Axon Guidance Signaling Pathway Research Articles

Comprehensive bioinformatics analysis of lncRNA regulation and screening for pathogenic genes in NF2-related schwannomatosis

Abstract Objectives NF2-related Schwannomatosis (NF2-SWN) is an autosomal dominant disease with full penetrance. Increasing data shows that long non-coding RNAs (lncRNA) can act as competitive endogenous RNAs (ceRNA), regulating target gene expression. This study aims to investigate lncRNAs in NF2-SWN that may be involved in regulating NF2 pathogenic genes. Methods Data were collected from three patients with NF2-SWN, including medical records, physical examination, imaging, pathology, and RNA from the tumor and adjacent tissues. differentially expressed genes (DEGs) between the two groups were screened by conducting gene differential analysis on the sequenced data. Next, GO & KEGG enrichment analysis was performed on DEGs, and an association network between lncRNA and NF2 was established to identify regulatory lncRNA. Finally, qRT-PCR was used to substantiate the expression patterns of critical lncRNAs and NF2 in NF2-SWN. Results Sequencing revealed 6433 DEGs involved in key biological processes and pathways, such as axon guidance, intracellular signal transduction, cell migration, phosphorylation, cell adhesion molecules, taste transduction, axon guidance, and ErbB signaling pathways, etc. The ceRNA correlation network identified four lncRNAs (CADM3-AS1, MTMR9LP, LOC101929536, PRDM16-DT) that may regulate the NF2 gene. As expected, qRT-PCR results revealed that compared with the control group, the expression levels of L0C10929536 and PRDM16-DT in the tumor group were significantly increased. In contrast, the expression levels of MTMR9LP and CADM3-AS1 genes were decreased. Conclusions Four identified lncRNAs could be crucial for NF2-SWN development, potentially serving as diagnosis biomarkers or therapeutic targets. This study contributes to the understanding of NF2-SWN’s molecular mechanism.

Linking gut microbiota dysbiosis to molecular pathways in Alzheimer’s disease

BackgroundAlzheimer’s disease (AD) is a progressive neurodegenerative disorder marked by cognitive decline and synaptic dysfunction. Emerging evidence suggests a significant relationship between gut microbiota and brain health, mediated through the gut-brain axis. Alterations in gut microbiota composition may influence AD progression by affecting molecular pathways and miRNA interactions. MethodsWe retrieved and analyzed microarray data from 34 tissue samples of AD patients and controls (GEO accession number GSE110298). Differentially expressed genes (DEGs) with the GCS score package in R, considering a p-value < 0.05 and logFC<-1 and logFC>1 to isolate significant gene clusters. Enrichment analysis of signaling pathways and gene ontology was conducted using Enrichr, KEGG, Panther, DAVID, and shiny GO databases. Protein-protein interactions were visualized with Networkanalyst and CytoScape. Gut microbiota in 200 CE patients was analyzed using next-generation sequencing (NGS) data from gutMDisorder and GMrepo databases. miRNA interactions were evaluated using miEAA, Targetscan, MienTurnet, and miRnet databases. ResultsSignificant reductions in microbial taxa, including Clostridia (LDA score −4.878208), Firmicutes (LDA score −4.817032), and Faecalibacterium (LDA score −4.40714), were observed in AD patients. Pathway analysis highlighted the involvement of Axon guidance, ErbB, and MAPK signaling pathways in AD. Venn diagram analysis identified 619 intersecting genes in brain and gut tissues, emphasizing pathways such as Axon Guidance and Cell Cycle. miRNA analysis revealed important regulatory miRNAs, including hsa-let-7c, hsa-mir-125b-2, and hsa-mir-145, which target key transcription factors involved in AD pathology. ConclusionThe study demonstrates significant dysbiosis in the gut microbiota of AD patients and underscores the potential role of gut microbiota in AD progression through altered signaling pathways and miRNA interactions. These findings highlight the need for further research into microbiota-based interventions as potential therapeutic strategies for AD.

Single-nuclei sequencing of uterine serous carcinoma reveals racial differences in immune signaling

Significant racial disparities exist between Black and White patients with uterine serous carcinoma (USC). While the reasons for these disparities are unclear, several studies have demonstrated significantly different rates of driver mutations between racial groups, including TP53. However, limited research has investigated the transcriptional differences of tumors or the composition of the tumor microenvironment (TME) between these groups. Here, we report the single-nuclei RNA-sequencing profiles of primary USC tumors from diverse racial backgrounds. We find that there are significant differences between the tumors of Black and White patients. Tumors from Black patients exhibited higher expression of specific genes associated with aggressiveness, such as PAX8, and axon guidance and synaptic signaling pathways. We also demonstrated that T cell populations are reduced in the tumor tissue compared to matched benign, while anti-inflammatory macrophage populations are retained within the TME. Furthermore, we investigated the connection between PAX8 overexpression and immunosuppression in USC through regulation of several cytokines and chemokines. Notably, we show that PAX8 activity can influence macrophage gene expression and protein secretion. These studies provide a detailed understanding of the USC transcriptome and TME, and identify differences in tumor biology from patients of different racial backgrounds.

