The landscape of somatic mutation in normal colorectal epithelial cells

2018 ◽  
Author(s):  
Henry Lee-Six ◽  
Peter Ellis ◽  
Robert J. Osborne ◽  
Mathijs A. Sanders ◽  
Luiza Moore ◽  
...  
Keyword(s):  
Normal Tissue ◽  
Somatic Mutations ◽  
Cell Lineage ◽  
Driver Mutations ◽  
Normal Cells ◽  
Genetic Changes ◽  
Adult Cell ◽  
Neoplastic Change ◽  
Cancer Types ◽  
Mutational Processes

AbstractThe colorectal adenoma-carcinoma sequence has provided a paradigmatic framework for understanding the successive somatic genetic changes and consequent clonal expansions leading to cancer. As for most cancer types, however, understanding of the earliest phases of colorectal neoplastic change, which may occur in morphologically normal tissue, is comparatively limited because of the difficulty of detecting somatic mutations in normal cells. Each colorectal crypt is a small clone of cells derived from a single recently-existing stem cell. Here, we whole genome sequenced hundreds of normal crypts from 42 individuals. Signatures of multiple mutational processes were revealed, some ubiquitous and continuous, others only found in some individuals, in some crypts or during some phases of the cell lineage from zygote to adult cell. Likely driver mutations were present in ∼1% of normal colorectal crypts in middle-aged individuals, indicating that adenomas and carcinomas are rare outcomes of a pervasive process of neoplastic change across morphologically normal colorectal epithelium.

scholarly journals The effects of mutational processes and selection on driver mutations across cancer types

2017 ◽  
Author(s):  
Daniel Temko ◽  
Ian PM Tomlinson ◽  
Simone Severini ◽  
Benjamin Schuster-Böckler ◽  
Trevor A Graham
Keyword(s):  
Driver Mutations ◽  
Sequencing Data ◽  
Epidemiological Evidence ◽  
Dna Mismatch ◽  
Cancer Types ◽  
Key Driver ◽  
Independent Effects ◽  
Mutational Processes ◽  
Mutation And Selection

ABSTRACTEpidemiological evidence has long associated environmental mutagens with increased cancer risk. However, links between specific mutation-causing processes and the acquisition of individual driver mutations have remained obscure. Here we have used public cancer sequencing data to infer the independent effects of mutation and selection on driver mutation complement. First, we detect associations between a range of mutational processes, including those linked to smoking, ageing, APOBEC and DNA mismatch repair (MMR) and the presence of key driver mutations across cancer types. Second, we quantify differential selection between well-known alternative driver mutations, including differences in selection between distinct mutant residues in the same gene. These results show that while mutational processes play a large role in determining which driver mutations are present in a cancer, the role of selection frequently dominates.

scholarly journals Author Correction: The effects of mutational processes and selection on driver mutations across cancer types

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Daniel Temko ◽  
Ian P. M. Tomlinson ◽  
Simone Severini ◽  
Benjamin Schuster-Böckler ◽  
Trevor A. Graham
Keyword(s):  
Driver Mutations ◽  
Cancer Types ◽  
Mutational Processes

scholarly journals Analysis of Mutations and Dysregulated Pathways Unravels Carcinogenic Effect and Clinical Actionability of Mutational Processes

2021 ◽  
Vol 9 ◽  
Author(s):  
Zedong Jiang ◽  
Gaoming Liao ◽  
Yiran Yang ◽  
Yujia Lan ◽  
Liwen Xu ◽  
...  
Keyword(s):  
Somatic Mutations ◽  
Strand Break ◽  
Driver Mutations ◽  
Cancer Genes ◽  
Carcinogenic Effect ◽  
Cancer Subtypes ◽  
Recurrent Mutations ◽  
Clinical Benefits ◽  
Mutational Processes ◽  
Mutational Process

Somatic mutations accumulate over time in cancer cells as a consequence of mutational processes. However, the role of mutational processes in carcinogenesis remains poorly understood. Here, we infer the causal relationship between mutational processes and somatic mutations in 5,828 samples spanning 34 cancer subtypes. We found most mutational processes cause abundant recurrent mutations in cancer genes, while exceptionally ultraviolet exposure and altered activity of the error-prone polymerase bring a large number of recurrent non-driver mutations. Furthermore, some mutations are specifically induced by a certain mutational process, such as IDH1 p.R132H which is mainly caused by spontaneous deamination of 5-methylcytosine. At the pathway level, clock-like mutational processes extensively trigger mutations to dysregulate cancer signal transduction pathways. In addition, APOBEC mutational process destroys DNA double-strand break repair pathway, and bladder cancer patients with high APOBEC activity, though with homologous recombination proficient, show a significantly longer overall survival with platinum regimens. These findings help to understand how mutational processes act on the genome to promote carcinogenesis, and further, presents novel insights for cancer prevention and treatment, as our results showing, APOBEC mutagenesis and HRD synergistically contributed to the clinical benefits of platinum-based treatment.

