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Using joint genomic-transcriptomic analysis of 243 samples, we reveal recurrent patterns of nongenetic evolution in ccRCC not exclusively governed by genetic factors, including T-cell depletion, tumor T-cell receptor coevolution, potential cGAS-STING repression, and increased cell proliferation. These patterns can aid clinical management and guide novel treatment approaches.
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http://dx.doi.org/10.1158/2159-8290.CD-24-0499 | DOI Listing |
Elife
September 2025
Institute of Ecology and Evolution, University of Oregon, Eugene, United States.
In recent decades, genome-wide association studies (GWAS) have been the major approach to understand the biological basis of individual differences in traits and diseases. However, GWAS approaches have limited predictive power to explain individual differences, particularly for complex traits and diseases in which environmental factors play a substantial role in their etiology. Indeed, individual differences persist even in genetically identical individuals, although fully separating genetic and environmental causation is difficult in most organisms.
View Article and Find Full Text PDFJ Exp Bot
August 2025
Florida Museum of Natural History, University of Florida, Gainesville, FL, United States.
Polyploidy or whole-genome duplication (WGD) is a significant evolutionary force. However, the mechanisms governing polyploid genome evolution remain unclear, limited largely by a lack of functional analysis tools in organisms that best exemplify the earliest stages of WGD. Tragopogon (Asteraceae) includes an evolutionary model system for studying the immediate consequences of polyploidy.
View Article and Find Full Text PDFNPJ Syst Biol Appl
August 2025
School of Mathematics, University of Minnesota, Minneapolis, MN, USA.
While cancer has traditionally been considered a genetic disease, mounting evidence indicates an important role for non-genetic (epigenetic) mechanisms. Common anti-cancer drugs have recently been observed to induce the adoption of non-genetic drug-tolerant cell states, thereby accelerating the evolution of drug resistance. This confounds conventional high-dose treatment strategies aimed at maximal tumor reduction, since high doses can simultaneously promote non-genetic resistance.
View Article and Find Full Text PDFBlood Adv
July 2025
The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States.
Non-genetic transcription evolution has been increasingly explored and recognized to drive tumor cell progression and therapeutic resistance. As the regulation hub of transcription machinery, cyclin-dependent kinase 9 (CDK9) is the gatekeeper of RNA polymerase II (Pol II) transcription, and CDK9 dysfunction results in transcriptomic reprogramming and tumor cell progression. We recently reported that the HSP90-MYC-CDK9 network drives therapeutic resistance in mantle cell lymphoma (MCL) through transcriptomic reprogramming.
View Article and Find Full Text PDFMol Cells
September 2025
Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea. Electronic address:
Attaining a complete understanding of the genetic architecture underlying common complex traits is challenging due to the substantial contributions of nongenetic factors and the involvement of numerous influencing genes. Genome-wide association studies (GWAS) have identified novel variants associated with such traits, but our understanding of the molecular genetic mechanisms underlying those associations remains limited. Additionally, variants without significant associations from GWAS can influence gene expression, contributing to individual-level variation in traits.
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