Identifying candidate genes associated with hippocampal dysfunction in a hemiparkinsonian rat model by transcriptomic profiling

ABSTRACT Parkinson’s disease (PD) often results in hippocampal dysfunction, which leads to cognitive and emotional challenges and synaptic irregularities. This study attempted to assess behavioral anomalies and identify differentially expressed genes (DEGs) within the hippocampus of a hemiparkinsonian rat model to potentially uncover novel genetic candidates linked to hippocampal dysfunction. Striatal 6-hydroxydopamine (6-OHDA) infusions were performed unilaterally in the brains of adult SD rats, while dopaminergic impairments were verified in rats with 6-OHDA-lesioned striata. RNA sequencing and gene expression analysis unveiled 1018 DEGs in the ipsilateral rat hippocampus following 6-OHDA infusion: 631 genes exhibited upregulation, while 387 genes were downregulated (with FDR-adjusted p-value < 0.05 and absolute fold-change > 1.5). Gene ontology analysis of DEGs indicated that alterations in the hippocampi of 6-OHDA-lesioned rats were primarily associated with synaptic signaling, axon development, behavior, postsynaptic membrane, synaptic membrane, neurotransmitter receptor activity, and peptide receptor activity. The Kyoto Encyclopedia of Genes and Genomes analysis of DEGs demonstrated significant enrichment of the neuroactive ligand–receptor interaction, calcium signaling pathway, cAMP signaling pathway, axon guidance, and notch signaling pathway in rat hippocampi that had been subjected to striatal 6-OHDA infusion. STRING analysis confirmed a notable upregulation of eight hub genes (Notch3, Gng4, Itga3, Grin2d, Hgf, Fgf11, Htr3a, and Col6a2), along with a significant downregulation of two hub genes (Itga11 and Plp1), as validated by reverse transcription-quantitative polymerase chain reaction. This study provides a comprehensive transcriptomic profile of the hippocampi in a hemiparkinsonian rat model, thereby offering insights into the signaling pathways underlying hippocampal dysfunction.

Discovery of long non-coding RNAs in naïve CD4+ T cells in response to initiating antiretroviral therapy at acute or chronic phase of HIV-1 infection

Long non-coding RNAs (lncRNAs) have gained prominence due to their involvement in various cellular processes, but their specific roles remain elusive. Dysregulation of lncRNAs has been implicated in the pathogenesis of several diseases. In this study, we aimed to shed light on the role of lncRNAs in individuals infected with human immunodeficiency virus type 1 (HIV-1) by examining their changes in the expression patterns related to the initiation of antiretroviral therapy (ART) during acute or chronic phases of infection, compared to healthy controls. We found 316 differentially expressed (DE) lncRNAs in patients receiving long-term ART, shedding light on their potential roles. We also observed interactions between these DE lncRNAs and specific microRNAs (miRNAs). Some of these miRNAs, such as hsa-miR-574-5p, hsa-miR-765, hsa-miR-6165, hsa-miR-1207-5p, and hsa-miR-378i, are associated with cancer progression or suppression, while others, including hsa-miR-328-5p, hsa-miR-4753-3p, and MiR-664, play roles in immune system regulation. Furthermore, our study revealed substantial enrichment in distinct Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as axon guidance, PI3K-Akt signaling, and MAPK signaling pathways. Although our results indicate possible molecular processes impacted by the discovered lncRNAs, we cannot explicitly establish causality or specific connections between lncRNAs and genes in these pathways, fostering more specific studies. Furthermore, Gene Ontology (GO) analysis highlighted terms such as cytoskeletal protein binding, ion channel function, synaptic processes, neuron projection, and the somatodendritic compartment, underscoring the relevance of lncRNAs in these cellular components within the context of HIV-1 infection and ART treatment. In conclusion, our study emphasizes the need for further exploration of lncRNAs as potential biomarkers and therapeutic targets in HIV-1-infected patients, with a particular focus on CD4+ T cells. Understanding the functions of lncRNAs in these contexts may pave the way for novel treatment strategies and improved patient outcomes, aligning with the broader goals of our research.

