Comprehensive analyses of brain cell communications based on multiple scRNA-seq and snRNA-seq datasets for revealing novel mechanism in neurodegenerative diseases

Mendelian randomization combined with single-cell sequencing data analysis of chemokines and chemokine receptors and key genes and molecular mechanisms associated with epilepsy

OBJECTIVE

To explore the functions and potential regulatory mechanisms of chemokine and chemokine receptor (CCR)-related genes in epilepsy.

METHODS

CCRs were identified as candidate genes and their causal relationship with epilepsy was rigorously evaluated via Mendelian randomization analysis. Subsequently, single-cell RNA sequencing (scRNA-seq) data were analyzed to identify and classify cell clusters into distinct types based on cellular annotation. Differential expression analysis was conducted to pinpoint key genes by overlapping the candidate gene set with differentially expressed genes (DEGs). Furthermore, potential therapeutic drugs for epilepsy were predicted, offering novel avenues for disease management and treatment.

RESULTS

In total, 6395 DEGs were identified across the six cell clusters. After their intersection, CCRL2, XCL2, CXCR5, CXCL1, and CX3CR1 were pinpointed as key genes. Microglia, T cells, B cells, and macrophages have been emerged as critical cells. Furthermore, CXCL1 was regulated by hsa-miR-570-3p and hsa-miR-532-5p. Notably, CXCR5, CXCL1, and CX3CR1 were associated with 27 drug compounds. This comprehensive study leveraged scRNA-seq and transcriptomic data to elucidate the roles of CCR-related genes in epilepsy. Notably, CCRL2, XCL2, CXCR5, CXCL1,and CX3CR1 were identified as key genes implicated in epilepsy, whereas microglia, T cells, B cells, and macrophages were recognized as critical contributors to the development of epilepsy.

CONCLUSIONS

Regulating the expression of CCRL2, XCL2, CXCR5, CXCL1, and CX3CR1, along with the activity of these immune cells may offer therapeutic potential for the alleviation of epilepsy.

Dynamic changes in lactate-related genes in microglia and their role in immune cell interactions after ischemic stroke

Objectives

This study aims to elucidate the dynamic changes in lactate-related genes (LRGs) in microglia following ischemic stroke (IS) and their associations with immune cells.

Methods

We performed differential expression analysis on bulk-sequencing (GSE30655 and GSE35338) and scRNA-seq data (GSE174574) to identify differentially expressed genes. These genes were intersected with lactate genes from MSigDB to identify post-stroke LRGs. We used t-SNE to visualize LRG distribution across cell types and selected microglia for cell-cell communication, pseudo time, and functional enrichment analyses. These findings were integrated with the GSE225948 scRNA-seq dataset to examine LRG trends in the chronic phase of IS. Finally, CIBERSORT was used to explore immune cell infiltration changes and LRG-immune cell associations post-IS.

Results

Nine LRGs were identified, including Spp1, Per2, Col4a1, Sfxn4, C1qbp, Myc, Apln, Cdo1, and Cav1, with Spp1, C1qbp, and Myc highly expressed in microglia. C1qbp and Myc are crucial in the acute phase, while Spp1 impacts both acute and chronic phases of IS. Microglia subcluster analysis revealed four subclusters (MG0-MG3). Immune cell infiltration analysis showed significant associations between these genes and immune cells.

Conclusion

In summary, Spp1, C1qbp, and Myc are LRGs that are predominantly expressed in microglia and play regulatory roles in various stages of IS.

