RNA sequencing screening of differentially expressed genes after spinal cord injury

Transcriptome profile analysis in spinal cord injury rats with transplantation of menstrual blood-derived stem cells

Introduction

Menstrual blood-derived stem cells (MenSCs) are vital in treating many degenerative and traumatic disorders. However, the underlying molecular mechanisms remain obscure in MenSCs-treating spinal cord injury (SCI) rats.

Methods

MenSCs were adopted into the injured sites of rat spinal cords at day 7 post surgery and the tissues were harvested for total RNA sequencing analysis at day 21 after surgery to investigate the expression patterns of RNAs. The differentially expressed genes (DEGs) were analyzed with volcano and heatmap plot. DEGs were sequentially analyzed by weighted gene co-expression network, functional enrichment, and competitive endogenous RNAs (ceRNA) network analysis. Next, expression of selected miRNAs, lncRNAs, circRNAs and mRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR). Bioinformatics packages and extra databases were enrolled to scoop the genes functions and their interaction relationships.

Results

A total of 89 lncRNAs, 65 circRNAs, 120 miRNAs and 422 mRNAs were significantly upregulated and 65 lncRNAs, 72 circRNAs, 74 miRNAs, and 190 mRNAs were significantly downregulated in the MenSCs treated rats compared to SCI ones. Current investigation revealed that MenSCs treatment improve the recovery of the injured rats and the most significantly involved pathways in SCI regeneration were cell adhesion molecules, nature killer cell mediated cytotoxicity, primary immunodeficiency, chemokine signaling pathway, T cell receptor signaling pathway and B cell receptor signaling pathway. Moreover, the lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA ceRNA network of SCI was constructed. Finally, the protein-protein interaction (PPI) network was constructed using the top 100 DE mRNAs. The constructed PPI network included 47 nodes and 70 edges.

Discussion

In summary, the above results revealed the expression profile and potential functions of differentially expressed (DE) RNAs in the injured spinal cords of rats in the MenSCs-treated and SCI groups, and this study may provide new clues to understand the mechanisms of MenSCs in treating SCI.

Mass cytometric analysis of the immune cell landscape after traumatic brain injury elucidates the role of complement and complement receptors in neurologic outcomes

Following traumatic brain injury (TBI), a neuroinflammatory response can persist for years and contribute to the development of chronic neurological manifestations. Complement plays a central role in post-TBI neuroinflammation, and C3 opsonins and the anaphylatoxins (C3a and C5a) have been implicated in promoting secondary injury. We used single cell mass cytometry to characterize the immune cell landscape of the brain at different time points after TBI. To specifically investigate how complement shapes the post-TBI immune cell landscape, we analyzed TBI brains in the context of CR2-Crry treatment, an inhibitor of C3 activation. We analyzed 13 immune cell types, including peripheral and brain resident cells, and assessed expression of various receptors. TBI modulated the expression of phagocytic and complement receptors on both brain resident and infiltrating peripheral immune cells, and distinct functional clusters were identified within same cell populations that emerge at different phases after TBI. In particular, a CD11c+ (CR4) microglia subpopulation continued to expand over 28 days after injury, and was the only receptor to show continuous increase over time. Complement inhibition affected the abundance of brain resident immune cells in the injured hemisphere and impacted the expression of functional receptors on infiltrating cells. A role for C5a has also been indicated in models of brain injury, and we found significant upregulation of C5aR1 on many immune cell types after TBI. However, we demonstrated experimentally that while C5aR1 is involved in the infiltration of peripheral immune cells into the brain after injury, it does not alone affect histological or behavioral outcomes. However, CR2-Crry improved post-TBI outcomes and reduced resident immune cell populations, as well as complement and phagocytic receptor expression, indicating that its neuroprotective effects are mediated upstream of C5a generation, likely via modulating C3 opsonization and complement receptor expression.

