An Integrative Transcriptomic Analysis for Identifying Novel Target Genes Corresponding to Severity Spectrum in Spinal Muscular Atrophy

Abstract

Spinal muscular atrophy (SMA) is an inherited neuromuscular disease resulting from a recessive mutation in the SMN1 gene. This disease affects multiple organ systems with varying degrees of severity. Exploration of the molecular pathological changes occurring in different cell types in SMA is crucial for developing new therapies. This study collected 39 human microarray datasets from ArrayExpress and GEO databases to build an integrative transcriptomic analysis for recognizing novel SMA targets. The transcriptomic analysis was conducted through combining weighted correlation network analysis (WGCNA) for gene module detection, gene set enrichment analysis (GSEA) for functional categorization and filtration, and Cytoscape (visual interaction gene network analysis) for target gene identification. Seven novel target genes (Bmp4, Serpine1, Gata6, Ptgs2, Bcl2, IL6 and Cntn1) of SMA were revealed, and are all known in the regulation of TNFα for controlling neural, cardiac and bone development. Sequentially, the differentially expressed patterns of these 7 target genes in mouse tissues (e.g., spinal cord, heart, muscles and bone) were validated in SMA mice of different severities (pre-symptomatic, mildly symptomatic, and severely symptomatic). In severely symptomatic SMA mice, TNFα was up-regulated with attenuation of Bmp4 and increase of Serpine1 and Gata6 (a pathway in neural and cardiac development), but not in pre-symptomatic and mildly symptomatic SMA mice. The severely symptomatic SMA mice also had the elevated levels of Ptgs2 and Bcl2 (a pathway in skeletal development) as well as IL6 and Cntn1 (a pathway in nervous system development). Thus, the 7 genes identified in this study might serve as potential target genes for future investigations of disease pathogenesis and SMA therapy.

Capacitive interdigitated system of high osteoinductive/conductive performance for personalized acting-sensing implants

“…Associations to bone metabolism (confirmed or putative) were also found for the 24 downregulated MVs proteins, including roles in stemness; commitment into the osteo-lineage or other lineages; functions in earlier osteodifferentiation stages; bone growth inhibition; and/or osteoclastogenesis promotion. Examples of downregulated proteins upon Stim are contactin ( CNTN1 ), which regulates TNFα in bone development 81 ; osteolectin ( CLEC11A ), which promotes osteogenesis 82 and is highly enriched in extracellular MSCs vesicles 83 ; PTX3 , an osteoblast differentiation promoter, highly expressed by precursor but not mature osteoblasts 84 ; TIE1 , a tyrosine-protein kinase receptor downregulated in neurotrophin-3-induced osteogenesis 85 ; peroxiredoxin-6 ( PRDX6 ), which inhibits osteogenic differentiation, impairing ALP activity and mineralized nodule formation 86 . Other downregulated proteins reported to decrease bone mass are ALDH1A1 , PGM1 , SERPIND1 , and the collagenolytic metalloendopeptidase MMP14 , all involved in RANKL-mediated osteoclast differentiation (Supplementary Table 2 ).…”

Viral mediated knockdown of GATA6 in SMA iPSC-derived astrocytes prevents motor neuron loss and microglial activation

“…Within these SMN-deficient SMA astrocytes, GATA6 does appear to be a main contributor of aberrant activation, confirming what transcriptome analyses, in vivo studies, and our own previous findings predicted. 32,36 In contrast, overexpressing GATA6 in the Ctrl astrocytes showed trending-but not significant-increases in these transcripts. This suggests that these inflammatory ligands are more tightly regulated by NFκB than GATA6, with GATA6 potentially competing with functional alternative regulators of NFκB in healthy SMN-expressing astrocytes.…”

“…30,31 One potential explanation for this effect is the noted change in astrocyte secreted factors, as SMA astrocytes show reduced GDNF release, abnormal microRNA production, and increased NFκB expression. [30][31][32][33][34] GATA6, a zinc finger transcription factor negatively regulated by SMN and associated with NFkB, 35,36 was accordingly found to be increased in SMA mouse and human samples. 36 Microglial activation has been noted late in the pathology of SMA mouse models, 37 but recent evidence demonstrates microglial phagocytosis of complement-tagged synapses on proprioceptive neurons in the SMA mouse spinal cord, indicating a role during disease progression.…”

“…[30][31][32][33][34] GATA6, a zinc finger transcription factor negatively regulated by SMN and associated with NFkB, 35,36 was accordingly found to be increased in SMA mouse and human samples. 36 Microglial activation has been noted late in the pathology of SMA mouse models, 37 but recent evidence demonstrates microglial phagocytosis of complement-tagged synapses on proprioceptive neurons in the SMA mouse spinal cord, indicating a role during disease progression. 38 It is not yet known how upregulated GATA6 changes the astrocyte phenotype in SMA, nor how this impacts astrocyte interactions with motor neurons and microglia.…”

Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging

“…Recently, high content analysis has been used to characterize multiple neurological cell types and their interactions in vivo and in vitro [25,26], providing insights into cell differentiation and neurological conditions [27][28][29][30][31]. Such work can benefit from a complementary IF method that is not constrained by limitations inherent in traditional antibody-based imaging.…”