Biology subjects

Mei, I.

Publications and source records attributed to Mei, I..

8 recordsLinked to original sources

bioRxiv2026

The nuclear membrane protein Samp1 links peripheral genome organization to the myogenic transcriptional program

Samp1 is an inner nuclear membrane protein required for myogenic differentiation and involved in chromatin organization at the nuclear periphery. Here, we investigated whether these functions are connected by studying the effects of Samp1 depletion during C2C12 myogenic differentiation using immunofluorescence microscopy, RNA sequencing, FRIC, and chromosome-positioning analysis. Samp1-depleted cells showed strongly reduced MyHC expression and virtually abrogated multinucleated fiber formation. Although cell-cycle withdrawal was not prevented, the transcriptional program driving differentiation was drastically perturbed, with reduced muscle-associated transcripts and incomplete repression of genes normally downregulated during myogenesis. Samp1 depletion also disrupted peripheral chromatin organization and prevented the accumulation of peripheral heterochromatin typically seen during differentiation. In addition, radial chromosome distribution was disrupted, evidenced by the failure of chromosome 8 to reposition to the nuclear periphery during differentiation. Together, these findings link the requirement for Samp1 in myogenic differentiation to its role in genome organization at the nuclear periphery.

cell biology↗

bioRxiv2025

A linear regression model predicts human brain ageing and reveals differential neuronal biological ageing relevant for Parkinson's disease susceptibility

Biological brain ageing is a major risk factor for neurodegenerative diseases, which are characterized by selective degeneration of particular neuron types. We analyzed the impact of ageing on the transcriptome of neurons in the ventral tegmental area (VTA), substantia nigra pars compacta (SNc) and locus coeruleus (LC), that show differential vulnerabilities to Parkinsons disease. Neurons were isolated from human post mortem brain tissues originating from 48 individuals ranging from 17 to 102 years of age and subjected to Smart-seq2 RNA sequencing. We identified 2,764 genes that were correlated with chronological ageing. This gene expression data was used to develop a feature selection-based Time Traversal algorithm, utilizing functionally grouped gene sets, GO terms, with high predictive accuracy of biological brain ageing. We identified 59 GO terms that can predict biological age using a linear regression model, where leave-one-out cross validation demonstrated a strong correlation between chronological age and predicted biological age (Pearson correlation coefficient = 0.946; adjusted R{superscript 2} = 0.771). The algorithm was validated on five independent datasets with high predictive performance, demonstrating shared ageing features across the human brain. Nonetheless, our analysis also highlights brain region and neuron type specificity in particular ageing features. Resilient neurons showed a weaker association with age-related transcriptional changes, indicating that they age slower than their vulnerable counterparts, thus revealing targets that may be used to slow down ageing and prevent disease development.

neuroscience↗

bioRxiv2025

Reevaluating the Role of Beta2-Microglobulin: New Insights on Selective Vulnerability in ALS Pathology

Amyotrophic lateral sclerosis (ALS) is characterized by the selective loss of motor neurons (MNs). Why these neurons show particular vulnerability in ALS is still debated, and also why certain MNs remain resilient. We investigated the importance of the human leukocyte antigen (HLA) and particularly beta2-microglobulin ({beta}2m) in MN susceptibility to ALS as these molecules have been implicated both in prolonging and shortening disease. RNA-sequencing demonstrated that disease-resistant oculomotor neurons (OMNs) and Onufs MNs had similar {beta}2m and HLA mRNA levels to vulnerable spinal MNs in control tissues. Thus, baseline differences in these transcripts do not explain the differential vulnerabilities of these neurons to disease. Nonetheless, the HLA protein level showed an inverse correlation with spinal MN size, where large MNs, which are lost early in ALS, had low HLA levels. HLA protein levels were also reduced in end-stage ALS patient spinal MNs, while remaining unchanged in OMNs with disease. Spinal MNs uniquely exhibited a significant upregulation of {beta}2m and HLA-C transcripts with disease, likely as a protective compensatory response. Thus, {beta}2m and HLA may relate to vulnerability to ALS. Cross-breeding of {beta}2m knockout mice with SOD1G93A ALS mice resulted in modest transient worsening of functional motor performance, but did not affect life span. There was partial preservation of innervation of particular muscles in SOD1G93A mice lacking {beta}2m, which was insufficient to improve motor behavior. These findings indicate that {beta}2m and HLAs are dynamically regulated in ALS, and may influence MN vulnerability, but they are not major disease modifiers in ALS.