Stereo-seq of the prefrontal cortex in aging and Alzheimer's disease

Aging increases the risk for Alzheimer's disease (AD), driving pathological changes like amyloid-β (Aβ) buildup, inflammation, and oxidative stress, especially in the prefrontal cortex (PFC). We present the first subcellular-resolution spatial transcriptome atlas of the human prefrontal cortex (PFC), generated with Stereo-seq from six male AD cases at varying neuropathological stages and six age-matched male controls. Our analyses revealed distinct transcriptional alterations across PFC layers, highlighted disruptions in laminar structure, and exposed AD-related shifts in layer-to-layer and cell-cell interactions. Notably, we identified genes highly upregulated in stressed neurons and nearby glial cells, where AD diminished stress-response interactions that promote Aβ clearance. Further, cell-type-specific co-expression analysis highlighted three neuronal modules linked to neuroprotection, protein dephosphorylation, and Aβ regulation, with all modules downregulated as AD progresses. We identified ZNF460 as a transcription factor regulating these modules, offering a potential therapeutic target. In summary, this spatial transcriptome atlas provides valuable insight into AD's molecular mechanisms.

Unraveling Neurological Drug Delivery: Polymeric Nanocarriers for Enhanced Blood-Brain Barrier Penetration

Treating neurological illnesses is challenging because the blood-brain barrier hinders therapeutic medications from reaching the brain. Recent advances in polymeric nanocarriers (PNCs), which improve medication permeability across the blood-brain barrier, may influence therapy strategies for neurological diseases. PNCs have several ways to deliver medications to the nervous system. This review article provides a summary of the parts and manufacturing methods involved in making PNCs. Additionally, it highlights the elements that result in PNCs having enhanced blood-brain barrier penetration. A combination of passive and active targeting strategies is used by PNCs intended to overcome the blood-brain barrier. Among these are micellar structures, nanogels, nanoparticles, cubosomes, and dendrimers. These nanocarriers, which are functionalized with certain ligands that target BBB transporters, enable the direct delivery of drugs to the brain. Mainly, the BBB prevents medications from entering the brain. Understanding the BBB's physiological and anatomical characteristics is necessary to get over this obstacle. Preclinical and clinical research demonstrates the safety and effectiveness of these PNCs, and their potential use in the treatment of neurological illnesses, including brain tumors, Parkinson's disease, and Alzheimer's disease, is discussed. Concerns that PNCs may have about their biocompatibility and possible toxicity are also covered in this review article. This study examines the revolutionary potential of PNCs in CNS drug delivery, potential roadblocks, ongoing research, and future opportunities for PNC design progress. PNCs open the door to more focused and efficient treatment for neurological illnesses by comprehending the subtleties of BBB penetration.

Single-cell analysis uncovers liver susceptibility to pancreatic cancer metastasis via myeloid cell characterization

The liver is the predominant metastatic site for diverse cancers, including pancreatic and colorectal cancers (CRC), etc. The high incidence of hepatic metastasis of pancreatic cancer is an important reason for its refractory and high mortality. Therefore, it is important to understand how metastatic pancreatic cancer affects the hepatic tumor immune microenvironment (TME) in patients. Here, we characterized the TME of liver metastases unique to pancreatic cancer by comparing them with CRC liver metastases. We integrated two single-cell RNA-seq (scRNA-seq) datasets including tumor samples of pancreatic cancer liver metastasis (P-LM), colorectal cancer liver metastasis (C-LM), primary pancreatic cancer (PP), primary colorectal cancer (PC), as well as samples of peripheral blood mono-nuclear cells (PBMC), adjacent normal pancreatic tissues (NPT), to better characterize the heterogeneities of the microenvironment of two kinds of liver metastases. We next performed comparative analysis on cellular compositions between P-LM and C-LM, found that Mph_SPP1, a subset of macrophages associated with angiogenesis and tumor invasion, was more enriched in the P-LM group, indicating this kind of macrophages provide a TME niche more vulnerable for pancreatic cancers. Analysis of the developmental trajectory implied that Mph_SPP1 may progressively be furnished with increased expression of genes regulating endothelium. Cell-cell communications analysis revealed that Mph_SPP1 potentially interacts with endothelial cells in P-LM via FN1/SPP1-ITGAV/ITGB1, implying this macrophage subset may construct an immunosuppressive TME for pancreatic cancer by regulating endothelial cells. We also found that Mph_SPP1 has a prognostic value in pancreatic adenocarcinoma that is not present in colon adenocarcinoma or rectum adenocarcinoma. This study provides a new perspective for understanding the characteristics of the hepatic TME in patients with liver metastatic cancer. And it provides a subset of macrophages specifically associated with the liver metastasis of pancreatic cancer, and its detection and intervention have potential value for preventing the metastasis of pancreatic cancer to the liver.

