Genetic intra-tumour heterogeneity fuels clonal evolution, but our understanding of clinically relevant clonal dynamics remain limited. We investigated spatial and temporal features of clonal diversification in clear cell renal cell carcinoma through a combination of modelling and real tumour analysis. We observe that the mode of tumour growth, surface or volume, impacts the extent of subclonal diversification, enabling interpretation of clonal diversity in patient tumours. Specific patterns of proliferation and necrosis explain clonal expansion and emergence of parallel evolution and microdiversity in tumours. In silico time-course studies reveal the appearance of budding structures before detectable subclonal diversification. Intriguingly, we observe radiological evidence of budding structures in early-stage clear cell renal cell carcinoma, indicating that future clonal evolution may be predictable from imaging. Our findings offer a window into the temporal and spatial features of clinically relevant clonal evolution.
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http://dx.doi.org/10.1038/s41559-021-01586-x | DOI Listing |
mSystems
January 2025
Institute for Infection Prevention and Control, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
The surveillance of mobile genetic elements facilitating the spread of antimicrobial resistance genes has been challenging. Here, we tracked both clonal and plasmid transmission in colistin- and carbapenem-resistant using short- and long-read sequencing technologies. We observed three clonal transmissions, all containing Incompatibility group (Inc) L plasmids and New Delhi metallo-beta-lactamase , although not co-located on the same plasmid.
View Article and Find Full Text PDFNat Cancer
January 2025
Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
Human tumors are diverse in their natural history and response to treatment, which in part results from genetic and transcriptomic heterogeneity. In clinical practice, single-site needle biopsies are used to sample this diversity, but cancer biomarkers may be confounded by spatiogenomic heterogeneity within individual tumors. Here we investigate clonally expressed genes as a solution to the sampling bias problem by analyzing multiregion whole-exome and RNA sequencing data for 450 tumor regions from 184 patients with lung adenocarcinoma in the TRACERx study.
View Article and Find Full Text PDFBiomark Res
January 2025
Department of Oncology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY, USA.
FMS-like tyrosine kinase 3 (FLT3) genetic variants are commonly seen in high-grade myeloid neoplasms and are typically gain-of-function mutations associated with a proliferative disease phenotype. Inactivating FLT3 variants have been less frequently described in non-malignant, autoimmune disorders and are uncommon in aplastic anemia (AA). Herein, we report the first to our knowledge, and unusual case of a germline, gain-of-function, FLT3 variant in a patient with severe AA treated successfully with immunosuppressive therapy.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, Rheinisch-Westfälische Technische Hochschule (RWTH) University Hospital, 52074 Aachen, Germany.
The oral-gut axis is a complex system linking the oral cavity and gastrointestinal tract, impacting host health and microbial composition. This study investigates genetic changes and adaptive mechanisms employed by streptococci-one of the few genera capable of colonizing oral and intestinal niches-within the same individual. We conducted whole-genome sequencing (WGS) on 218 streptococcal isolates from saliva and fecal samples of 14 inflammatory bowel disease (IBD) patients and 12 healthy controls.
View Article and Find Full Text PDFCancers (Basel)
December 2024
IBSAL, IBMCC, CSIC, Centro de Investigación del Cáncer, University of Salamanca, 37007 Salamanca, Spain.
Adult B-cell acute lymphoblastic leukemia (B-ALL) is characterized by genetic heterogeneity and a high relapse rate, affecting over 40% of adults. However, the mechanisms leading to relapse in adults are poorly understood. Forty-four adult B-ALL patients were studied at both diagnosis and relapse by next-generation sequencing (NGS).
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