Abstract 5876: ALDH3A1 as a predictive marker for gemcitabine treatment in pancreatic cancer

Abstract Background: Pancreatic cancer is one of the incurable cancer. The currently preferred chemotherapy regimens, including gemcitabine, do not extend patient survival by more than a year, and studies on drug resistance mechanisms or biomarkers for the drug sensitivity are very limited. Aldehyde dehydrogenase (ALDH) is a family of enzymes that play an essential role in cell survival and protection. In cancer cells, it is thought that overexpression of the ALDHs confers a survival advantage to the cells, which is associated with a poor prognosis. In this study, we analyzed the drug sensitivity between ALDH3A1 expression and gemcitabine in PDAC cells. Method: In this study, we investigated the relationship between ALDH3A1 expression and gemcitabine sensitivity using 8 pancreatic cancer cell line. We observed changes in the pattern of ALDH3A1 expression in established gemcitabine resistance pancreatic cancer cell line. Following this, we functionally inhibited ALDH3A1 to determine its impact on gemcitabine sensitivity using shRNA method. To elucidate the molecular mechanisms related with ALDH3A1, we performed multi-omics analysis such as transcriptomics and proteomics. Results: As a results, there was a negative correlation between ALDH3A1 expression (Protein &amp; mRNA) and gemcitabine resistance 8 pancreatic cancer cell lines. However, in established gemcitabine resistance BxPC3 cells compared to control cells, gemcitabine resistance increased more than 1000 fold while the protein expression was decreased. In these results correlated with inhibition of ALDH3A1 expression using shALDH3A1 experiments both change ALDH3A1 expression and gemcitabine resistance. In biological phenotype experiments, cell proliferation and migration increased in the ALDH3A1 inhibition groups. When using combination treatment of gemcitabine and CB29, a known ALDH3A1 inhibitor, drug resistance increased by more than 2,000 fold in the combination treatment groups. In RNAseq analysis, Adherens junction, Ras signaling, Axon guidance, and JAK-STAT signaling pathway related genes were up regulated in shALDH3A1 treatment group compared control. Conclusion: In this study, we demonstrated the negative correlation between ALDH3A1 and gemcitabine resistant in pancreatic cancer cell lines and suggesting that it may serves as a predictive marker for gemcitabine treatment in pancreatic cancer patients. Keywords: Pancreatic ductal adenocarcinoma (PDAC), Aldehyde dehydrogenase 3 family member A1 (ALDH3A1), Gemcitabine sensitivity. Citation Format: Jin Su Kim, Ji Young Keum, Chan Hee Park, Seungmin Bang. ALDH3A1 as a predictive marker for gemcitabine treatment in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5876.

Former smoking associated with epigenetic modifications in human granulosa cells among women undergoing assisted reproduction

Smoking exposure during adulthood can disrupt oocyte development in women, contributing to infertility and possibly adverse birth outcomes. Some of these effects may be reflected in epigenome profiles in granulosa cells (GCs) in human follicular fluid. We compared the epigenetic modifications throughout the genome in GCs from women who were former (N = 15) versus never smokers (N = 44) undergoing assisted reproductive technologies (ART). This study included 59 women undergoing ART. Smoking history including time since quitting was determined by questionnaire. GCs were collected during oocyte retrieval and DNA methylation (DNAm) levels were profiled using the Infinium MethylationEPIC BeadChip. We performed an epigenome-wide association study with robust linear models, regressing DNAm level at individual loci on smoking status, adjusting for age, ovarian stimulation protocol, and three surrogate variables. We performed differentially methylated regions (DMRs) analysis and over-representation analysis of the identified CpGs and corresponding gene set. 81 CpGs were differentially methylated among former smokers compared to never smokers (FDR < 0.05). We identified 2 significant DMRs (KCNQ1 and RHBDD2). The former smoking-associated genes were enriched in oxytocin signaling, adrenergic signaling in cardiomyocytes, platelet activation, axon guidance, and chemokine signaling pathway. These epigenetic variations have been associated with inflammatory responses, reproductive outcomes, cancer development, neurodevelopmental disorder, and cardiometabolic health. Secondarily, we examined the relationships between time since quitting and DNAm at significant CpGs. We observed three CpGs in negative associations with the length of quitting smoking (p < 0.05), which were cg04254052 (KCNIP1), cg22875371 (OGDHL), and cg27289628 (LOC148145), while one in positive association, which was cg13487862 (PLXNB1). As a pilot study, we demonstrated epigenetic modifications associated with former smoking in GCs. The study is informative to potential biological pathways underlying the documented association between smoking and female infertility and biomarker discovery for smoking-associated reproductive outcomes.