The Stress Response of the Holothurian Central Nervous System: A Transcriptomic Analysis

Injury to the central nervous system (CNS) results in permanent damage and lack of function in most vertebrate animals, due to their limited regenerative capacities. In contrast, echinoderms can fully regenerate their radial nerve cord (RNC) following transection, with little to no scarring. Investigators have associated the regenerative capacity of some organisms to the stress response and inflammation produced by the injury. Here, we explore the gene activation profile of the stressed holothurian CNS. To do this, we performed RNA sequencing on isolated RNC explants submitted to the stress of transection and enzyme dissection and compared them with explants kept in culture for 3 days following dissection. We describe stress-associated genes, including members of heat-shock families, ubiquitin-related pathways, transposons, and apoptosis that were differentially expressed. Surprisingly, the stress response does not induce apoptosis in this system. Other genes associated with stress in other animal models, such as hero proteins and those associated with the integrated stress response, were not found to be differentially expressed either. Our results provide a new viewpoint on the stress response in the nervous system of an organism with amazing regenerative capacities. This is the first step in deciphering the molecular processes that allow echinoderms to undergo fully functional CNS regeneration, and also provides a comparative view of the stress response in other organisms.

Molecular diagnostics in neurotrauma: Are there reliable biomarkers and effective methods for their detection?

To date, a large number of studies are being carried out in the field of neurotrauma, researchers not only establish the molecular mechanisms of the course of the disorders, but are also involved in the search for effective biomarkers for early prediction of the outcome and therapeutic intervention. Particular attention is paid to traumatic brain injury and spinal cord injury, due to the complex cascade of reactions in primary and secondary injury that affect pathophysiological processes and regenerative potential of the central nervous system. Despite a wide range of methods available methods to study biomarkers that correlate with the severity and degree of recovery in traumatic brain injury and spinal cord injury, development of reliable test systems for clinical use continues. In this review, we evaluate the results of recent studies looking for various molecules acting as biomarkers in the abovementioned neurotrauma. We also summarize the current knowledge of new methods for studying biological molecules, analyzing their sensitivity and limitations, as well as reproducibility of results. In this review, we also highlight the importance of developing reliable and reproducible protocols to identify diagnostic and prognostic biomolecules.

Analysis of gene expression profiles in two spinal cord injury models

Objectives

To analyze the changes of gene expression at different timepoints after spinal cord injury (SCI) with tenth segment thoracic injury.

Methods

Two SCI models, the complete paraplegia (H) and Allen’s strike (D) methods were applied to induce SCI in rats, and transcriptome sequencing was performed 1, 3, 7, 14, 56, and 70 days after SCI, respectively. Principal component analysis, differentially expressed gene analysis, and hierarchical clustering analysis were applied to analyze the differentially expressed genes (DEGs). Gene Ontology GO enrichment analysis, Kyoto Encyclopedia of Genes and Genomes enrichment analysis, and Gene Set Enrichment Analysis revealed the pathway of gene enrichment.

Results

There were 1,907, 3,120, 3,728, 978, 2,319, and 3,798 DEGs in the complete paraplegia group and 2,380, 878, 1,543, 6,040, 1,945, and 3,850 DEGs in the Allen’s strike method group and after SCI at 1, 3, 7, 14, 56, and 70 days, respectively. The transcriptome contours of D1, H1, D3, and H14 were clustered with C; the H56, D56, H70, and D70 transcriptome contours were similar and clustered together. H3, D7, and H7 were clustered together, and D14 was clustered separately. The transcriptome differences of the two SCI models were mainly concentrated during the first 2 weeks after SCI. The DEGs after SCI in the complete paraplegia group were more concentrated. Most of the early transcriptional regulation stabilized within 2 weeks after injury.

Conclusions

There were DEGs between the two SCI models. Through the gene changes and pathway enrichment of the entire time period after SCI, the molecular mechanism of SCI repair was revealed in depth, which provided a reference for SCI treatment in the future.

The Time Sequence of Gene Expression Changes after Spinal Cord Injury

Gene expression changes following spinal cord injury (SCI) are time-dependent, and an accurate understanding of these changes can be crucial in determining time-based treatment options in a clinical setting. We performed RNA sequencing of the contused spinal cord of rats at five different time points from the very acute to chronic stages (1 hour, 1 day, 1 week, 1 month, and 3 months) following SCI. We identified differentially expressed genes (DEGs) and Gene Ontology (GO) terms at each time point, and 14,257 genes were commonly expressed at all time points. The biological process of the inflammatory response was increased at 1 hour and 1 day, and the cellular component of the integral component of the synaptic membrane was increased at 1 day. DEGs associated with cell activation and the innate immune response were highly enriched at 1 week and 1 month, respectively. A total of 2841 DEGs were differentially expressed at any of the five time points, and 18 genes (17 upregulated and 1 downregulated) showed common expression differences at all time points. We found that interleukin signaling, neutrophil degranulation, eukaryotic translation, collagen degradation, LGI–ADAM interactions, GABA receptor, and L1CAM-ankyrin interactions were prominent after SCI depending on the time post injury. We also performed gene–drug network analysis and found several potential antagonists and agonists which can be used to treat SCI. We expect to discover effective treatments in the clinical field through further studies revealing the efficacy and safety of potential drugs.