Exploring molecular mechanisms of diazinon toxicity in HT22 hippocampal neurons through integrated miRNA and mRNA profiling

Diazinon (DZN), a persistent organophosphate insecticide, has been associated with neurotoxic effects, particularly in the hippocampus. However, the specific molecular mechanisms of DZN-induced hippocampal toxicity remain unknown. In this study, we analyzed the mRNA and miRNA expression patterns of HT22 cells following exposure to DZN (125 μM), and the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted subsequently. The integration of miRNA sequencing (miRNA-seq) and mRNA sequencing (mRNA-seq) data identified 33 differentially expressed miRNAs (DEMIs, 15 up-regulated and 18 down-regulated) and 271 differentially expressed mRNAs (DEMs, 69 up-regulated and 202 down-regulated) targeted by the DEMIs. Moreover, the 3 most central mRNAs (ITGAV, FN1, and EGFR) and 7 associated miRNAs (mmu-miR-700-5p, mmu-miR-26a-2-3p, mmu-miR-452-3p, mmu-miR-25-3p, mmu-miR-582-5p, mmu-miR-467a-5p, and mmu-miR-467b-5p) were screened and validated using quantitative real-time PCR. Furthermore, the GO analysis revealed that the identified DEMs were enriched in biological adhesion extracellular matrix, and growth factor binding, while the KEGG analysis suggested that the enriched DEMs were involved in ECM-receptor interaction, mTOR signaling pathway, MAPK signaling pathway, and AMPK signaling pathway. Our results may aid in elucidating the underlying mechanisms associated with DZN-induced hippocampal toxicity and provide valuable insights into the pathogenesis of neurotoxicity triggered by other organophosphorus pesticides.

Investigating causality and shared genetic architecture between body mass index and cognitive function: a genome-wide cross-trait analysis and bi-directional Mendelian randomization study

Background and objectives

Observational studies have established a connection between body mass index (BMI) and an increased risk of cognitive decline. However, a comprehensive investigation into the causal relationships between BMI and cognitive function across diverse age groups, as well as the genetic underpinnings of this relationship, has been notably lacking. This study aims to investigate causality and the shared genetic underpinnings of between BMI and cognitive function by conducting a thorough genome-wide analysis, thereby provide valuable insights for developing personalized intervention strategies to promote cognitive health.

Methods

Genetic associations between BMI and cognitive function were thoroughly investigated through covariate genetic analysis and chained imbalance score regression, utilizing data from genome-wide association studies (GWAS). Bi-directional Mendelian Randomization (MR) was employed to uncover associations and potential functional genes were further scrutinized through Cross-trait meta-analysis and Summary-data-based MR (SMR). Subsequently, a detailed examination of the expression profiles of the identified risk SNPs in tissues and cells was conducted.

Results

The study found a significant negative correlation between BMI and cognitive function (β = -0.16, P = 1.76E-05), suggesting a causal linkage where higher BMI values were predictive of cognitive impairment. We identified 5 genetic loci (rs6809216, rs7187776, rs11713193, rs13096480, and rs13107325) between BMI and cognitive function by cross-trait meta-analysis and 5 gene-tissue pairs were identified by SMR analysis. Moreover, two novel risk genes TUFM and MST1R were shared by both cross-trait analysis and SMR analysis, which had not been observed in previous studies. Furthermore, significant enrichment of single nucleotide polymorphisms (SNPs) at tissue- and cell-specific levels was identified for both BMI and cognitive function, predominantly within the brain.

