Publications by authors named "Miho Oka"
Article Synopsis
- The study investigates the early stages of tumor development, specifically focusing on lung adenocarcinomas like adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma.
- Researchers conducted comprehensive genomic analysis on 76 lung cancer samples, combining sequencing data with transcriptomic and epigenomic information.
- Findings indicate that very early-stage tumors have minimal somatic mutations, primarily in key driver mutations, leading to copy number changes and global DNA hypomethylation as the disease progresses, particularly in Noguchi type B tumors.
Atrial fibrillation (AF) is the most frequent persistent arrhythmia. Many genes have been reported as a genetic background for AF. However, most transcriptome analyses of AF are limited to the atrial samples and have not been evaluated by multiple cardiac regions.
View Article and Find Full Text PDFComparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans.
Biomolecules
June 2022
The heart is a significant organ in mammalian life, and the heartbeat mechanism has been an essential focus of science. However, few studies have focused on species differences. Accordingly, challenges remain in studying genes that have universal functions across species and genes that determine species differences.
View Article and Find Full Text PDFArticle Synopsis
- Researchers analyzed non-small cell lung cancer from 20 Japanese patients using a combination of short and long read sequencing, achieving long phased DNA segments with high accuracy.
- The study found that mutations in cancer genomes are not evenly spread across both chromosome copies, with large chromosomal rearrangements occurring more frequently on one chromosome, particularly in EGFR mutation-positive lung adenocarcinomas.
- The integration of epigenomic and transcriptomic data indicated that the two copies of chromosomes can have different transcriptional and epigenetic states, highlighting the role of distinct chromosomal backgrounds in cancer development.
RNA-seq using long-read sequencing, such as nanopore and SMRT (Single Molecule, Real-Time) sequencing, enabled the identification of the full-length structure of RNA molecules. Several tools for long-read RNA-seq were developed recently. In this section, we introduce an analytical pipeline of long-read RNA-seq for isoform identification and the estimation of expression levels using minimap2, TranscriptClean, and TALON.
View Article and Find Full Text PDFArticle Synopsis
- - The study utilized long-read sequencing to catalog aberrant splicing isoforms in non-small-cell lung cancers, identifying 2021 novel isoforms and potential neoantigens.
- - Researchers discovered that removing certain factors increased the levels of these aberrant transcripts, and they validated some isoforms through proteome analysis and T-cell response tests.
- - Findings show that long-read sequencing is crucial for accurately identifying these isoforms, which could have implications for cancer diagnosis and treatment based on the data from The Cancer Genome Atlas.
Lysosomes are acidic organelles responsible for degrading both exogenous and endogenous materials. The small GTPase Arl8 localizes primarily to lysosomes and is involved in lysosomal function. In the present study, using Arl8b gene-trapped mutant (Arl8b ) mice, we show that Arl8b is required for the development of dorsal structures of the neural tube, including the thalamus and hippocampus.
View Article and Find Full Text PDFThe small GTPase Arl8b localizes primarily to lysosomes and is involved in lysosomal motility and fusion. Here, we show that Arl8b is required for lysosomal degradation of maternal proteins in the visceral yolk sac endoderm (VYSE), an apical cell layer of the visceral yolk sac, of mouse embryos. The VYSE actively takes up maternal materials from uterine fluid and degrades them in lysosomes to provide breakdown products to the embryo.
View Article and Find Full Text PDF