Biology subjects

Ai, S.

Publications and source records attributed to Ai, S..

8 recordsLinked to original sources

bioRxiv2025

NuMA promotes constitutive heterochromatin compaction by stabilizing linker histone H1 on chromatin

Heterochromatin has been widely recognized to exert pivotal functions of silencing specific genes and maintenance of genome stability. However, the mechanisms underlying heterochromatin formation and maintenance remain to be fully elucidated. Here, we discovered that the critical mitotic regulator NuMA, as a nucleoskeleton protein, is required for constitutive heterochromatin organization at the level of nucleosomes in the interphase. Depletion of NuMA results in shortened nucleosome repeat length (NRL), dispersed nucleosome clutches and increased chromatin accessibility in heterochromatin regions. Afterwards, epigenetic maintenance and transcription repression in constitutive heterochromatin are disrupted upon NuMA-depletion, particularly the up-regulated transcription level of the non-coding long terminal repeat (LTR) elements, indicating the crucial roles of NuMA in cell differentiation and senescence. We revealed that such functions of NuMA rely on its interaction with linker histone H1, which stabilizes H1s binding to chromatin and facilitates nucleosome stacking. We provided direct structural evidence of NuMAs stabilization effect at the highest spatial resolution of nucleosomes through in situ cryo-ET. Notably, we found that NuMA oligomerizes into quasi-meshwork in nucleoplasm and highly co-localizes with H1 on the chromatin, providing the organization basis for NuMA as a nucleoskeleton protein in chromatin architecture regulation. Collectively, our findings illuminate the concerted effect of nucleoskeleton protein and linker histone on chromatin compaction at the level of nucleosomes, which unveil a new layer of mechanisms by which nucleoskeleton regulates heterochromatin formation and maintenance.

biophysics↗

bioRxiv2025

Effect of Shufeng Xingbi Therapy on Th1/Th2 immune balance and intestinal flora in rats with allergic rhinitis

ObjectiveTo study the effect of Shufeng Xingbi Therapy (SFXBT) on Th1/Th2 immune balance and intestinal flora in allergic rhinitis (AR) rats. Methods32 SD rats were randomly divided into control group, OVA group, antibiotic + SFXBT group and acetic acid + SFXBT group. Evaluate the AR behavioral score, observe the pathological changes of nasal mucosa with H&E, detect the composition and content of colonic contents with 16S rDNA, the levels of serum IgE, IL-4 and short-chain fatty acid (SCFAs) with ELISA, the mRNA expressions of STAT5, STAT6 and GATA3 in nasal mucosa with RT-qPCR, and the protein expressions of IL-4, STAT5, STAT6 and GATA3 in nasal mucosa with Western Blot. ResultsCompared with the OVA group, the AR behavioral score in the antibiotic + SFXBT group and acetic acid + SFXBT group decreased (P < 0.01), and the pathological changes of nasal mucosa were alleviated. At the door level, the relative abundance of Firmicutes in feces increased significantly, while the relative abundance of Bacteroidetes decreased significantly. At the genus level, The relative abundance of fecal Lactobacillus, Romboutsia, Allobaculum and Dubosiella increased significantly, the levels of serum IgE and IL-4 decreased (P < 0.05), the content of SCFAs increased significantly (P < 0.05), and the expression levels of STAT5, STAT6 and GATA3 mRNA and protein in nasal mucosa decreased significantly (P < 0.05). ConclusionShufeng Xingbi Therapy can significantly improve the inflammatory symptoms of nasal mucosa in AR rats, and its mechanism may be closely related to regulating Th1/Th2 immune balance and intestinal flora.

immunology↗

bioRxiv2024

CCR2 limits inflammatory functions of CD8 TRM cells that impair recognition memory during recovery from WNV encephalitis