Conclusion

This study uncovers a causal relationship between BMI and cognitive function, with the discovery of TUFM and MST1R as shared genetic factors associated with both conditions. This novel finding offers new insights into the development of preventative strategies for cognitive decline in obese individuals, and further enhances our understanding of the underlying pathophysiology of these conditions. Furthermore, these findings could serve as a guide for the development of innovative therapeutic approaches to address cognitive decline in obese individuals.

Bibliometric and visual analysis of single-cell multiomics in neurodegenerative disease arrest studies

Background

Neurodegenerative diseases are progressive disorders that severely diminish the quality of life of patients. However, research on neurodegenerative diseases needs to be refined and deepened. Single-cell polyomics is a technique for obtaining transcriptomic, proteomic, and other information from a single cell. In recent years, the heat of single-cell multiomics as an emerging research tool for brain science has gradually increased. Therefore, the aim of this study was to analyze the current status and trends of studies related to the application of single-cell multiomics in neurodegenerative diseases through bibliometrics.

Result

A total of 596 publications were included in the bibliometric analysis. Between 2015 and 2022, the number of publications increased annually, with the total number of citations increasing significantly, exhibiting the fastest rate of growth between 2019 and 2022. The country/region collaboration map shows that the United States has the most publications and cumulative citations, and that China and the United States have the most collaborations. The institutions that produced the greatest number of articles were Harvard Medical School, Skupin, Alexander, and Wiendl. Among the authors, Heinz had the highest output. Mathys, H accumulated the most citations and was the authoritative author in the field. The journal Nature Communications has published the most literature in this field. A keyword analysis reveals that neurodegenerative diseases and lesions (e.g., Alzheimer's disease, amyloid beta) are the core and foundation of the field. Conversely, single-cell multiomics related research (e.g., single-cell RNA sequencing, bioinformatics) and brain nerve cells (e.g., microglia, astrocytes, neural stem cells) are the hot frontiers of this specialty. Among the references, the article "Single-cell transcriptomic analysis of Alzheimer's disease" is the most frequently cited (1,146 citations), and the article "Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq" was the most cited article in the field.

Conclusion

The objective of this study is to employ bibliometric methods to visualize studies related to single-cell multiomics in neurodegenerative diseases. This will enable us to summarize the current state of research and to reveal key trends and emerging hotspots in the field.

Spatial Dissection of the Distinct Cellular Responses to Normal Aging and Alzheimer's Disease in Human Prefrontal Cortex at Single-Nucleus Resolution

Aging significantly elevates the risk for Alzheimer's disease (AD), contributing to the accumulation of AD pathologies, such as amyloid-β (Aβ), inflammation, and oxidative stress. The human prefrontal cortex (PFC) is highly vulnerable to the impacts of both aging and AD. Unveiling and understanding the molecular alterations in PFC associated with normal aging (NA) and AD is essential for elucidating the mechanisms of AD progression and developing novel therapeutics for this devastating disease. In this study, for the first time, we employed a cutting-edge spatial transcriptome platform, STOmics® SpaTial Enhanced Resolution Omics-sequencing (Stereo-seq), to generate the first comprehensive, subcellular resolution spatial transcriptome atlas of the human PFC from six AD cases at various neuropathological stages and six age, sex, and ethnicity matched controls. Our analyses revealed distinct transcriptional alterations across six neocortex layers, highlighted the AD-associated disruptions in laminar architecture, and identified changes in layer-to-layer interactions as AD progresses. Further, throughout the progression from NA to various stages of AD, we discovered specific genes that were significantly upregulated in neurons experiencing high stress and in nearby non-neuronal cells, compared to cells distant from the source of stress. Notably, the cell-cell interactions between the neurons under the high stress and adjacent glial cells that promote Aβ clearance and neuroprotection were diminished in AD in response to stressors compared to NA. Through cell-type specific gene co-expression analysis, we identified three modules in excitatory and inhibitory neurons associated with neuronal protection, protein dephosphorylation, and negative regulation of Aβ plaque formation. These modules negatively correlated with AD progression, indicating a reduced capacity for toxic substance clearance in AD subject samples. Moreover, we have discovered a novel transcription factor, ZNF460, that regulates all three modules, establishing it as a potential new therapeutic target for AD. Overall, utilizing the latest spatial transcriptome platform, our study developed the first transcriptome-wide atlas with subcellular resolution for assessing the molecular alterations in the human PFC due to AD. This atlas sheds light on the potential mechanisms underlying the progression from NA to AD.