Long-read sequencing unveils novel somatic variants and methylation patterns in the genetic information system of early lung cancer

Lung cancer poses a global health challenge, necessitating advanced diagnostics for improved outcomes. Intensive efforts are ongoing to pinpoint early detection biomarkers, such as genomic variations and DNA methylation, to elevate diagnostic precision. We conducted long-read sequencing on cancerous and adjacent non-cancerous tissues from a patient with lung adenocarcinoma. We identified somatic structural variations (SVs) specific to lung cancer by integrating data from various SV calling methods and differentially methylated regions (DMRs) that were distinct between these two tissue samples, revealing a unique methylation pattern associated with lung cancer. This study discovered over 40,000 somatic SVs and over 180,000 DMRs linked to lung cancer. We identified approximately 700 genes of significant relevance through comprehensive analysis, including genes intricately associated with many lung cancers, such as NOTCH1, SMOC2, CSMD2, and others. Furthermore, we observed that somatic SVs and DMRs were substantially enriched in several pathways, such as axon guidance signaling pathways, which suggests a comprehensive multi-omics impact on lung cancer progression across various biological investigation levels. These datasets can potentially serve as biomarkers for early lung cancer detection and may hold significant value in clinical diagnosis and treatment applications.

Bioinformatics and system biology approaches for identifying potential therapeutic targets for prostate cancer

Prostate cancer (PCa) is the primary cause of cancer-related deaths among men, and its incidence increases with age. Despite the availability of treatments, the high costs and complications associated with current cancer therapies pose challenges. Therefore, there is an urgent need to explore globally accessible and effective alternative medications to support prostate cancer treatment. Bioinformatics and system biology approaches were utilized to investigate repurposed medicines for prostate cancer treatment guided by host genomic biomarkers. The investigation identified 120 common differentially expressed genes (DEGs) and 24 hub genes (HubGs) as potential therapeutic targets by analyzing gene expression patterns and protein-protein interaction (PPI) networks. The top 10 hub genes CDK1, CCNA2, RRM2, ASPM, MELK, HJURP, DLGAP5, NCAPG, TTK, and HMMR are associated with the development and progression of prostate cancer. The DEGs enrichment analysis revealed significant axon guidance, cell-cell adhesion, extracellular space, and calcium signaling pathways associated with prostate cancer. Gene regulatory network analysis revealed transcription factors (FOXC1, GATA2 and E2F1 etc.) and micro-RNAs (hsa-mir-16–5p, hsa-mir-24–3p and hsa-mir-34a-5p etc.) as regulators of hub genes. The potential drug candidates, includingindirubin-3′-Monoxime (−7.7 kcal/mol), benzene sulfonamide (−8.8 kcal/mol), and cladribine (−6.6 kcal/mol) have been identified as the top 3 candidate drugs against CDK1, CCNA2 and RRM2, respectively. Besides, these drugs exhibit strong binding affinity with the target proteins and suggest their potential for repurposing in the treatment of prostate cancer. Collectively, the findings present valuable insights for advancing prostate cancer research, potentially leading to a deeper understanding and novel treatment strategies for relevant diseases.

Co-exposure to low-dose lead, cadmium, and mercury promotes memory deficits in rats: Insights from the dynamics of dendritic spine pruning in brain development

Lead (Pb), cadmium (Cd), and mercury (Hg) are environmentally toxic heavy metals that can be simultaneously detected at low levels in the blood of the general population. Although our previous studies have demonstrated neurodevelopmental toxicity upon co-exposure to these heavy metals at these low levels, the precise mechanisms remain largely unknown. Dendritic spines are the structural foundation of memory and undergo significant dynamic changes during development. This study focused on the dynamics of dendritic spines during brain development following Pb, Cd, and Hg co-exposure-induced memory impairment. First, the dynamic characteristics of dendritic spines in the prefrontal cortex were observed throughout the life cycle of normal rats. We observed that dendritic spines increased rapidly from birth to their peak value at weaning, followed by significant pruning and a decrease during adolescence. Dendritic spines tended to be stable until their loss in old age. Subsequently, a rat model of low-dose Pb, Cd, and Hg co-exposure from embryo to adolescence was established. The results showed that exposure to low doses of heavy metals equivalent to those detected in the blood of the general population impaired spatial memory and altered the dynamics of dendritic spine pruning from weaning to adolescence. Proteomic analysis of brain and blood samples suggested that differentially expressed proteins upon heavy metal exposure were enriched in dendritic spine-related cytoskeletal regulation and axon guidance signaling pathways and that cofilin was enriched in both of these pathways. Further experiments confirmed that heavy metal exposure altered actin cytoskeleton dynamics and disturbed the dendritic spine pruning-related LIM domain kinase 1-cofilin pathway in the rat prefrontal cortex. Our findings demonstrate that low-dose Pb, Cd, and Hg co-exposure may promote memory impairment by perturbing dendritic spine dynamics through dendritic spine pruning-related signaling pathways.