scholarly journals Comprehensive analysis of clustered mutations in cancer reveals recurrent APOBEC3 mutagenesis of ecDNA

2021 ◽  
Author(s):  
Erik N Bergstrom ◽  
Jens-Christian Luebeck ◽  
Mia Petljak ◽  
Vineet Bafna ◽  
Paul S. Mischel ◽  
...  
Keyword(s):  
Somatic Mutations ◽  
Human Cancer ◽  
Cancer Genes ◽  
Base Substitutions ◽  
Cancer Genomes ◽  
Cancer Types ◽  
Mutational Processes ◽  
Comprehensive Characterization

Clustered somatic mutations are common in cancer genomes with prior analyses revealing several types of clustered single-base substitutions, including doublet- and multi-base substitutions, diffuse hypermutation termed omikli, and longer strand-coordinated events termed kataegis. Here, we provide a comprehensive characterization of clustered substitutions and clustered small insertions and deletions (indels) across 2,583 whole-genome sequenced cancers from 30 cancer types. While only 3.7% of substitutions and 0.9% of indels were found to be clustered, they contributed 8.4% and 6.9% of substitution and indel drivers, respectively. Multiple distinct mutational processes gave rise to clustered indels including signatures enriched in tobacco smokers and homologous-recombination deficient cancers. Doublet-base substitutions were caused by at least 12 mutational processes, while the majority of multi-base substitutions were generated by either tobacco smoking or exposure to ultraviolet light. Omikli events, previously attributed to the activity of APOBEC3 deaminases, accounted for a large proportion of clustered substitutions. However, only 16.2% of omikli matched APOBEC3 patterns with experimental validation confirming additional mutational processes giving rise to omikli. Kataegis was generated by multiple mutational processes with 76.1% of all kataegic events exhibiting AID/APOBEC3-associated mutational patterns. Co-occurrence of APOBEC3 kataegis and extrachromosomal-DNA (ecDNA) was observed in 31% of samples with ecDNA. Multiple distinct APOBEC3 kataegic events were observed on most mutated ecDNA. ecDNA containing known cancer genes exhibited both positive selection and kataegic hypermutation. Our results reveal the diversity of clustered mutational processes in human cancer and the role of APOBEC3 in recurrently mutating and fueling the evolution of ecDNA.

scholarly journals The effects of mutational processes and selection on driver mutations across cancer types

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Daniel Temko ◽  
Ian P. M. Tomlinson ◽  
Simone Severini ◽  
Benjamin Schuster-Böckler ◽  
Trevor A. Graham
Keyword(s):  
Driver Mutations ◽  
Cancer Types ◽  
Mutational Processes

scholarly journals Signaling levels mold the RAS mutation tropism of urethane

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Siqi Li ◽  
Christopher M Counter
Keyword(s):  
Human Cancer ◽  
Driver Mutations ◽  
Normal Cells ◽  
Ras Mutation ◽  
Oncogenic Ras ◽  
Ras Genes ◽  
Specific Subset ◽  
Oncogenic Mutations ◽  
Cancer Types ◽  
Oncogenic Stress

RAS genes are commonly mutated in human cancer. Despite many possible mutations, individual cancer types often have a ‘tropism’ towards a specific subset of RAS mutations. As driver mutations, these patterns ostensibly originate from normal cells. High oncogenic RAS activity causes oncogenic stress and different oncogenic mutations can impart different levels of activity, suggesting a relationship between oncoprotein activity and RAS mutation tropism. Here, we show that changing rare codons to common in the murine Kras gene to increase protein expression shifts tumors induced by the carcinogen urethane from arising from canonical Q61 to biochemically less active G12 Kras driver mutations, despite the carcinogen still being biased towards generating Q61 mutations. Conversely, inactivating the tumor suppressor p53 to blunt oncogenic stress partially reversed this effect, restoring Q61 mutations. One interpretation of these findings is that the RAS mutation tropism of urethane arises from selection in normal cells for specific mutations that impart a narrow window of signaling that promotes proliferation without causing oncogenic stress.

scholarly journals Disruption of ubiquitin mediated proteolysis is a widespread mechanism of tumorigenesis

2018 ◽  
Author(s):  
Francisco Martinez-Jimenez ◽  
Ferran Muinos ◽  
Erika Lopez-Arribillaga ◽  
Nuria Lopez-Bigas ◽  
Abel Gonzalez-Perez
Keyword(s):  
Random Forest ◽  
Positive Selection ◽  
Somatic Mutations ◽  
Random Forest Classifier ◽  
Human Proteome ◽  
Cancer Development ◽  
Driver Mutations ◽  
Primary Tumors ◽  
E3 Ligases ◽  
Cancer Types