Central nervous system (CNS) resident memory CD8 T cells (TRM) that express IFN-{gamma} contribute to neurodegenerative processes, including synapse loss, leading to memory impairments. Here, we show that CCR2 signalling in CD8 TRM that persist within the hippocampus after recovery from CNS infection with West Nile virus (WNV) significantly prevents the development of memory impairments. Using CCR2-deficient mice, we determined that CCR2 expression is not essential for CNS T cell recruitment or virologic control during acute WNV infection. However, transcriptomic analyses of forebrain CCR2+ versus CCR2- CD8 TRM during WNV recovery reveal that CCR2 signalling significantly regulates hippocampal CD8 TRM phenotype and function via extrinsic and intrinsic effects, decreasing the expression of CD103 and granzyme A and IFN-{gamma}, respectively. Consistent with this, WNV-recovered Cd8acreCcr2fl/fl mice exhibit decreased recognition memory. Our findings highlight a neuroprotective role for CCR2 in limiting CD8 T cell-mediated neuroinflammation and cognitive deficits, providing insights into potential therapeutic targets for CNS infections.

immunology↗

bioRxiv2023

Neural mechanism of attention modulation during non-movement decision-making

Decision-making is a cognitive process, in which participants need to attend to relevant information and ignore the irrelevant information. Previous studies have described a set of cortical areas important for attention. It is unclear whether subcortical areas also serve a role. The subthalamic nucleus (STN), a part of basal ganglia, is traditionally considered a critical node in the cortico-basal ganglia-thalamus-cortico network. Given the location of the STN and its widespread connections with cortical and subcortical brain regions, the STN plays an important role in motor and non-motor cognitive processing. We would like to know if STN is also related to fluctuations in attentional task performance, and how the STN interacts with prefrontal cortical regions during the process. We examined neural activities within STN covaried with lapses of attention (defined as behavior error). We found that decreased neural activities in STN were associated with sustained attention. By examining connectivity across STN and various sub-regions of the prefrontal cortex (PFC), we found that decreased connectivity across areas was associated with sustained attention. Our results indicated that decreased STN activities were associated with sustained attention, and the STN-PFC circuit supported this process. Significance StatementAttention is a core internal state variable that governs the allocation of limited resources depending on the task demands in various cognitive processes. If the subcortical area, subthalamic nucleus (STN), related to attentional fluctuations, and how the STN interacted with cortical regions during the process remains unclear. In this study, we examined neural activities within STN, and connectivity between STN and various prefrontal sub-regions during sustained attention and lapses of attention. We found both neural activities within STN and connectivity between STN-PFC circuit decreased during sustained attention. These findings indicated that decreased STN activities were associated with sustained attention, and the STN-PFC circuit supported this process.

neuroscience↗

bioRxiv2021

Single-cell RNA transcriptome analysis reveals CXCL16/CXCR6 as maintenance factors for CNS tissue resident T cells that drive synapse elimination during viral recovery

BackgroundEmerging RNA viruses that target the central nervous system (CNS) lead to cognitive sequelae in survivors. Studies in humans and mice infected with West Nile virus (WNV), a re-emerging RNA virus associated with learning and memory deficits, revealed microglial-mediated synapse elimination within the hippocampus. Moreover, CNS resident memory T (TRM) cells activate microglia, limiting synapse recovery and inducing spatial learning defects in WNV-recovered mice. The signals involved in T cell-microglia interactions are unknown. MethodsHere, we examined the murine WNV-recovered forebrain using single-cell RNA sequencing to identify putative ligand-receptor pairs involved in intercellular communication between T cells and microglia. Clustering and differential gene analyses were followed by protein validation, genetic and antibody-based approaches utilizing an established murine model of WNV recovery in which microglia and complement promote ongoing hippocampal synaptic loss. ResultsProfiling of host transcriptome at 25 days post-infection revealed a shift in forebrain homeostatic microglia to activated subpopulations with transcriptional signatures that have previously been observed in studies of neurodegenerative diseases. Importantly, CXCL16/CXCR6, a chemokine signaling pathway involved in TRM cell biology, was identified as critically regulating CXCR6 expressing CD8+ TRM cell numbers within the WNV-recovered forebrain. We demonstrate that CXCL16 is highly expressed by all myeloid cells, and its unique receptor, CXCR6, is highly expressed on all CD8+ T cells. Using genetic and pharmacological approaches, we demonstrate that CXCL16/CXCR6 is required not only for the maintenance of WNV-specific, CD8 TRM cells in the post-infectious CNS, but also contributes to their expression of TRM cell markers. Moreover, CXCR6+CD8+ T cells are required for glial activation and ongoing synapse elimination. ConclusionsWe provide a comprehensive assessment of the role of CXCL16/CXCR6 as an interaction link between microglia and CD8+ T cells that maintains forebrain TRM cells, microglial and astrocyte activation, and ongoing synapse elimination in virally recovered animals. We also show that therapeutic targeting of CXCL16 during recovery may reduce CNS CD8+ TRM cells.