neuroscience↗

bioRxiv2024

Posterior specification of multi-lineage axial assembloids from human pluripotent stem cells.

Elongation of the posterior body axis is driven by multi-potent neuromesodermal progenitors (NMPs), which both self-renew and simultaneously generate neural tube, neural crest, and presomitc mesoderm lineages at successive anterior posterior (A-P) levels. The ensuing diversification of these three NMP lineages is remarkably extensive, and also essential for an immense range of clinically important adult posterior body tissues. Here, we describe a human pluripotent stem cell protocol that successfully specifies authentic NMPs using a cocktail of seven factors (7F). 7F-NMPs express requisite markers, exhibit co-linear HOX activation, and can be purposely specified into each of the three NMP daughter lineages, demonstrating genuine multi-potency. 3D assembly of neural tube, neural crest, and presomitic mesoderm spheroids followed by long-term floating culture derives mature, multi-compartment Posterior Axial Assembloids, or PAXAs. PAXAs constitute a complex heterogeneous tissue containing spinal motor neurons and interneurons, central and peripheral glia, connective tissues, muscle satellite cells and contractile muscle fibres. Together, 7F-NMP and PAXA protocols establish a versatile in vitro platform to model mechanisms of human posterior body axis development, and for the study of a wide range of human diseases.

cell biology↗

bioRxiv2024

Transcriptional modulation unique to vulnerable motor neurons predict ALS across species and SOD gene mutations

Amyotrophic lateral sclerosis (ALS) is characterized by the progressive loss of motor neurons that innervate skeletal muscles. However, certain motor neuron groups including ocular motor neurons, are relatively resilient. To reveal key drivers of resilience versus vulnerability in ALS, we investigate the transcriptional dynamics of four distinct motor neuron populations in SOD1G93A ALS mice using LCM-seq and single molecule fluorescent in situ hybridization. We find that resilient ocular motor neurons regulate few genes in response to disease. Instead, they exhibit high baseline gene expression of neuroprotective factors including En1, Pvalb, Cd63 and Gal, some of which vulnerable motor neurons upregulate during disease. Vulnerable motor neuron groups upregulate both detrimental and regenerative responses to ALS and share pathway activation, indicating that breakdown occurs through similar mechanisms across vulnerable neurons, albeit with distinct timing. Meta-analysis across four rodent mutant SOD1 motor neuron transcriptome datasets identify a shared vulnerability code of 39 genes including e.g Atf4, Nupr1, Ddit3 and Penk, involved in apoptosis, as well as a proregenerative and anti-apoptotic signature consisting of Atf3, Vgf, Ina, Sprr1a, Fgf21, Gap43, Adcyap1, and Mt1. Machine learning using genes upregulated in SOD1G93A spinal motor neuron predicts disease in human stem cell-derived SOD1E100G motor neurons, and shows that dysregulation of VGF, INA, PENK and NTS are strong disease-predictors across species and SOD1 mutations. Our study reveals motor neuron population-specific gene expression and temporal disease-induced regulation that together provide a basis to explain ALS selective vulnerability and resilience and that can be used to predict disease.

neuroscience↗

bioRxiv2023

Human motor neurons are rare and can be transcriptomically divided into known subtypes

