CASZ1 induces skeletal muscle and rhabdomyosarcoma differentiation through a feed-forward loop with MYOD and MYOG

Liu, Zhihui; Zhang, Xiyuan; Lei, Haiyan; Lam, Norris; Carter, Sakereh; Yockey, Oliver; Xu, Max; Mendoza, Arnulfo; Hernandez, Edjay Ralph; Wei, Jun S.; Khan, Javed; Yohe, Marielle E.; Shern, Jack F.; Thiele, Carol J.

doi:10.1038/s41467-020-14684-4

Cited by 40 publications

(55 citation statements)

References 54 publications

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“…By sequencing open chromatin, ATAC-seq can be used to study carcinogenesis. Transcription factors can affect the epigenetic modification of genes, thereby regulating gene expression, leading to the occurrence of cancer (13). People with specific gene mutations must avoid exposure to some environmental factors to reduce their risk of cancer.…”

Section: Discussionmentioning

confidence: 99%

“…Liu et al used ATAC-seq to reveal that CASZ1 regulates skeletal muscle genes by chromatin accessibility. The loss of CASZ1 activity impairs embryonal rhabdomyosarcoma differentiation and contributes to tumorigenesis (13). ATACseq analysis demonstrated that hypoxia treatment significantly reduced chromatin accessibility at RAR/RXR binding sites, while acetate supplementation restored chromatin accessibility and promoted tumor cell differentiation (14).…”

Section: Introductionmentioning

confidence: 99%

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Bibliometric Analysis of ATAC-Seq and Its Use in Cancer Biology via Nucleic Acid Detection

et al. 2020

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Assay for transposase-accessible chromatin using sequencing (ATAC-seq) is associated with significant progress in biological research and has attracted increasing attention. However, the impact of ATAC-seq on cancer biology has not been objectively analyzed. We categorized 440 ATAC-seq publications according to the publication date, type, field, and country. R 3.6.2 was used to analyze the distribution of research fields. VOSviewer was used for country co-authorship and author co-authorship analyses, and GraphPad Prism 8 was used for correlation analyses of the factors that may affect the number of articles published in different countries. We found that ATAC-seq plays roles in carcinogenesis, anticancer immunity, targeted therapy, and metastasis risk predictions and is most frequently used in studies of leukemia among all types of cancer. We found a significantly strong correlation between the top 10 countries in terms of the number of publications and the gross expenditure on research and development (R&D), the number of universities, and the number of researchers. At present, ATAC-seq technology is undergoing a period of rapid development, making it inseparable from the emphasis and investment in scientific research by many countries. Collectively, ATAC-seq has advantages in the study of the cancer mechanisms because it can detect nucleic acids and thus has good application prospects in the field of cancer, especially in leukemia studies. As a country's economic strength increases and the emphasis on scientific research deepens, ATAC-seq will definitely play a more significant role in the field of cancer biology.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Bibliometric Analysis of ATAC-Seq and Its Use in Cancer Biology via Nucleic Acid Detection

et al. 2020

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“…ATAC-seq was performed as previously described 69,70 . Approximately, 50,000 KCNR cells were pelleted and the Tn5 transposition reaction was performed with the Nextera kit (Illumina), according to the manufacturer’s protocol.…”

Section: Methodsmentioning

confidence: 99%

Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation

Gryder¹,

Banerjee²,

Bagchi³

et al. 2020

Preprint

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Temporal regulation of super-enhancer (SE) driven lineage specific transcription factors (TFs) underlies normal developmental programs. Neuroblastoma (NB) arises from an inability of sympathoadrenal progenitors to exit a self-renewal program and terminally differentiate. To identify critical SEs driving TF regulators of NB, we utilized NB cells in which all-trans retinoic acid (ATRA) induces growth arrest and differentiation. H3K27ac ChIP-seq paired with RNA-seq over a time course of ATRA treatment revealed SEs moving in a coordinated manner with four distinct temporal patterns (clusters). SEs that decreased with ATRA linked to 24 TFs involved in stem cell development/specialization (MYCN, GATA3, SOX11) along with LMO1, a transcriptional coregulator and oncogene identified via a genome-wide association study (GWAS) of NB. H3K27ac levels and GATA3 binding at the NB-associated rs2168101 site of the LMO1 SE were reduced with ATRA treatment, resulting in 1.46 fold decreased LMO1 expression. The SOX11 SE was lost coincident with a 50% decrease in mRNA after 8 days of ATRA treatment. CRISPR-Cas9 screening and siRNA inhibition showed a dependency on SOX11 for cell growth in NB cell lines. Silencing of the SOX11 SE using dCAS9-KRAB targeted guides caused a 40% decrease in SOX11 mRNA and inhibited cell growth. Three other TF SE clusters had sequential waves of activation at 2, 4 and 8 days of ATRA treatment and involved TFs regulating neural development (GATA2 and SOX4). Silencing of the gained SOX4 SE using dCAS9-KRAB targeting, caused a 50% decrease in SOX4 expression and attenuated expression of ATRA-induced differentiation genes. Our study has identified candidate oncogenic lineage drivers of NB self-renewal and TFs critical for implementing a differentiation program.

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“…Except that, p38 signaling pathway and wnt pathway were both proved to be responsible for the process [27,28]. As for the myogenic genes, MRFs, myoD, myoG, etc [29,30] were all reported as myogenic related genes.…”

Section: Discussionmentioning

confidence: 95%

Identification of key pathways and hub genes in the myogenic process of pluripotent stem cell: A bioinformatics study

Fei¹,

Liu²,

Zhang³

et al. 2020

Preprint

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Purpose: The study aims to determine the process of myoginc differentiation in human pluripotent stem cells and to figure out that the key pathways and hub genes in the process, which do helpful for the further research of muscular regeneration.Method: Three gene expression profiles, GSE131125, GSE148994, GSE149055, about the comparisons of pluripotent stem cells and myogenic stem cells from the Gene Expression Omnibus (GEO) data base. Common differentially expressed genes (DEGs) were obtained and for the further analysis as Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and GSEA analysis and protein‑protein interaction (PPI) network. In vitro cell research to verify the hub genes and key pathways.Result:824 DEGs were co-expressed in the three GSEs. 19 hub genes were identified from the PPI network. The GO and KEGG pathway analysis were performed to determine the functions of DEGs. GSEA analysis indicated the differentiated cells were enriched in muscle cell development and myogenesis.Conclusion: Our research revealed the main hub genes and modules in the myogeinc process of stem cells which contribute to further study about the molecular mechanism of myogenesis regeneration. Paving a way for more accurate treatment for muscle dysfunction.

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CASZ1 induces skeletal muscle and rhabdomyosarcoma differentiation through a feed-forward loop with MYOD and MYOG

Cited by 40 publications

References 54 publications

Bibliometric Analysis of ATAC-Seq and Its Use in Cancer Biology via Nucleic Acid Detection

Bibliometric Analysis of ATAC-Seq and Its Use in Cancer Biology via Nucleic Acid Detection

Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation

Identification of key pathways and hub genes in the myogenic process of pluripotent stem cell: A bioinformatics study

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