E3 ligases and degrons --the sequences they recognize in target proteins-- are key parts of the ubiquitin-mediated proteolysis system. There are several examples of alterations of these two components of the system that play a role in cancer. Here, we uncovered the landscape of the contribution of such alterations to tumorigenesis across cancer types. We first systematically identified novel instances of degrons across the human proteome using a random forest classifier, and validated them exploiting somatic mutations across more than 7,000 tumors. We detected signals of positive selection across these novel degrons and revealed new instances involved in cancer development. Overall, we estimated that at least one in seven driver mutations across primary tumors affect either degrons or E3 ligases.

scholarly journals Mutational likeliness and entropy help to identify driver mutations and their functional role in cancer

2018 ◽  
Author(s):  
Giorgio Mattiuz ◽  
Salvatore Di Giorgio ◽  
Lorenzo Tofani ◽  
Antonio Frandi ◽  
Francesco Donati ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Somatic Mutations ◽  
Driver Mutations ◽  
Cancer Evolution ◽  
Loss Of Function ◽  
Driver Genes ◽  
Cancer Driver ◽  
Cancer Genomes ◽  
Passenger Mutations ◽  
Mutational Processes

AbstractAlterations in cancer genomes originate from mutational processes taking place throughout oncogenesis and cancer progression. We show that likeliness and entropy are two properties of somatic mutations crucial in cancer evolution, as cancer-driver mutations stand out, with respect to both of these properties, as being distinct from the bulk of passenger mutations. Our analysis can identify novel cancer driver genes and differentiate between gain and loss of function mutations.

scholarly journals A body map of somatic mutagenesis in morphologically normal human tissues

2020 ◽  
Author(s):  
Ruoyan Li ◽  
Lin Di ◽  
Jie Li ◽  
Wenyi Fan ◽  
Yachen Liu ◽  
...  
Keyword(s):  
Somatic Mutations ◽  
Genomic Analysis ◽  
Driver Mutations ◽  
Human Tissues ◽  
Normal Tissues ◽  
Variable Extent ◽  
Normal Human ◽  
Body Map ◽  
Somatic Mutagenesis ◽  
Mutational Processes

AbstractSomatic mutations accumulated in normal tissues are associated with aging and disease. Here, we performed a comprehensive genomic analysis of 1,737 morphologically normal tissue biopsies (~ 600 cells each), mostly from the epithelia, of nine organs from five donors. We found that somatic mutation accumulations and clonal expansions are widespread, although with variable extent, in morphologically normal human tissues. Somatic copy number alterations were rarely detected, except for tissues from esophagus and cardia. Endogenous mutational processes like SBS1 and SBS5 are ubiquitous among normal tissues though exhibiting different relative activities. Exogenous mutational processes like SBS22 were found in different tissues from the same donor. We reconstructed the spatial somatic clonal architecture with sub-millimeter resolution. In epithelial tissues from esophagus and cardia, macroscopic somatic clones expanded to several millimeters were frequently seen, whereas in tissues from colon, rectum, and duodenum somatic clones were microscopic in size and evolved independently. Our study depicted a body map of somatic mutations and clonal expansions from the same individuals, and it revealed that the degree of somatic clonal expansion and enrichment of driver mutations are highly organ specific.

scholarly journals Genomic Determinants of Homologous Recombination Deficiency across Human Cancers

Cancers ◽  
2021 ◽  
Vol 13 (18) ◽  
pp. 4572
Author(s):  
Tao Qing ◽  
Xinfeng Wang ◽  
Tomi Jun ◽  
Li Ding ◽  
Lajos Pusztai ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Copy Number ◽  
Somatic Mutations ◽  
Synthetic Lethality ◽  
Driver Mutations ◽  
Multiple Cancer ◽  
Clinical Biomarkers ◽  
Somatic Alterations ◽  
Cancer Types ◽  
Prostate Cancers

Germline BRCA1/2 mutations associated with HRD are clinical biomarkers for sensitivity to poly-ADP ribose polymerase inhibitors (PARPi) treatment in breast, ovarian, pancreatic, and prostate cancers. However, it remains unclear whether other mutations may also lead to HRD and PARPi sensitivity across a broader range of cancer types. Our goal was to determine the germline or somatic alterations associated with the HRD phenotype that might therefore confer PARPi sensitivity. Using germline and somatic genomic data from over 9000 tumors representing 32 cancer types, we examined associations between HRD scores and pathogenic germline variants, somatic driver mutations, and copy number deletions in 30 candidate genes involved in homologous recombination. We identified several germline and somatic mutations (e.g., BRCA1/2, PALB2, ATM, and ATR mutations) associated with HRD phenotype in ovarian, breast, pancreatic, stomach, bladder, and lung cancer. The co-occurrence of germline BRCA1 variants and somatic TP53 mutations was significantly associated with increasing HRD in breast cancer. Notably, we also identified multiple somatic copy number deletions associated with HRD. Our study suggests that multiple cancer types include tumor subsets that show HRD phenotype and should be considered in the future clinical studies of PARPi and synthetic lethality strategies exploiting HRD, which can be caused by a large number of genomic alterations.

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