) were decreased after low temperature stress in hemolymph of Lvp70S6K-silenced shrimp at 1.5 h. Silencing of LvPTEN significantly increased Lvp70S6K, LvPI3K, LvAKT and LvmTOR expression. In summary, these results indicated that Lvp70S6K play a crucial role in oxidative and apoptosis, which was able to negatively regulate by PTEN.

Functional analysis target of rapamycin (TOR) on the Penaeus vannamei in response to acute low temperature stress.

Target of rapamycin (TOR) is an atypical of Ser/Thr protein kinase that plays an important role in many aspects such as cell growth, reproduction, differentiation, cell cycle regulation, autophagy and apoptosis. However, little information is known about the enzyme in crustaceans. Here, a novel TOR was identified from shrimp Penaeus vannamei (PvTOR) and its biological functions were investigated in response low temperature stress. The PvTOR gene encoded a polypeptide of 2464 amino acids with an estimated molecular mass of 279.4 kD and a predicted isoelectronic point (pI) of 7.30. Phylogenetic analysis revealed that PvTOR shared high similarity with other known species. PvTOR mRNA was detected in all the tested tissues and highest transcription in muscle and hepatopancreas. PvTOR transcriptional level was up-regulated significantly at 1.5 h and 3 h, and down-regulated at 12 h and 24 h after low temperature stress. TEM and autophagy indicator system GFP-PvLC3 suggested that low temperature induced autophagy generation. ROS, Ca2+ concentration and apoptosis rate were increased significantly in TOR-knockdown shrimp after low temperature stress. The autophagy associated gene ATG8II/I, PvBeclin-1, PvATG14, apoptosis gene PvPARP, Pvcasp-3, PvBAX and Pvp53 transcripts, and casp-3/8 activity in hemocyte were increased significantly in TOR-knockdown group shrimp at 3 h after low temperature stress. Additionally, THC counts of TOR-knockdown group were significantly higher than the dsGFP group. In summary, these results suggested that PvTOR plays an important role in the adaptation mechanisms of shrimp at low temperature by regulating autophagy and apoptosis.

Molecular cloning, characterization and expression analysis of S- adenosyl- L-homocysteine hydrolase (SAHH) during the pathogenic infection of Litopenaeus vannamei by Vibrio alginolyticus.

SAHH is an enzyme, playing a significant role in the catalyzation of the S-adenosyl homocysteine (SAH) into homocysteine (Hcy) and adenosine (Ado). However, little is known information of the enzyme in crustaceans. In the present study, SAHH cDNA was cloned from Litopenaeus vannamei (LvSAHH). The full length of the LvSAHH was found, containing a 5' UTR of 119 bp, an ORF of 1236 bp and a 3' UTR of 549 bp. The LvSAHH gene encoded a polypeptide of 411 amino acids with an estimated molecular mass of 45.55 kD and a predicted isoelectronic point (pI) of 5.63. Comparison of the deduced amino acid sequence showed that LvSAHH has high identity (70 %-82%) with other known species. qRT-PCR analysis revealed that LvSAHH mRNA was broadly expressed in all of the examined tissues, while the highest expression level was observed in muscle, followed by the expression in stomach, gill, pleopod, hepatopancreas, heart, eye and intestine. Subcellular localization analysis revealed that LvSAHH was predominantly localized in the cytoplasm and nucleus. LvSAHH mRNA expression levels in hepatopancreas and gill were significantly up-regulated from 6 to 48 h after V. alginolyticus injection and reached the highest level (15-fold and 8-fold, p < 0.01) at 24 h, respectively. Additionally, the Toll-like receptors (TLR) and interleukins-16 (IL-16) were detected in hepatopancreas and gill of LvSAHH-knockdown SAHH. LvRack1, LvToll1, LvToll2, LvToll3 and LvIL-16 transcripts were decreased significantly in LvSAHH-knockdown shrimp at 24 h post V. alginolyticus stimulation in hepatopancreas and gill. But LvToll3 was no significant difference in gill. In summary, these results indicated that LvSAHH may play a regulatory role in the invertebrate innate immune defense by regulating TLR and IL-16 expression.