RESUMO
Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-tumor heterogeneity. Here, we present CNAqc, an evolution-inspired method to perform the computational validation of clonal and subclonal CNAs detected from bulk DNA sequencing. CNAqc is validated using single-cell data and simulations, is applied to over 4000 TCGA and PCAWG samples, and is incorporated into the validation process for the clinically accredited bioinformatics pipeline at Genomics England. CNAqc is designed to support automated quality control procedures for tumor somatic data validation.
Assuntos
Variações do Número de Cópias de DNA , Neoplasias , Humanos , Algoritmos , Polimorfismo de Nucleotídeo Único , Neoplasias/genética , Neoplasias/patologia , Genômica/métodos , Biologia Computacional/métodosRESUMO
The evolutionary dynamics of tumor initiation remain undetermined, and the interplay between neoplastic cells and the immune system is hypothesized to be critical in transformation. Colorectal cancer (CRC) presents a unique opportunity to study the transition to malignancy as pre-cancers (adenomas) and early-stage cancers are frequently resected. Here, we examine tumor-immune eco-evolutionary dynamics from pre-cancer to carcinoma using a computational model, ecological analysis of digital pathology data, and neoantigen prediction in 62 patient samples. Modeling predicted recruitment of immunosuppressive cells would be the most common driver of transformation. As predicted, ecological analysis reveals that progressed adenomas co-localized with immunosuppressive cells and cytokines, while benign adenomas co-localized with a mixed immune response. Carcinomas converge to a common immune "cold" ecology, relaxing selection against immunogenicity and high neoantigen burdens, with little evidence for PD-L1 overexpression driving tumor initiation. These findings suggest re-engineering the immunosuppressive niche may prove an effective immunotherapy in CRC.
Assuntos
Adenoma , Carcinoma , Neoplasias Colorretais , Evolução Biológica , Neoplasias Colorretais/patologia , Humanos , ImunoterapiaRESUMO
Central to tumor evolution is the generation of genetic diversity. However, the extent and patterns by which de novo karyotype alterations emerge and propagate within human tumors are not well understood, especially at single-cell resolution. Here, we present 3D Live-Seq-a protocol that integrates live-cell imaging of tumor organoid outgrowth and whole-genome sequencing of each imaged cell to reconstruct evolving tumor cell karyotypes across consecutive cell generations. Using patient-derived colorectal cancer organoids and fresh tumor biopsies, we demonstrate that karyotype alterations of varying complexity are prevalent and can arise within a few cell generations. Sub-chromosomal acentric fragments were prone to replication and collective missegregation across consecutive cell divisions. In contrast, gross genome-wide karyotype alterations were generated in a single erroneous cell division, providing support that aneuploid tumor genomes can evolve via punctuated evolution. Mapping the temporal dynamics and patterns of karyotype diversification in cancer enables reconstructions of evolutionary paths to malignant fitness.
Assuntos
Neoplasias Colorretais/genética , Neoplasias Colorretais/patologia , Análise de Célula Única/métodos , Proliferação de Células/genética , Cromatina/genética , Cromossomos Humanos , Dosagem de Genes , Humanos , Cariótipo , Cariotipagem , Microscopia Confocal , Mitose , Organoides/crescimento & desenvolvimento , Organoides/patologia , Fuso Acromático/genéticaRESUMO
Cancers accumulate mutations that lead to neoantigens, novel peptides that elicit an immune response, and consequently undergo evolutionary selection. Here we establish how negative selection shapes the clonality of neoantigens in a growing cancer by constructing a mathematical model of neoantigen evolution. The model predicts that, without immune escape, tumor neoantigens are either clonal or at low frequency; hypermutated tumors can only establish after the evolution of immune escape. Moreover, the site frequency spectrum of somatic variants under negative selection appears more neutral as the strength of negative selection increases, which is consistent with classical neutral theory. These predictions are corroborated by the analysis of neoantigen frequencies and immune escape in exome and RNA sequencing data from 879 colon, stomach and endometrial cancers.
Assuntos
Antígenos de Neoplasias/genética , Imunidade Celular/genética , Neoplasias/genética , Seleção Genética/genética , Evolução Clonal/genética , Exoma/genética , Humanos , Linfócitos do Interstício Tumoral/imunologia , Modelos Teóricos , Mutação/genética , Neoplasias/imunologia , Neoplasias/patologia , Seleção Genética/imunologia , Sequenciamento do ExomaRESUMO
The MAPT H1c haplotype is a risk factor for the neurodegenerative tauopathies progressive supranuclear palsy (PSP) and Alzheimer's disease. We hypothesise that the effect of the H1c haplotype relates to an increase in MAPT expression leading to an increase in tau neurofibrillary tangle deposition. We have evaluated the effect of the MAPT H1c haplotype on the expression of MAPT using allele specific expression, comparing the relative levels of MAPT H1 and H2 RNA derived from post-mortem human brain, unaffected by neurodegenerative disease. Using three assays spanning the MAPT gene we did not detect any effect of H1c on MAPT expression as compared with other haplotypes. We did, however, detect an effect of age on expression of MAPT H1 with a relative decrease in MAPT H1 expression with increased age. Our data suggest that there is an interaction between age and the expression of MAPT.