Time-Course of Transcriptomic Change in the Lungs of F344 Rats Repeatedly Exposed to a Multiwalled Carbon Nanotube in a 2-Year Test.

Despite intensive toxicological studies of carbon nanotubes (CNTs) over the last two decades, only a few studies have demonstrated their pulmonary carcinogenicities in chronic animal experiments, and the underlying molecular mechanisms are still unclear. To obtain molecular insights into CNT-induced lung carcinogenicity, we performed a transcriptomic analysis using a set of lung tissues collected from rats in a 2-year study, in which lung tumors were induced by repeated intratracheal instillations of a multiwalled carbon nanotube, MWNT-7. The RNA-seq-based transcriptome identified a large number of significantly differentially expressed genes at Year 0.5, Year 1, and Year 2. Ingenuity Pathway Analysis revealed that macrophage-elicited signaling pathways such as phagocytosis, acute phase response, and Toll-like receptor signaling were activated throughout the experimental period. At Year 2, cancer-related pathways including ERBB signaling and some axonal guidance signaling pathways such as EphB4 signaling were perturbed. qRT-PCR and immunohistochemistry indicated that several key molecules such as Osteopontin/Spp1, Hmox1, Mmp12, and ERBB2 were markedly altered and/or localized in the preneoplastic lesions, suggesting their participation in the induction of lung cancer. Our findings support a scenario of inflammation-induced carcinogenesis and contribute to a better understanding of the molecular mechanism of MWCNT carcinogenicity.

Integrated transcriptome and metabolome analysis to investigate the mechanism of intranasal insulin treatment in a rat model of vascular dementia.

Introduction: Insulin has an effect on neurodegenerative diseases. However, the role and mechanism of insulin in vascular dementia (VD) and its underlying mechanism are unknown. In this study, we aimed to investigate the effects and mechanism of insulin on VD. Methods: Experimental rats were randomly assigned to control (CK), Sham, VD, and insulin (INS) + VD groups. Insulin was administered by intranasal spray. Cognitive function was evaluated using the Morris's water maze. Nissl's staining and immunohistochemical staining were used to assess morphological alterations. Apoptosis was evaluated using TUNEL-staining. Transcriptome and metabolome analyses were performed to identify differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs), respectively. Results: Insulin significantly improved cognitive and memory functions in VD model rats (p < 0.05). Compared with the VD group, the insulin + VD group exhibited significantly reduced the number of Nissl's bodies numbers, apoptosis level, GFAP-positive cell numbers, apoptosis rates, and p-tau and tau levels in the hippocampal CA1 region (p < 0.05). Transcriptomic analysis found 1,257 and 938 DEGs in the VD vs. CK and insulin + VD vs. VD comparisons, respectively. The DEGs were mainly enriched in calcium signaling, cAMP signaling, axon guidance, and glutamatergic synapse signaling pathways. In addition, metabolomic analysis identified 1 and 14 DEMs between groups in negative and positive modes, respectively. KEGG pathway analysis indicated that DEGs and DEMs were mostly enriched in metabolic pathway. Conclusion: Insulin could effectively improve cognitive function in VD model rats by downregulating tau and p-tau expression, inhibiting astrocyte inflammation and neuron apoptosis, and regulating genes involved in calcium signaling, cAMP signaling, axon guidance, and glutamatergic synapse pathways, as well as metabolites involved in metabolic pathway.

Expression profiles and potential roles of serum tRNA‑derived fragments in diabetic nephropathy.

Diabetic nephropathy (DN) is one of the most important causes of end-stage renal disease and current treatments are ineffective in preventing its progression. Transfer RNA (tRNA)-derived fragments (tRFs), which are small non-coding fragments derived from tRNA precursors or mature tRNAs, have a critical role in various human diseases. The present study aimed to investigate the expression profile and potential functions of tRFs in DN. High-throughput sequencing technology was employed to detect the differential serum levels of tRFs between DN and diabetes mellitus and to validate the reliability of the sequencing results using reverse transcription-quantitative PCR. Ultimately, six differentially expressed (DE) tRFs were identified (P<0.05; |log2fold change| ≥1), including three upregulated (tRF5-GluCTC, tRF5-AlaCGC and tRF5-ValCAC) and three downregulated tRFs (tRF5-GlyCCC, tRF3-GlyGCC and tRF3-IleAAT). Potential functions and regulatory mechanisms of these DE tRFs were further evaluated using an applied bioinformatics-based analysis. Gene ontology analysis revealed that the DE tRFs are mainly enriched in biological processes, including axon guidance, Rad51 paralog (Rad51)B-Rad51C-Rad51D-X-Ray repair cross-complementing 2 complex, nuclear factor of activated T-cells protein binding and fibroblast growth factor-activated receptor activity. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that they are associated with axon guidance, neurotrophin signaling, mTOR signaling, AMPK signaling and epidermal growth factor receptor family signaling pathways. In conclusion, the present findings indicated that tRFs were DE in DN and may be involved in the regulation of DN pathology through multiple pathways, thereby providing a new perspective for the study of DN therapeutic targets.