Circular Ribonucleic Acid Expression Alteration in the Spinal Cord Tissue after Spinal Cord Injury in Rats

BACKGROUND AND PURPOSE

Increased researches focus into pathophysiological mechanisms of spinal cord injury (SCI), particularly toward the relationship between relevant biomarkers and the degree of SCI and prognosis. Circular ribonucleic acids (circRNAs) possess microRNA (miRNA) binding sites that can play the role of miRNA sponges and thus participate in the expression of parental gene modification. This study focused on rat SCI models and explore the relationship between circRNAs and SCI at a genomic level.

METHODS

We first established a rat SCI model and extracted the target spinal cord tissue according to 4 time points. Then investigated the alterations in the circRNA expression by high-throughput whole transcriptome sequencing, analyzed data by gene ontology and the Kyoto Encyclopedia of Genes and Genomes, and constructed the circRNA-miRNA network.

RESULTS

A total of 178 circRNAs were dysregulated (89 upregulated/89 downregulated). Differential circRNAs were found to be mainly involved in the composition of specific organelles in the cytoplasm and are mainly involved in the energy transfer process associated with electron transfer (and similar activities). In all the signaling pathways identified in this study, the MAPK, Wnt, and mTOR signaling pathways are intimately associated with the pathophysiological process of rats post-SCI. In this study, 10 circRNAs with obvious dysregulation were selected for prediction, 26 miRNAs with additional interactions were obtained, and a network diagram of circRNAs-miRNAs was constructed. In this manner, one can understand in further detail the pathogenesis of SCI and to provide new strategies for the prevention, diagnosis, and treatment of SCI-related injuries at the genetic level.

A 3D Fiber-Hydrogel Based Non-Viral Gene Delivery Platform Reveals that microRNAs Promote Axon Regeneration and Enhance Functional Recovery Following Spinal Cord Injury

Current treatment approaches toward spinal cord injuries (SCI) have mainly focused on overcoming the inhibitory microenvironment that surrounds lesion sites. Unfortunately, the mere modulation of the cell/tissue microenvironment is often insufficient to achieve desired functional recovery. Therefore, stimulating the intrinsic growth ability of injured neurons becomes crucial. MicroRNAs (miRs) play significant roles during axon regeneration by regulating local protein synthesis at growth cones. However, one challenge of using miRs to treat SCI is the lack of efficient delivery approaches. Here, a 3D fiber-hydrogel scaffold is introduced which can be directly implanted into a spinal cord transected rat. This 3D scaffold consists of aligned electrospun fibers which provide topographical cues to direct axon regeneration, and collagen matrix which enables a sustained delivery of miRs. Correspondingly, treatment with Axon miRs (i.e., a cocktail of miR-132/miR-222/miR-431) significantly enhances axon regeneration. Moreover, administration of Axon miRs along with anti-inflammatory drug, methylprednisolone, synergistically enhances functional recovery. Additionally, this combined treatment also decreases the expression of pro-inflammatory genes and enhance gene expressions related to extracellular matrix deposition. Finally, increased Axon miRs dosage with methylprednisolone, significantly promotes functional recovery and remyelination. Altogether, scaffold-mediated Axon miR treatment with methylprednisolone is a promising therapeutic approach for SCI.

Targeting senescent cells improves functional recovery after spinal cord injury

Persistent senescent cells (SCs) are known to underlie aging-related chronic disorders, but it is now recognized that SCs may be at the center of tissue remodeling events, namely during development or organ repair. In this study, we show that two distinct senescence profiles are induced in the context of a spinal cord injury between the regenerative zebrafish and the scarring mouse. Whereas induced SCs in zebrafish are progressively cleared out, they accumulate over time in mice. Depletion of SCs in spinal-cord-injured mice, with different senolytic drugs, improves locomotor, sensory, and bladder functions. This functional recovery is associated with improved myelin sparing, reduced fibrotic scar, and attenuated inflammation, which correlate with a decreased secretion of pro-fibrotic and pro-inflammatory factors. Targeting SCs is a promising therapeutic strategy not only for spinal cord injuries but potentially for other organs that lack regenerative competence.