We performed single-nucleus RNA-sequencing on adult human spinal cord using a neuronal nuclei enrichment strategy. We obtained transcriptomic profiles of >14,000 spinal neurons, including a small population of motor neurons that shares similarities with mouse motor neurons and can be subdivided into alpha and gamma subtypes. We sought to compare our results to those from a recent study by Yadav and colleagues, which provides a single-nucleus transcriptomic atlas of the human spinal cord. While most neuronal nuclei from both studies share similar features, our results from motor neurons differ substantially. We reanalyzed their RNA-sequencing data and provide evidence that the authors incorrectly identified cholinergic cellular debris as motor neuron nuclei in their dataset, raising doubts about their conclusions regarding motor neurons. Our findings underscore the challenges associated with transcriptionally profiling motor neurons from the spinal cord because of their rarity. We propose specific enrichment strategies and recommend important quality control measures for future transcriptional profiling studies involving human spinal cord tissue and rare cell types.

neuroscience↗

bioRxiv2023

Single cell RNA sequencing in isogenic FUS and TARDBP mutant ALS lines reveals early mitochondrial dysfunction as a common pathway in motor neurons

Mutations in the RNA/DNA-binding proteins FUS and TDP-43 cause the fatal disease amyotrophic lateral sclerosis (ALS). The precise mechanisms behind the selective motor neuron degeneration remain unclear and it is uncertain if ALS-causative mutations trigger motor neuron death through shared or distinct pathogenic pathways. To address these two questions, we performed single-cell RNA sequencing across neuron types derived from isogenic induced pluripotent stem cell lines, harbouring FUS P525L, FUS R495X, TARDBP M337V mutations or FUS knockout. The mutations elicited 5- to 15-fold greater transcriptional responses in motor neurons than interneurons. Approximately 20% of transcripts uniquely dysregulated in motor neurons were shared across FUS mutations, with half being driven by FUS gain-of-function. Among these, a majority pointed towards mitochondrial impairments, with attenuated pathways shared with the TARDBP M337V mutation. Meta-analysis demonstrated convergence on mitochondrial dysfunction with C9orf72-ALS patient-derived motor neurons. We observed impaired mitochondrial motility across ALS motor axons, even in isogenic FUS R244C motor neurons, which retain FUS in the nucleus, demonstrating shared toxic gain-of-function mechanisms across FUS- and TARDBP-ALS, uncoupled from protein mislocalization. These early signs of mitochondrial dysfunction unique to motor neurons could have profound implications for their survival and represent promising therapeutic targets across multiple ALS forms.

neuroscience↗

bioRxiv2022

Expression of substance P, NPY and their Receptors Is Altered in Major Depression

BACKGROUNDMajor depressive disorder (MDD) is a serious disease and a burden to patients, families and society. Rodent experiments and human studies suggest that several neuropeptide systems, including substance P(SP)/tachykinin, neuropeptide Y(NPY) and their G protein-coupled receptors are involved in mood regulation. METHODSWe assessed the transcript levels (qPCR) of SP/tachykinin and NPY systems in five regions from postmortem brains of male and female depressed subjects who committed suicide (DSS) and controls: dorsolateral prefrontal cortex (DLPFC), anterior cingulate cortex (ACC), the dorsal raphe nucleus (DRN), locus coeruleus (LC) and medullary raphe nuclei (MRN). We also analysed human LC neurons isolated using LCM with Smart-seq2 RNA sequencing. RESULTSTranscripts for all nine members were detected in male and female controls with marked regional variations of the raw CT values and with the highest levels for several tachykinin and tachykinin receptor transcripts in the DRN and for NPY and NPYR transcripts in the PFC regions. Significant sex differences for controls were recorded only in the DRN (NPYR2 >in females) and LC (TAC3 and NPY >in females). Elevated expression in DSS was recorded in (i) DLPFC for SP, TAC and TAC3 in females, SP in males, and NPYR1 in both sexes; and (ii) LC for all tachykinin family transcripts in females, SP, TACR1 and TACR3 in males, NPY in both sexes, and NPYR1 in males. CONCLUSIONSThe selective perturbation of neuropeptide systems in MDD patients may assist in the search for novel treatment strategies for subjects afflicted by this grave disorder.

neuroscience↗