Weighted gene co-expression network analysis identifies the prognosis-related models of left- and right-sided colon cancer.

Left-sided colon cancer (LC) and right-sided colon cancer (RC) are 2 essentially different diseases, and the potential mechanisms regulating them remain unidentified. In this study, we applied weighted gene co-expression network analysis (WGCNA) to confirm a yellow module, mainly enriched in metabolism-related signaling pathways related to LC and RC. Based on the RNA-seq data of colon cancer in The Cancer Genome Atlas (TCGA) and GSE41258 dataset with their corresponding clinical information, a training set (TCGA: LC: n = 171; RC: n = 260) and a validation set (GSE41258: LC: n = 94; RC: n = 77) were divided. Least absolute shrinkage and selection operator (LASSO) penalized COX regression analysis identified 20 prognosis-related genes (PRGs) and helped constructed 2 risk (LC-R and RC-R) models in LC and RC, respectively. The model-based risk scores accurately performed in risk stratification for colon cancer patients. The high-risk group of the LC-R model showed associations with ECM-receptor interaction, focal adhesion, and PI3K-AKT signaling pathway. Interestingly, the low-risk group of the LC-R model showed associations with immune-related signaling pathways like antigen processing and presentation. On the other hand, the high-risk group of the RC-R model showed enrichment for cell adhesion molecules and axon guidance signaling pathways. Furthermore, we identified 20 differentially expressed PRGs between LC and RC. Our findings provide new insights into the difference between LC and RC, and uncover the potential biomarkers for the treatment of LC and RC.

Identification of immunodiagnostic blood biomarkers associated with spinal cord injury severity.

Blood always shows some immune changes after spinal cord injury (SCI), and detection of such changes in blood may be helpful for diagnosis and treatment of SCI. However, studies to date on blood immune changes after SCI in humans are not comprehensive. Therefore, to obtain the characteristics of blood immune changes and immunodiagnostic blood biomarkers of SCI and its different grades, a human blood transcriptome sequencing dataset was downloaded and analyzed to obtain differentially expressed immune-related genes (DEIGs), related functions and signaling pathways related to SCI and its various grades. Characteristic biomarkers of SCI and its different grades were identified by using weighted gene coexpression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) logistic regression. Expression of biomarkers was verified through experiments. The area under the curve (AUC) of biomarkers was calculated to evaluate their diagnostic value, and differences in immune cell content were examined. In this study, 17 kinds of immune cells with different contents between the SCI group and healthy control (HC) group were identified, with 7 immune cell types being significantly increased. Differences in the content of immune cells between different grades of SCI and the HC group were also discovered. DEIGs were identified, with alteration in some immune-related signaling pathways, vascular endothelial growth factor signaling pathways, and axon guidance signaling pathways. The SCI biomarkers identified and those of American Spinal Injury Society Impairment Scale (AIS) A and AIS D of SCI have certain diagnostic sensitivity. Analysis of the correlation of immune cells and biomarkers showed that biomarkers of SCI, AIS A grade and AIS D grade correlated positively or negatively with some immune cells. CKLF, EDNRB, FCER1G, SORT1, and TNFSF13B can be used as immune biomarkers for SCI. Additionally, GDF11and HSPA1L can be used as biomarkers of SCI AIS A grade; PRKCA and CMTM2 can be used as biomarkers of the SCI AIS D grade. Detecting expression of these putative biomarkers and changes in related immune cells may be helpful for predicting the severity of SCI.

Identification of miRNA-mediated gene regulatory networks in L-methionine exposure counteracts cocaine-conditioned place preference in mice.

