Pancreatic Cancer Cell Fraction Estimation in a DNA Sample

Ishihara, Hiroki; Yamashita, Satoshi; Amano, Ryosuke; Kimura, Kenjiro; Hirakawa, Kosei; Ueda, Takako; Murakami, Yoshiki; Tamori, Akihiro; Tanabe, Kazunari; Kawada, Norifumi; Hagihara, Atsushi

doi:10.1159/000491637

Cited by 8 publications

(11 citation statements)

References 33 publications

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“…HOXC-AS3, an antisense transcript of HOXC10, mediates gene transcriptional regulation in the tumorigenesis of GC by binding to YBX1 (Zhang et al, 2018). Genome-wide screening isolated HOXB-AS4 as specifically methylated in pancreatic cancer cells, which was useful to assess a cancer cell fraction in DNA samples (Ishihara et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of DNA Methylation and Long Non-Coding RNA Expression in Gastric Cancer

Song

Guan

2020

Front. Genet.

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Abnormal DNA methylation, an epigenetic modification, has increasingly been linked to the pathogenesis of many human cancers. However, there has been little focus on the DNA methylation patterns of genes encoding long noncoding RNAs (lncRNAs) in gastric cancer (GC). This study comprehensively determined DNA methylation and lncRNA expression profiles in GC through genome-wide analysis. Differentially methylated loci and lncRNAs were identified by integrating multi-omics data. In total, 548 differentially methylated CpG sites in lncRNA promoters and 2,399 differentially expressed lncRNAs were screened that were capable of distinguishing GC from normal tissues. Among them, 22 differentially methylation sites in 17 lncRNAs were inversely related to expression levels. Further analysis of DNA methylation status and gene expression level in GC revealed that three CpG sites (cg01550148, cg22497867, and cg20001829) and two lncRNAs (RP11-366F6.2 and RP5-881L22.5) were significantly associated with GC patient overall survival. Molecular function analysis showed that these abnormally methylated lncRNAs were mainly involved in transcriptional activator activity. Our study identified several lncRNAs regulated by aberrant DNA methylation that have clinical utility as novel prognostic biomarkers in GC. These findings help improve the understanding of methylated patterns of lncRNAs and further our knowledge of the role of epigenetics in cancer development.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of DNA Methylation and Long Non-Coding RNA Expression in Gastric Cancer

Song

Guan

2020

Front. Genet.

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“…LincNORS is a splicered lincRNA generated at MIR193BHG site, this lincRNA fine-tunes cytosterol/steroid biosynthetic by inhibiting the expression of multiple pathway components [ 12 ]. Genome-wide screening found HOXB-AS4 as specifically methylated in pancreatic cancer cells [ 13 ].…”

Section: Discussionmentioning

confidence: 99%

An epithelial-mesenchymal transition-related long non-coding RNA signature to predict overall survival and immune microenvironment in kidney renal clear cell carcinoma

Zhang

Cheng

et al. 2021

Bioengineered

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“…When occurring at a gene promoter, DNA methylation typically represses gene transcription. In human pancreatic cancer cells, CAR was identified among the methylated genes [155]. In HepG2 cells, berberine, an isoquinoline alkaloid, inhibits expression of CAR and of its target genes CYP2B6 and CYP3A4 [156].…”

Section: Dna Methylationmentioning

confidence: 99%

Regulation of CAR and PXR Expression in Health and Disease

Daujat-Chavanieu

Gerbal‐Chaloin

2020

Cells

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Pregnane X receptor (PXR, NR1I2) and constitutive androstane receptor (CAR, NR1I3) are members of the nuclear receptor superfamily that mainly act as ligand-activated transcription factors. Their functions have long been associated with the regulation of drug metabolism and disposition, and it is now well established that they are implicated in physiological and pathological conditions. Considerable efforts have been made to understand the regulation of their activity by their cognate ligand; however, additional regulatory mechanisms, among which the regulation of their expression, modulate their pleiotropic effects. This review summarizes the current knowledge on CAR and PXR expression during development and adult life; tissue distribution; spatial, temporal, and metabolic regulations; as well as in pathological situations, including chronic diseases and cancers. The expression of CAR and PXR is modulated by complex regulatory mechanisms that involve the interplay of transcription factors and also post-transcriptional and epigenetic modifications. Moreover, many environmental stimuli affect CAR and PXR expression through mechanisms that have not been elucidated.

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Pancreatic Cancer Cell Fraction Estimation in a DNA Sample

Cited by 8 publications

References 33 publications

Genome-Wide Identification and Characterization of DNA Methylation and Long Non-Coding RNA Expression in Gastric Cancer

Genome-Wide Identification and Characterization of DNA Methylation and Long Non-Coding RNA Expression in Gastric Cancer

An epithelial-mesenchymal transition-related long non-coding RNA signature to predict overall survival and immune microenvironment in kidney renal clear cell carcinoma

Regulation of CAR and PXR Expression in Health and Disease

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