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Multiomics integration and machine learning reveal prognostic programmed cell death signatures in gastric cancer.
Sci Rep
December 2024
Clinical Teaching Hospital of Medical School, Nanjing Children's Hospital, Nanjing University, Nanjing, 210008, China.
Gastric cancer (GC) is characterized by notable heterogeneity and the impact of molecular subtypes on treatment and prognosis. The role of programmed cell death (PCD) in cellular processes is critical, yet its specific function in GC is underexplored. This study applied multiomics approaches, integrating transcriptomic, epigenetic, and somatic mutation data, with consensus clustering algorithms to classify GC molecular subtypes and assess their biological and immunological features.
View Article and Find Full Text PDFWhole-genome Sequencing Analysis of Bile Tract Cancer Reveals Mutation Characteristics and Potential Biomarkers.
Cancer Genomics Proteomics
December 2024
Division of Surgical Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
Background/aim: Bile tract cancer (BTC) is a malignant tumor with a poor prognosis. Recent studies have reported the heterogeneity of the genomic background and gene alterations in BTC, but its genetic heterogeneity and molecular profiles remain poorly understood. Whole-genome sequencing may enable the identification of novel actionable gene mutations involved in BTC carcinogenesis, malignant progression, and treatment resistance.
View Article and Find Full Text PDFWhole exome-seq and RNA-seq data reveal unique neoantigen profiles in Kenyan breast cancer patients.
Front Oncol
December 2024
Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya.
Background: The immune response against tumors relies on distinguishing between self and non-self, the basis of cancer immunotherapy. Neoantigens from somatic mutations are central to many immunotherapeutic strategies and understanding their landscape in breast cancer is crucial for targeted interventions. We aimed to profile neoantigens in Kenyan breast cancer patients using genomic DNA and total RNA from paired tumor and adjacent non-cancerous tissue samples of 23 patients.
View Article and Find Full Text PDFAlterations in DNA Damage Repair Genes Before and After Neoadjuvant Cisplatin-based Chemotherapy in Muscle-invasive Bladder Cancer.
Eur Urol Open Sci
January 2025
Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
Background And Objective: The role of genetic variants in response to systemic therapy in muscle-invasive bladder cancer (MIBC) is still elusive. We assessed variations in genes involved in DNA damage repair (DDR) before and after cisplatin-based neoadjuvant chemotherapy (NAC) and correlation of alteration patterns with DNA damage and response to therapy.
Methods: Matched tissue from 46 patients with MIBC was investigated via Ion Torrent-based next-generation sequencing using a self-designed panel of 30 DDR genes.
DEMETER DNA demethylase reshapes the global DNA methylation landscape and controls cell identity transition during plant regeneration.
BMC Genomics
December 2024
Department of Biological Sciences, Seoul National University, Seoul, Korea.
Background: Plants possess a high potential for somatic cell reprogramming, enabling the transition from differentiated tissue to pluripotent callus, followed by the formation of de novo shoots during plant regeneration. Despite extensive studies on the molecular network and key genetic factors involved in this process, the underlying epigenetic landscape remains incompletely understood.
Results: Here, we explored the dynamics of the methylome and transcriptome during the two-step plant regeneration process.
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