Project description:Esophageal squamous cell carcinoma (ESCC) is characterized as a metabolic disorder characterized by lipid metabolic reprogramming. To investigate the regional characteristics of ESCC patients in Xinjiang Province, China, and lipid metabolism, in this study, we described the characteristics of the serum lipid composition in Kazakh ESCC patients by performing an integrated analysis of the transcriptome and lipidomic data. Serum samples from 30 Kazakh ESCC patients and 30 healthy individuals were subjected to targeted lipid metabolomics analysis via UPLC‒MS/MS, while 3 tumor samples and matched adjacent normal tissues from 30 ESCC patients were subjected to transcriptome analysis. Compared with those in the healthy group, we observed obvious changes in the serum lipid subclass content, chain length and unsaturation in the ESCC patients. Integrated lipidomic and transcriptomic analyses revealed that unsaturated fatty acid biosynthesis, fatty acid metabolism, lipid degradation, cholesterol metabolism and the AMPK signaling pathway were enriched in tumor tissues. In addition, RT–qPCR results demonstrated that genes closely related to these pathways were differentially expressed between the ESCC group and the healthy control group. Considering the key role of AMPK in lipid metabolism, we conducted a targeted lipid metabolomics analysis on AMPK-knockdown esophageal cancer cells by UPLC‒MS/MS. These findings suggested that AMPK might be correlated with lipid metabolism in Kazakh ESCC patients, identifying potential therapeutic targets of AMPK and other lipid metabolism-related markers against the progression of ESCC.
2024-01-17 | GSE253171 | GEO
Project description:Whole exome sequences of kazakh individuals
| PRJNA559979 | ENA
Project description:Whole genome sequencing of Kazakh healthy individuals
Project description:In this study, two accessions of Arabidopsis thaliana (Columbia and Landsberg erecta) were crossed and tetrads were obtained using thanks to the the quartet mutation, which keeps the 4 haploid pollen grains from a single meiosis attached together. By fertilising a plant (of ecotype Columbia) with a single tetrad, then selecting seeds from siliques containing exactly four seeds and finally sequencing the 4 developed plants, we can access the complete history of meiotic recombination events occurring in a single male meiosis. Comparison of the genomic sequences (WGS) of the 4 plants in a tetrad makes it possible to identify meiotic COs and NCOS events in each tetrad thanks to the numerous polymorphisms specific to each of the parental genomes. The analysis of the WGS tetrads data consists of genotyping a series of SNV markers (differentiating Columbia and Landsberg) positioned on the five chromosomes for the 4 (M1, M2, M3, M4) individuals of a tetrad, representing the 4 chromatids of each chromosomes. A total of 20 tetrads, the F1 and the two parental accessions Columbia and Landsberg erecta were sequenced.
Project description:Investigate long non-coding RNA (lncRNA) expression characteristics in the peripheral blood lymphocytes of Xinjiang Kazakh people with essential hypertension.
Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).
