It holds great promises to precisely stratify cancer subtypes to improve cancer diagnosis, therapy and prognosis. In the past, the diagnosis of pathological subtypes mainly relied on hematoxylin-eosin staining and immunohistochemistry. With the development of sequencing technologies, genotype and phenotype analysis of individuals has become possible and precision medicine is on the rise in healthcare. As different tumor subtypes have different cell-of-origin, risk factors and clinical phenotypes, they generate unique combinations of mutation types, termed "Mutational Signatures". Herein, using the exome sequencing data from The Cancer Genome Atlas (TCGA), we evaluated the utility of mutational landscape for differentiating cell-of-origin within three common cancers (kidney, lung and esophageal cancers). We found that mutational signatures predicted histological subtypes of kidney cancers, clear cell renal cell carcinoma (KIRC) vs. chromophobe renal cell carcinoma (KICH), which had different cell-of-origin, with 100% accuracy (95% CI: 0.93-1.00). The mutational signatures also predicted histological subtypes of lung cancers (lung adenocarcinoma vs. lung squamous cell carcinoma) and esophageal cancers (esophageal adenocarcinoma vs. esophageal squamous cell carcinoma) with 78% (95% CI: 0.66-0.86) and 84% accuracy (95% CI: 0.60-0.97), respectively. Collectively, mutational signatures-based subtyping is good at pathological classification, personalized diagnosis, especially early detection for common cancers.
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http://dx.doi.org/10.16288/j.yczz.18-208 | DOI Listing |
Funct Integr Genomics
January 2025
Institute of Infectious Diseases, Guangdong Province, Guangzhou Eighth People's Hospital, Guangzhou Medical University, 8 Huaying Road, Baiyun District, Guangzhou, 510440, China.
Hepatocellular carcinoma (HCC) remains a malignant and life-threatening tumor with an extremely poor prognosis, posing a significant global health challenge. Despite the continuous emergence of novel therapeutic agents, patients exhibit substantial heterogeneity in their responses to anti-tumor drugs and overall prognosis. The pentose phosphate pathway (PPP) is highly activated in various tumor cells and plays a pivotal role in tumor metabolic reprogramming.
View Article and Find Full Text PDFClin Exp Med
January 2025
Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
Lung cancer is one of the major causes of cancer morbidity and mortality. Subtyping of non-small cell lung cancer is necessary owing to different treatment options. This study is to evaluate the value of immunohistochemical expression of glypican-1 in the diagnosis of lung squamous cell carcinoma (SCC).
View Article and Find Full Text PDFFunct Integr Genomics
January 2025
School of Medical Technology, Tianjin Medical University, Tianjin, 300203, China.
Clear cell renal cell carcinoma (ccRCC) is a highly malignant tumor characterized by a significant propensity for recurrence and metastasis. DNA methylation has emerged as a critical epigenetic mechanism with substantial utility in cancer diagnosis. In this study, multi-omics data were utilized to investigate the target genes regulated by the transcription factor MYC-associated zinc finger protein (MAZ) in ccRCC, leading to the identification of thymidine phosphorylase (TYMP) as a gene with notably elevated expression in ccRCC.
View Article and Find Full Text PDFOphthalmology
January 2025
Cornea and External Disease, Department of Ophthalmology, Morsani College of Medicine, University of South Florida, Tampa, Florida; Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, Florida.
Nucleic Acids Res
January 2025
Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania.
The expansion of single-cell analytical techniques has empowered the exploration of diverse biological questions at the individual cells. Droplet-based single-cell RNA sequencing (scRNA-seq) methods have been particularly widely used due to their high-throughput capabilities and small reaction volumes. While commercial systems have contributed to the widespread adoption of droplet-based scRNA-seq, their relatively high cost limits the ability to profile large numbers of cells and samples.
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