Background and Aims: Methionine has been proven to inhibit addictive behaviors of cocaine dependence. This study aimed to identify the potential mechanisms of MET relating to its inhibitory effects on cocaine induced cellular and behavioral changes. Methods: MRNA and miRNA high-throughput sequencing of the prefrontal cortex in a mouse model of cocaine conditioned place preference (CPP) combined with L-methionine was performed. Differentially expressed miRNAs (DE-miRNAs) and differentially expressed genes (DEGs) regulated by cocaine and inhibited by L-methionine were identified. DEGs were mapped to STRING database to construct a protein-protein interaction (PPI) network. Then, the identified DEGs were subjected to the DAVID webserver for functional annotation. Finally, miRNA-mRNA regulatory network and miRNA-mRNA-TF regulatory networks were established to screen key DE-miRNAs and coregulation network in Cytoscape. Results: Sequencing data analysis showed that L-methionine reversely regulated genes and miRNAs affected by cocaine. Pathways associated with drug addiction only enriched in CS-down with MC-up genes targeted by DE-miRNAs including GABAergic synapse, Glutamatergic synapse, Circadian entrainment, Axon guidance and Calcium signaling pathway. Drug addiction associated network was formed of 22 DEGs including calcium channel (Cacna1c, Cacna1e, Cacna1g and Cacng8), ephrin receptor genes (Ephb6 and Epha8) and ryanodine receptor genes (Ryr1 and Ryr2). Calcium channel gene network were identified as a core gene network modulated by L-methionine in response to cocaine dependence. Moreover, it was predicted that Grin1 and Fosb presented in TF-miRNA-mRNA coregulation network with a high degree of interaction as hub genes and interacted calcium channels. Conclusion: These identified key genes, miRNA and coregulation network demonstrated the efficacy of L-methionine in counteracting the effects of cocaine CPP. To a certain degree, it may provide some hints to better understand the underlying mechanism on L-methionine in response to cocaine abuse.

Selection of MicroRNAs Associated between Neural Stem Cells and Multiple Sclerosis

Background: Diagnosis and treatment of multiple sclerosis (MS) in its advanced state have been one of the medical community's concerns so far. Cell therapy has been a modern and successful treatment. However, it has not yet been effective enough to treat MS. This study aimed to find the relationship between neural stem cells (NSCs) and MS, and by considering important signaling pathways of pathogenesis, the most important microRNAs (miRNAs) for its diagnosis and treatment were investigated. Materials and Methods: Using the bioinformatics approaches and appropriate databases, the relationship between NSCs and MS were recognized, and after obtaining common genes between them, the protein products by them were evaluated. Finally, after nominating essential genes, we isolated and analyzed the microarrays involved in these pathways. Results: In the first step, 76 upregulated and 1600 down-regulated common genes between NSCs and MS were recognized. Upregulated genes obtained axon guidance, NCAM, and RHO signaling pathways, and the cell cycle, RNA metabolism, and DNA repair signaling pathways by down-regulated genes. Then, high-expression PAK3, ROBO2, and LIMK2, and low-expression AURKA, BIRC5, BLM, and BRCA1 proteins were identified. Accordingly, high-expression miRNAs included hsa-miR-4790-5p, hsa-miR-4281, and hsa-miR-4327, but low-expression miRNAs included hsa-miR-103b, hsa-miR-638, and hsa-miR-4537 were recognized. Conclusion: Our study indicated that the abovementioned important miRNAs have a major role in diagnosing and treating MS.

Exploration of the relationship between gut microbiota and fecal microRNAs in patients with major depressive disorder

Microbiota-gut-brain axis signaling plays a pivotal role in mood disorders. The communication between the host and the gut microbiota may involve complex regulatory networks. Previous evidence showed that host-fecal microRNAs (miRNAs) interactions partly shaped gut microbiota composition. We hypothesized that some miRNAs are correlated with specific bacteria in the fecal samples in patients with major depressive disorder (MDD), and these miRNAs would show enrichment in pathways associated with MDD. MDD patients and healthy controls were recruited to collect fecal samples. We performed 16S ribosome RNA sequence using the Illumina MiSeq sequencers and analysis of 798 fecal miRNAs using the nCounter Human-v2 miRNA Panel in 20 subjects. We calculated the Spearman correlation coefficient for bacteria abundance and miRNA expressions, and analyzed the predicted miRNA pathways by enrichment analysis with false-discovery correction (FDR). A total of 270 genera and 798 miRNAs were detected in the fecal samples. Seven genera (Anaerostipes, Bacteroides, Bifidobacterium, Clostridium, Collinsella, Dialister, and Roseburia) had fold changes greater than one and were present in over 90% of all fecal samples. In particular, Bacteroides and Dialister significantly differed between the MDD and control groups (p-value < 0.05). The correlation coefficients between the seven genera and miRNAs in patients with MDD showed 48 pairs of positive correlations and 36 negative correlations (p-value < 0.01). For miRNA predicted functions, there were 57 predicted pathways with a p-value < 0.001, including MDD-associated pathways, axon guidance, circadian rhythm, dopaminergic synapse, focal adhesion, long-term potentiation, and neurotrophin signaling pathway. In the current pilot study, our findings suggest specific genera highly correlated with the predicted miRNA functions, which might provide clues for the interaction between host factors and gut microbiota via the microbiota-gut-brain axis. Follow-up studies with larger sample sizes and refined experimental design are essential to dissect the roles between gut microbiota and miRNAs for depression.

