CCR7-mediated T follicular helper cell differentiation is associated with the pathogenesis and immune microenvironment of spinal cord injury-induced immune deficiency syndrome

Identification and validation of biomarkers associated with mitochondrial dysfunction and ferroptosis in rat spinal cord injury

Introduction

Mitochondrial dysfunction and ferroptosis have been implicated in the pathophysiological processes following spinal cord injury (SCI), with evidence suggesting their interplay influences neuronal cell survival and repair mechanisms. This study seeks to identify mitochondria- and ferroptosis-related biomarkers through comprehensive bioinformatics analysis.

Methods

Mitochondria- and ferroptosis-associated differentially expressed genes (DEGs) were identified through the integration of differential expression analysis and weighted gene co-expression network analysis. Two machine learning algorithms, least absolute shrinkage and selection operator (LASSO) and Boruta, were employed to isolate SCI-associated feature genes. Biomarkers were subsequently identified by analyzing their expression levels. An artificial neural network (ANN) diagnostic model was constructed to predict SCI likelihood based on these biomarkers. Further evaluations were performed using enrichment analysis, immune infiltration profiling, molecular modulation assessment, and drug prediction. The biomarkers' expression levels were validated using RT-qPCR.

Results

In this study, two biomarkers, Hcrt and Cdca2, linked to mitochondrial function and ferroptosis in SCI, were found to be highly expressed in SCI samples. Tissue-specific analysis from the GTEx database revealed expression of these biomarkers in brain and spinal cord tissues. The ANN model, constructed using these biomarkers, accurately discriminated between SCI and control samples. Enrichment analysis highlighted several co-enriched pathways for Hcrt and Cdca2, including "ubiquitin-mediated proteolysis," "endocytosis," and the "neurotrophin signaling pathway." Immune infiltration analysis, based on the Wilcoxon test, demonstrated significant differences in T follicular helper cell levels, which were lower in SCI samples compared to controls. Notably, T follicular helper cells exhibited a positive correlation with Hcrt and a negative correlation with Cdca2. Furthermore, seven transcription factors, including CEBPB, FOXC1, and GATA2, were identified as potential co-regulators of Hcrt and Cdca2. Drug prediction analysis revealed stable interactions of Cdca2 with pinosylvin, zinc acetate dihydrate, hydroquinone, lucanthone, and dasatinib. RT-qPCR validation confirmed the expression patterns of Hcrt and Cdca2 in alignment with the dataset, showing statistically significant differences.

Discussion

This study identifies Hcrt and Cdca2 as biomarkers related to mitochondrial function and ferroptosis in SCI, providing new insights for the diagnosis and mechanistic understanding of SCI.

Screening biomarkers for spinal cord injury using weighted gene co-expression network analysis and machine learning

JOURNAL/nrgr/04.03/01300535-202412000-00028/figure1/v/2024-04-08T165401Z/r/image-tiff Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal cord injury. They can greatly affect nerve regeneration and functional recovery. However, there is still limited understanding of the peripheral immune inflammatory response in spinal cord injury. In this study, we obtained microRNA expression profiles from the peripheral blood of patients with spinal cord injury using high-throughput sequencing. We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus (GEO) database (GSE151371). We identified 54 differentially expressed microRNAs and 1656 differentially expressed genes using bioinformatics approaches. Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways, such as neutrophil extracellular trap formation pathway, T cell receptor signaling pathway, and nuclear factor-κB signal pathway, were abnormally activated or inhibited in spinal cord injury patient samples. We applied an integrated strategy that combines weighted gene co-expression network analysis, LASSO logistic regression, and SVM-RFE algorithm and identified three biomarkers associated with spinal cord injury: ANO10, BST1, and ZFP36L2. We verified the expression levels and diagnostic performance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve. Quantitative polymerase chain reaction results showed that ANO10 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients. We also constructed a small RNA-mRNA interaction network using Cytoscape. Additionally, we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal cord injury patients using the CIBERSORT tool. The proportions of naïve B cells, plasma cells, monocytes, and neutrophils were increased while the proportions of memory B cells, CD8+ T cells, resting natural killer cells, resting dendritic cells, and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects, and ANO10, BST1 and ZFP26L2 were closely related to the proportion of certain immune cell types. The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal cord injury and suggest that ANO10, BST1, and ZFP36L2 are potential biomarkers for spinal cord injury. The study was registered in the Chinese Clinical Trial Registry (registration No. ChiCTR2200066985, December 12, 2022).

Peripheral immune reactions following human traumatic spinal cord injury: the interplay of immune activation and suppression

Traumatic spinal cord injury (SCI) damages the nerve tissue of the spinal cord, resulting in loss of motor and/or sensory functions at and below the injury level. SCI provokes a long-lasting immune response that extends beyond the spinal cord and induces changes in the composition and function of the peripheral immune system. Seemingly contradictory findings have been observed, as both systemic immune activation, including inflammation and autoimmunity, and immune suppression have been reported. Differences in the levels and functions of various cell types and components of both the innate and adaptive immune system supporting these changes have been described at (sub)acute and chronic stages post-injury. Further research is needed for a more comprehensive understanding of the peripheral immune reactions following SCI, their possible correlations with clinical characteristics, and how these immune responses could be targeted to facilitate the therapeutic management of SCI. In this review, we provide an overview of the current literature discussing changes in the peripheral immune system and their occurrence over time following a traumatic SCI.

Abnormal Characterization and Distribution of Circulating Regulatory T Cells in Patients with Chronic Spinal Cord Injury According to the Period of Evolution

Spinal cord injury (SCI) is a progressive and complex neurological disorder accompanied by multiple systemic challenges. Peripheral immune dysfunction is a major event occurring after SCI, especially in its chronic phase. Previous works have demonstrated significant changes in different circulating immune compartments, including in T cells. However, the precise characterization of these cells remains to be fully unraveled, particularly when considering important variants such as the time since the initial injury. In the present work, we aimed to study the level of circulating regulatory T cells (Tregs) in SCI patients depending on the duration of evolution. For this purpose, we studied and characterized peripheral Tregs from 105 patients with chronic SCI using flow cytometry, with patients classified into three major groups depending on the time since initial injury: short period chronic (SCI-SP, <5 years since initial injury); early chronic (SCI-ECP, from 5-15 years post-injury) and late chronic SCI (SCI-LCP, more than 15 years post-injury. Our results show that both the SCI-ECP and SCI-LCP groups appeared to present increased proportions of CD4+ CD25+/low Foxp3+ Tregs in comparison to healthy subjects, whereas a decreased number of these cells expressing CCR5 was observed in SCI-SP, SCI-ECP, and SCI-LCP patients. Furthermore, an increased number of CD4+ CD25+/high/low Foxp3 with negative expression of CD45RA and CCR7 was observed in SCI-LCP patients when compared to the SCI-ECP group. Taken together, these results deepen our understanding of the immune dysfunction reported in chronic SCI patients and how the time since initial injury may drive this dysregulation.