Comparative transcriptomic profiling of peripheral efferent and afferent nerve fibres at different developmental stages in mice

Wang, Hongkui; Zhou, Youlang; Ma, Cong; Zhang, Li; Gu, Xiaosong; Tang, Xin

doi:10.1038/s41598-018-30463-0

Cited by 3 publications

(2 citation statements)

References 53 publications

(58 reference statements)

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“…In this developmental switch, transcription regulators involved in MN differentiation at the early developmental stage are downregulated, while genes participating in synaptogenesis and neuronal functions are upregulated. The expression changes of similar or the same gene sets have been reported in MN maturation in other in vivo model systems ( Goulding, 2009 ; Moreno and Ribera, 2010 ; Stifani, 2014 ; Wang et al, 2018 ), further demonstrating the high quality and identity of iPSC-MNs prepared with this coculture system.…”

Section: Discussionsupporting

confidence: 70%

Assembling a Coculture System to Prepare Highly Pure Induced Pluripotent Stem Cell-Derived Neurons at Late Maturation Stages

Akter,

Sepehrimanesh,

et al. 2024

eNeuro

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Generation of human induced pluripotent stem cell (hiPSC)-derived motor neurons (MNs) offers an unprecedented approach to modeling movement disorders such as dystonia and amyotrophic lateral sclerosis. However, achieving survival poses a significant challenge when culturing induced MNs, especially when aiming to reach late maturation stages. Utilizing hiPSC-derived motor neurons and primary mouse astrocytes, we assembled two types of coculture systems: direct coculturing of neurons with astrocytes, and indirect coculture using culture inserts that physically separate neurons and astrocytes. Both systems significantly enhance neuron survival. Compared with these two systems, no significant differences in neurodevelopment, maturation, and survival within 3 weeks, allowing to prepare neurons at maturation stages. Using the indirect coculture system, we obtained highly pure MNs at the late mature stage from hiPSCs. Transcriptomic studies of hiPSC-derived MNs showed a typical neurodevelopmental switch in gene expression from the early immature stage to late maturation stages. Mature genes associated with neurodevelopment and synaptogenesis are highly enriched in MNs at late stages, demonstrating that these neurons achieve maturation. This study introduces a novel tool for the preparation of highly pure hiPSC-derived neurons, enabling the determination of neurological disease pathogenesis in neurons at late disease onset stages through biochemical approaches, which typically necessitate highly pure neurons. This advancement is particularly significant in modeling age-related neurodegeneration.Significance StatementAchieving survival poses a significant challenge for long-term neural cell cultures. Utilizing hiPSC-derived motor neurons and primary mouse astrocytes, we established an indirect coculture system using culture inserts that physically separate neurons and astrocytes, thereby facilitating neuronal maturation. Transcriptomic studies revealed the typical neurodevelopmental switch in gene expression from the early immature stage to late maturation stages, indicating the high quality and maturation of neurons prepared with culture inserts. This study introduces a novel tool for the preparation of highly pure hiPSC-derived neurons, enabling the determination of neurological disease pathogenesis in neurons at late disease onset stages through biochemical approaches, which typically necessitate highly pure neurons. This advancement is particularly significant in modeling age-related neurodegeneration.

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Section: Discussionsupporting

confidence: 70%

Assembling a Coculture System to Prepare Highly Pure Induced Pluripotent Stem Cell-Derived Neurons at Late Maturation Stages

Akter,

Sepehrimanesh,

et al. 2024

eNeuro

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“…Ingenuity pathway analysis (IPA) (http://ingenuity.com/ index.html, Ingenuity Systems, Redwood City, CA) online software was used to identify canonical pathways and gene networks. The Ingenuity Pathway Knowledge Base was used for a deep analysis of molecular networks and revealed interactions among DEGs (FC >2, P<0.01) (34,35). The Build Connect tool in IPA was used to create connections between molecules, with direct (solid line) or indirect (dot line) relationships shown.…”

Section: Regulatory Network Analysismentioning

confidence: 99%

RNA sequencing (RNA-seq) analysis of gene expression provides new insights into hindlimb unloading-induced skeletal muscle atrophy

Cui¹,

Yang²,

Gu³

et al. 2020

Ann Transl Med

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Background: Weightlessness-induced skeletal muscle atrophy, accompanied by complex biochemical and physiological changes, has potentially damaged consequences. However, there is still an insufficient effective strategy to treat skeletal muscle atrophy. Therefore, exploring the molecular mechanisms regulating skeletal muscle atrophy and effective protection is necessary.Methods: RNA sequencing (RNA-seq) analysis was used to detect differentially expressed genes (DEGs) in the soleus muscle at 12, 24, 36 hours, three days, and seven days after hindlimb unloading in rats. Pearson correlation heatmaps and principal component analysis (PCA) were applied to analyze DEGs' expression profiles. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for cluster analysis of DEGs. Ingenuity pathway analysis (IPA) was used to analyze specific biological processes further.

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Cell type mapping of inflammatory muscle diseases highlights selective myofiber vulnerability in inclusion body myositis

Wischnewski,

Thäwel,

Ikenaga

et al. 2024

Nat Aging

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Inclusion body myositis (IBM) is the most prevalent inflammatory muscle disease in older adults with no effective therapy available. In contrast to other inflammatory myopathies such as subacute, immune-mediated necrotizing myopathy (IMNM), IBM follows a chronic disease course with both inflammatory and degenerative features of pathology. Moreover, causal factors and molecular drivers of IBM progression are largely unknown. Therefore, we paired single-nucleus RNA sequencing with spatial transcriptomics from patient muscle biopsies to map cell-type-specific drivers underlying IBM pathogenesis compared with IMNM muscles and noninflammatory skeletal muscle samples. In IBM muscles, we observed a selective loss of type 2 myonuclei paralleled by increased levels of cytotoxic T and conventional type 1 dendritic cells. IBM myofibers were characterized by either upregulation of cell stress markers featuring GADD45A and NORAD or protein degradation markers including RNF7 associated with p62 aggregates. GADD45A upregulation was preferentially seen in type 2A myofibers associated with severe tissue inflammation. We also noted IBM-specific upregulation of ACHE encoding acetylcholinesterase, which can be regulated by NORAD activity and result in functional denervation of myofibers. Our results provide promising insights into possible mechanisms of myofiber degeneration in IBM and suggest a selective type 2 fiber vulnerability linked to genomic stress and denervation pathways.

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Comparative transcriptomic profiling of peripheral efferent and afferent nerve fibres at different developmental stages in mice

Cited by 3 publications

References 53 publications

Assembling a Coculture System to Prepare Highly Pure Induced Pluripotent Stem Cell-Derived Neurons at Late Maturation Stages

Assembling a Coculture System to Prepare Highly Pure Induced Pluripotent Stem Cell-Derived Neurons at Late Maturation Stages

RNA sequencing (RNA-seq) analysis of gene expression provides new insights into hindlimb unloading-induced skeletal muscle atrophy

Cell type mapping of inflammatory muscle diseases highlights selective myofiber vulnerability in inclusion body myositis

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