Characterization of the Nucleus Pulposus Progenitor Cells via Spatial Transcriptomics

Loss of refreshment in nucleus pulposus (NP) cellularity leads to intervertebral disc (IVD) degeneration. Nevertheless, the cellular sequence of NP cell differentiation remains unclear, although an increasing body of literature has identified markers of NP progenitor cells (NPPCs). Notably, due to their fragility, the physical enrichment of NP-derived cells has limited conventional transcriptomic approaches in multiple studies. To overcome this limitation, a spatially resolved transcriptional atlas of the mouse IVD is generated via the 10x Genomics Visium platform dividing NP spots into two clusters. Based on this, most reported NPPC-markers, including Cathepsin K (Ctsk), are rare and predominantly located within the NP-outer subset. Cell lineage tracing further evidence that a small number of Ctsk-expressing cells generate the entire adult NP tissue. In contrast, Tie2, which has long suggested labeling NPPCs, is actually neither expressed in NP subsets nor labels NPPCs and their descendants in mouse models; consistent with this, an in situ sequencing (ISS) analysis validated the absence of Tie2 in NP tissue. Similarly, no Tie2-cre-mediated labeling of NPPCs is observed in an IVD degenerative mouse model. Altogether, in this study, the first spatial transcriptomic map of the IVD is established, thereby providing a public resource for bone biology.

Autism Spectrum Disorder- and/or Intellectual Disability-Associated Semaphorin-5A Exploits the Mechanism by Which Dock5 Signalosome Molecules Control Cell Shape

Autism spectrum disorder (ASD) is a neurodevelopmental disorder that includes autism, Asperger's syndrome, and pervasive developmental disorder. Individuals with ASD may exhibit difficulties in social interactions, communication challenges, repetitive behaviors, and restricted interests. While genetic mutations in individuals with ASD can either activate or inactivate the activities of the gene product, impacting neuronal morphogenesis and causing symptoms, the underlying mechanism remains to be fully established. Herein, for the first time, we report that genetically conserved Rac1 guanine-nucleotide exchange factor (GEF) Dock5 signalosome molecules control process elongation in the N1E-115 cell line, a model line capable of achieving neuronal morphological changes. The increased elongation phenotypes observed in ASD and intellectual disability (ID)-associated Semaphorin-5A (Sema5A) Arg676-to-Cys [p.R676C] were also mediated by Dock5 signalosome molecules. Indeed, knockdown of Dock5 using clustered regularly interspaced short palindromic repeat (CRISPR)/CasRx-based guide(g)RNA specifically recovered the mutated Sema5A-induced increase in process elongation in cells. Knockdown of Elmo2, an adaptor molecule of Dock5, also exhibited similar recovery. Comparable results were obtained when transfecting the interaction region of Dock5 with Elmo2. The activation of c-Jun N-terminal kinase (JNK), one of the primary signal transduction molecules underlying process elongation, was ameliorated by either their knockdown or transfection. These results suggest that the Dock5 signalosome comprises abnormal signaling involved in the process elongation induced by ASD- and ID-associated Sema5A. These molecules could be added to the list of potential therapeutic target molecules for abnormal neuronal morphogenesis in ASD at the molecular and cellular levels.