immunology↗

bioRxiv2021

Targeting interferon-{lambda} signaling promotes recovery from central nervous system autoimmunity

Type III interferons (IFNLs) are newly discovered cytokines, acting at epithelial and other barriers, that exert immunomodulatory functions in addition to their primary roles in antiviral defense. Here we define a role for IFNLs in maintaining autoreactive T cell effector function and limiting recovery in a murine model of multiple sclerosis (MS), experimental autoimmune encephalomyelitis (EAE). Genetic or antibody-based neutralization of the IFNL receptor (IFNLR) resulted in lack of disease maintenance during EAE, with loss of CNS Th1 effector responses and limited axonal injury. Phenotypic effects of IFNLR signaling were traced to increased antigen presenting cell (APC) function, with associated increase in T cell production of IFN{gamma} and GM-CSF. Consistent with this, IFNL levels within lesions of CNS tissues derived from MS patients were elevated compared to MS normal appearing white matter (NAWM). Furthermore, expression of IFNLR was selectively elevated in MS active lesions compared to inactive lesions or NAWM. These findings suggest IFNL signaling as a potential therapeutic target to prevent chronic autoimmune neuroinflammation.

immunology↗

bioRxiv2019

CoBATCH for high-throughput single-cell epigenomic profiling

An efficient, generalizable method for genome-wide mapping of single-cell histone modifications or chromatin-binding proteins is so far lacking. Here we develop CoBATCH, combinatorial barcoding and targeted chromatin release, for single-cell profiling of genomic distribution of chromatin-binding proteins in cell culture and tissue. Protein A in fusion to Tn5 transposase is enriched through specific antibodies to genomic regions and Tn5 generates indexed chromatin fragments ready for the library preparation and sequencing. Importantly, through a combinatorial barcoding strategy, we are able to measure epigenomic features up to tens of thousands single cells per experiment. CoBATCH produces not only high signal-to-noise features, but also ~10,000 reads per cells, allowing for efficiently deciphering epigenetic heterogeneity of cell populations and subtypes and inferring developmental histories. Thus, obviating specialized device, CoBATCH is easily deployable for any laboratories in life science and medicine.

genomics↗

bioRxiv2018

The long noncoding RNA Hand2as orchestrates heart development through regulation of precise expression of HAND2

Rigorous exploration and dissection of potential actions and effects of long noncoding RNA (lncRNA) in animals remain challenging. Here using multiple knockout mouse models and single-cell RNA sequencing, we demonstrate that the divergent lncRNA Hand2as has a key, complex modulatory effect on the expression of its neighboring gene HAND2 and subsequently on heart development and function, largely independent of Hand2as transcription and transcripts. Full-length deletion of Hand2as in mouse causes moderate yet prevalent upregulation of HAND2 in hundreds of cardiac cells, resulting in profound biological consequences, including dysregulated cardiac gene programs, congenital heart defects and perinatal lethality. We propose a cis-functional role for the Hand2as locus in dampening HAND2 expression to restrain cardiomyocyte proliferation, thereby orchestrating a balanced development of cardiac cell lineages. This study highlights the need for complementary genetic and single-cell approaches to delineate the function and primary molecular effects of an lncRNA in animals.\n\nImpact statementThe long noncoding RNA Hand2as critically controls the precise expression of its neighboring gene HAND2, thereby balancing cardiac lineages and expression programs that are essential for heart development and function.

developmental biology↗