The mutational landscape of human somatic and germline cells

AbstractDuring the course of a lifetime normal human cells accumulate mutations. Here, using multiple samples from the same individuals we compared the mutational landscape in 29 anatomical structures from soma and the germline. Two ubiquitous mutational signatures, SBS1 and SBS5/40, accounted for the majority of acquired mutations in most cell types but their absolute and relative contributions varied substantially. SBS18, potentially reflecting oxidative damage, and several additional signatures attributed to exogenous and endogenous exposures contributed mutations to subsets of cell types. The mutation rate was lowest in spermatogonia, the stem cell from which sperm are generated and from which most genetic variation in the human population is thought to originate. This was due to low rates of ubiquitous mutation processes and may be partially attributable to a low cell division rate of basal spermatogonia. The results provide important insights into how mutational processes affect the soma and germline.

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Elevated somatic mutation burdens in normal human cells due to defective DNA polymerases

10.1101/2020.06.23.167668 ◽

2020 ◽

Cited By ~ 2

Author(s):

Philip S. Robinson ◽

Tim H.H. Coorens ◽

Claire Palles ◽

Emily Mitchell ◽

Federico Abascal ◽

...

Keyword(s):

Somatic Mutation ◽

Normal Tissue ◽

Familial Cancer ◽

Dna Polymerases ◽

Cell Types ◽

Early Embryogenesis ◽

High Fidelity ◽

Mutational Signatures ◽

Exonuclease Domain ◽

Normal Human

ABSTRACTMutation accumulation over time in normal somatic cells contributes to cancer development and is proposed as a cause of ageing. DNA polymerases Pol ε and Pol δ replicate DNA with high fidelity during normal cell divisions. However, in some cancers defective proofreading due to acquired mutations in the exonuclease domains of POLE or POLD1 causes markedly elevated somatic mutation burdens with distinctive mutational signatures. POLE and POLD1 exonuclease domain mutations also cause familial cancer predisposition when inherited through the germline. Here, we sequenced normal tissue DNA from individuals with germline POLE or POLD1 exonuclease domain mutations. Increased mutation burdens with characteristic mutational signatures were found to varying extents in all normal adult somatic cell types examined, during early embryogenesis and in sperm. Mutation burdens were further markedly elevated in neoplasms from these individuals. Thus human physiology is able to tolerate ubiquitously elevated mutation burdens. Indeed, with the exception of early onset cancer, individuals with germline POLE and POLD1 exonuclease domain mutations are not reported to show abnormal phenotypic features, including those of premature ageing. The results, therefore, do not support a simple model in which all features of ageing are attributable to widespread cell malfunction directly resulting from somatic mutation burdens accrued during life.

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Heritable tumor cell division rate heterogeneity induces clonal dominance

10.1101/097683 ◽

2017 ◽

Author(s):

Margriet M. Palm ◽

Marjet Elemans ◽

Joost B. Beltman

Keyword(s):

Stem Cells ◽

Cancer Stem Cells ◽

Lineage Tracing ◽

Hierarchical Organization ◽

Rate Heterogeneity ◽

Division Rate ◽

Cell Division Rate ◽

Mutational Processes ◽

Selection Of

AbstractTumors consist of a hierarchical population of cells that differ in their phenotype and genotype. This hierarchical organization of cells means that a few clones (i.e., cells and several generations of offspring) are abundant while most are rare, which is called clonal dominance. Such dominance also occurred in published in vitro iterated growth and passage experiments with tumor cells in which genetic barcodes were used for lineage tracing. A potential source for such heterogeneity is that dominant clones derive from cancer stem cells with an unlimited self-renewal capacity. Furthermore, ongoing evolution within the growing population may also induce clonal dominance. To understand how clonal dominance developed in the iterated growth and passage experiments, we built a computational model that accurately simulates these experiments. The model simulations reproduced the clonal dominance that developed in in vitro iterated growth and passage experiments when the division rates vary between cells, due to a combination of initial variation and of ongoing mutational processes. In contrast, the experimental results can neither be reproduced with a model that considers random growth and passage, nor with a model based on cancer stem cells. Altogether, our model suggests that in vitro clonal dominance develops due to selection of fast-dividing clones.