Transcriptome analysis of molecular mechanisms underlying facial nerve injury repair in rats

Although the transcriptional alterations inside the facial nucleus after facial nerve injury have been well studied, the gene expression changes in the facial nerve trunk after injury are still unknown. In this study, we established an adult rat model of facial nerve crush injury by compressing the right lateral extracranial nerve trunk. Transcriptome sequencing, differential gene expression analysis, and cluster analysis of the injured facial nerve trunk were performed, and 39 intersecting genes with significant variance in expression were identified. Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the 39 intersecting genes revealed that these genes are mostly involved in leukocyte cell-cell adhesion and phagocytosis and have essential roles in regulating nerve repair. Quantitative real-time polymerase chain reaction assays were used to validate the expression of pivotal genes. Finally, nine pivotal genes that contribute to facial nerve recovery were identified, including Arhgap30, Akr1b8, C5ar1, Csf2ra, Dock2, Hcls1, Inpp5d, Sla, and Spi1. Primary Schwann cells were isolated from the sciatic nerve of neonatal rats. After knocking down Akr1b8 in Schwann cells with an Akr1b8-specific small interfering RNA plasmid, expression levels of monocyte chemoattractant protein-1 and interleukin-6 were decreased, while cell proliferation and migration were not obviously altered. These findings suggest that Akr1b8 likely regulates the interaction between Schwann cells and macrophages through regulation of cytokine expression to promote facial nerve regeneration. This study is the first to reveal a transcriptome change in the facial nerve trunk after facial nerve injury, thereby revealing the potential mechanism underlying repair of facial nerve injury. This study was approved by the Animal Ethics Committee of Nantong University, China in 2018 (approval No. S20180923-007).

RNA interference in glial cells for nerve injury treatment

Drivers of RNA interference are potent for manipulating gene and protein levels, which enable the restoration of dysregulated mRNA expression that is commonly associated with injuries and diseases. This review summarizes the potential of targeting neuroglial cells, using RNA interference, to treat nerve injuries sustained in the central nervous system. In addition, the various methods of delivering these RNA interference effectors will be discussed.

Expression of long non-coding RNAs in complete transection spinal cord injury: a transcriptomic analysis

Long non-coding RNAs (lncRNAs) are abundantly expressed in the central nervous system and exert a critical role in gene regulation via multiple biological processes. To uncover the functional significance and molecular mechanisms of lncRNAs in spinal cord injury (SCI), the expression signatures of lncRNAs were profiled using RNA sequencing (RNA-seq) technology in a Sprague-Dawley rat model of the 10^th thoracic vertebra complete transection SCI. Results showed that 116 of 14,802 detected lncRNAs were differentially expressed, among which 16—including eight up-regulated (H19, Vof16, Hmox2-ps1, LOC100910973, Ybx1-ps3, Nnat, Gcgr, LOC680254) and eight down-regulated (Rmrp, Terc, Ngrn, Ppp2r2b, Cox6a2, Rpl37a-ps1, LOC360231, Rpph1)—demonstrated fold changes > 2 in response to transection SCI. A subset of these RNA-seq results was validated by quantitative real-time PCR. The levels of 821 mRNAs were also significantly altered post-SCI; 592 mRNAs were up-regulated and 229 mRNAs were down-regulated by more than 2-fold. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that differentially expressed mRNAs were related to GO biological processes and molecular functions such as injury and inflammation response, wound repair, and apoptosis, and were significantly enriched in 15 KEGG pathways, including cell phagocytosis, tumor necrosis factor alpha pathway, and leukocyte migration. Our results reveal the expression profiles of lncRNAs and mRNAs in the rat spinal cord of a complete transection model, and these differentially expressed lncRNAs and mRNAs represent potential novel targets for SCI treatment. We suggest that lncRNAs may play an important role in the early immuno-inflammatory response after spinal cord injury. This study was approved by the Administration Committee of Experimental Animals, Guangdong Province, China.