Identification of circRNAs linked to Alzheimer’s disease and related dementias

AbstractBackgroundAlthough linear mRNA transcriptome study has been well performed for Alzheimer’s disease (AD), little is known for the non‐coding RNA. Circular RNAs(circRNAs) are particularly notable because of their selective expression in the brain and differential regulation in neurological disease conditions, including AD. CircRNAs are formed from back‐splicing events, and they majorly function as sponges for microRNA and RNA‐binding proteins. Our study examines circRNA expression patterns associated with AD and related dementias in different brain regions.MethodTo detect and quantify cortical circRNAs, we used Mount Sinai Brain Bank (MSBB) rRNA‐depleted RNA sequencing(RNAseq) data derived from inferior frontal gyrus tissue of 278 subjects(216 AD cases, 62 controls) by applying DCC and Circexplor3. To detect hippocampal circRNAs, we generated rRNA‐depleted RNAseq data from 207 human postmortem hippocampal region samples(186 AD, 21 controls) obtained from the BU Alzheimer Disease Research Center. Differentially expressed circRNAs were identified using limma and DESeq2. Both cortical and hippocampal circRNA candidates were further validated using RT‐qPCR in a smaller independent cohort of patients.ResultWe identified over 300 circRNA significantly associated with AD condition (FDR&lt;0.05). Interestingly, a major fraction of these circRNAs are derived from genes involved in excitatory synaptic transmission, axon guidance, and calcium signaling pathways. CircRNA from AD‐linked genes, including APP, PICALM and PSEN1, were identified as top candidates associated with AD in cortex. In the hippocampus, we find circSLC8A1 and circHOMER1 among the top differentially regulated circRNAs. We also find expression of circHOMER1, circMLIP, circATRNL1 among others to be correlated with AD traits of clinical dementia, BRAAK pathology, and amyloid plaque. Our analysis of AD‐only patients and AD patients with vascular or Lewy body dementia revealed differential expression of 39 circRNAs common among all three disease conditions.ConclusionCircRNAs are a novel class of regulatory RNAs but their role in AD pathogenesis is just beginning to be explored. Our study identified circRNA whose expression is linked to AD and are correlated with indices of tauopathy and cognitive loss in cortex and hippocampus. Furthermore, particular circRNAs were differentially expressed among patients with AD or other dementias, suggesting that circRNA might be useful disease biomarkers or targets for disease intervention.

Sexually‐dimorphic effects of C3aR1 disruption in a mouse model of Alzheimer’s disease

AbstractBackgroundThe complement system can act as part of the innate immune system as well as the adaptive immune system. Complement activation in the brain has been shown to play a role in neurogenesis, synaptic pruning and plasticity. It has also been specifically involved in microglial function, since our group has previously shown that when the complement component 3a receptor 1 (C3aR1) is disrupted in mice, phagocytosis by primary microglia cells is impaired as compared to WT microglia. Therefore, it is hypothesized that complement might have neuroprotective effects early in life but neurotoxic effects later in life or within a disease context, such as during Alzheimer’s disease (AD) impeding to effectively clear hallmarks of the disease.MethodWe performed bulk RNA sequencing (RNAseq) analysis from cortex tissue of 8mo old male and female wild‐type, C3aR1 knock‐out (KO), 5xFAD and 5xFAD‐C3aR1 KO mice. We also performed Barnes Maze on these mice to assess spatial learning and memory, as well as biochemical assays to measure several AD markers.ResultData obtained from RNAseq analysis has shown a sexually‐dimorphic trend in various differentially‐expressed genes (DEGs). For instance, when comparing 5xFAD‐C3aR1 KO with 5xFAD mice, male mice show downregulated DEGs in axon guidance and calcium signaling pathways according to KEGG pathway terms, but this is not seen in females. Similarly, barnes maze has shown sexually‐dimorphic differences, with 5xFAD‐C3aR1 KO male mice showing improve memory and learning when compared to 5xFAD mice, and no differences are seen in female mice.ConclusionInterestingly, other studies in humans have shown increased complement proteins in the cerebrospinal fluid of men, compared to women, showing the importance of studying the complement system in both males and females. Assessing these sexually‐dimorphic differences in this AD mouse model is also important, given that generally not only female mice present more aggressive phenotypes of AD, but also AD in humans is more prevalent in women.