Gene chip methods are applied to the study of gene expression. The differentially expressed genes in different specimens may be detected with parallel analysis by gene chip, which has greatly improved the traditional experiments in that only a single or several gene expressions need to be observed for each test, thereby speeding up the identification of differentially expressed genes and the construction of differential expression profiles. Many studies have applied this technology for Barrett's metaplasia and adenocarcinoma, and identified a number of candidate genes useful as biomarkers in cancer staging, prediction of recurrence, prognosis and treatment selection. This review described the gene expression profile and molecular changes related to Barrett's metaplasia and adenocarcinoma of the esophagus, with emphasis on its prognostic value and possibilities for targeted therapy in a clinical setting.
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http://dx.doi.org/10.1111/j.1751-2980.2008.00324.x | DOI Listing |
PLoS Pathog
January 2025
Department of Cancer and Genomic Sciences, College of Medicine and Health, University of Birmingham, Birmingham, United Kingdom.
Upon infection, human papillomavirus (HPV) manipulates host cell gene expression to create an environment that is supportive of a productive and persistent infection. The virus-induced changes to the host cell's transcriptome are thought to contribute to carcinogenesis. Here, we show by RNA-sequencing that oncogenic HPV18 episome replication in primary human foreskin keratinocytes (HFKs) drives host transcriptional changes that are consistent between multiple HFK donors.
View Article and Find Full Text PDFPLoS One
January 2025
Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam bin Abdulaziz University, Al-kharj, Saudi Arabia.
The Tapetum Determinant 1 (TPD1) family proteins are known to play a crucial role in the regulation of reproduction in plants, including Cenchrus americanus (pearl millet). However, members of TPD1 family proteins have not been fully identified. The current study aims to identify and characterize the TPD1 family proteins in Cenchrus americanus (L.
View Article and Find Full Text PDFJ Cell Mol Med
January 2025
Department of Cardiology, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province, China.
It is critical to appreciate the role of the tumour-associated microenvironment (TME) in developing strategies for the effective therapy of cancer, as it is an important factor that determines the evolution and treatment response of tumours. This work combines machine learning and single-cell RNA sequencing (scRNA-seq) to explore the glioma tumour microenvironment's TME. With the help of genome-wide association studies (GWAS) and Mendelian randomization (MR), we found genetic variants associated with TME elements that affect cancer and cardiovascular disease outcomes.
View Article and Find Full Text PDFPlant Genome
March 2025
Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy.
Wheat breeders are constantly looking for genes and alleles that increase grain yield. One key strategy is finding new genetic resources in the wild and domesticated gene pools of related species with genes affecting grain size. This study explored a natural population of Triticum turgidum (L.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
Genome-wide identification of binding profiles for DNA-binding proteins from the limited number of intracellular pathogens in infection studies is crucial for understanding virulence and cellular processes but remains challenging, as the current ChIP-exo is designed for high-input bacterial cells (>1010). Here, we developed an optimized ChIP-mini method, a low-input ChIP-exo utilizing a 5,000-fold reduced number of initial bacterial cells and an analysis pipeline, to identify genome-wide binding dynamics of DNA-binding proteins in host-infected pathogens. Applying ChIP-mini to intracellular Salmonella Typhimurium, we identified 642 and 1,837 binding sites of H-NS and RpoD, respectively, elucidating changes in their binding position and binding intensity during infection.
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