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RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer

10.1101/2020.11.21.392878 ◽

2020 ◽

Author(s):

Damian Wojtowicz ◽

Jan Hoinka ◽

Bayarbaatar Amgalan ◽

Yoo-Ah Kim ◽

Teresa M. Przytycka

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Mutational Signatures ◽

Dna Damage And Repair ◽

Therapeutic Implications ◽

Mutational Landscape ◽

Repair Processes ◽

Cancer Genomes ◽

Current Paradigm ◽

Mutational Processes

AbstractMany mutagenic processes leave characteristic imprints on cancer genomes known as mutational signatures. These signatures have been of recent interest regarding their applicability in studying processes shaping the mutational landscape of cancer. In particular, pinpointing the presence of altered DNA repair pathways can have important therapeutic implications. However, mutational signatures of DNA repair deficiencies are often hard to infer. This challenge emerges as a result of deficient DNA repair processes acting by modifying the outcome of other mutagens. Thus, they exhibit non-additive effects that are not depicted by the current paradigm for modeling mutational processes as independent signatures. To close this gap, we present RepairSig, a method that accounts for interactions between DNA damage and repair and is able to uncover unbiased signatures of deficient DNA repair processes. In particular, RepairSig was able to replace three MMR deficiency signatures previously proposed to be active in breast cancer, with just one signature strikingly similar to the experimentally derived signature. As the first method to model interactions between mutagenic processes, RepairSig is an important step towards biologically more realistic modeling of mutational processes in cancer. The source code for RepairSig is publicly available at https://github.com/ncbi/RepairSig.

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Increased somatic mutation burdens in normal human cells due to defective DNA polymerases

Nature Genetics ◽

10.1038/s41588-021-00930-y ◽

2021 ◽

Author(s):

Philip S. Robinson ◽

Tim H. H. Coorens ◽

Claire Palles ◽

Emily Mitchell ◽

Federico Abascal ◽

...

Keyword(s):

Somatic Mutation ◽

Normal Tissue ◽

Familial Cancer ◽

Dna Polymerases ◽

Cell Types ◽

Early Embryogenesis ◽

Premature Aging ◽

Mutational Signatures ◽

Normal Human ◽

Tumor Dna

AbstractMutation accumulation in somatic cells contributes to cancer development and is proposed as a cause of aging. DNA polymerases Pol ε and Pol δ replicate DNA during cell division. However, in some cancers, defective proofreading due to acquired POLE/POLD1 exonuclease domain mutations causes markedly elevated somatic mutation burdens with distinctive mutational signatures. Germline POLE/POLD1 mutations cause familial cancer predisposition. Here, we sequenced normal tissue and tumor DNA from individuals with germline POLE/POLD1 mutations. Increased mutation burdens with characteristic mutational signatures were found in normal adult somatic cell types, during early embryogenesis and in sperm. Thus human physiology can tolerate ubiquitously elevated mutation burdens. Except for increased cancer risk, individuals with germline POLE/POLD1 mutations do not exhibit overt features of premature aging. These results do not support a model in which all features of aging are attributable to widespread cell malfunction directly resulting from somatic mutation burdens accrued during life.

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Tracking HIV-1-Infected Cell Clones Using Integration Site-Specific qPCR

Viruses ◽

10.3390/v13071235 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1235

Author(s):

Leah D. Brandt ◽

Shuang Guo ◽

Kevin W. Joseph ◽

Jana L. Jacobs ◽

Asma Naqvi ◽

...

Keyword(s):

Integration Site ◽

Cell Types ◽

Sequencing Data ◽

Site Specific ◽

Cell Clones ◽

Droplet Pcr ◽

Relative Rarity ◽

Deep Integration ◽

Multiple Samples ◽

Hiv 1

Efforts to cure HIV-1 infection require better quantification of the HIV-1 reservoir, particularly the clones of cells harboring replication-competent (intact) proviruses, termed repliclones. The digital droplet PCR assays commonly used to quantify intact proviruses do not differentiate among specific repliclones, thus the dynamics of repliclones are not well defined. The major challenge in tracking repliclones is the relative rarity of the cells carrying specific intact proviruses. To date, detection and accurate quantification of repliclones requires in-depth integration site sequencing. Here, we describe a simplified workflow using integration site-specific qPCR (IS-qPCR) to determine the frequencies of the proviruses integrated in individual repliclones. We designed IS-qPCR to determine the frequencies of repliclones and clones of cells that carry defective proviruses in samples from three donors. Comparing the results of IS-qPCR with deep integration site sequencing data showed that the two methods yielded concordant estimates of clone frequencies (r = 0.838). IS-qPCR is a potentially valuable tool that can be applied to multiple samples and cell types over time to measure the dynamics of individual repliclones and the efficacy of treatments designed to eliminate them.

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Spatial Distribution of Cell Division Rate Can Be Deduced from that of p34cdc2 Kinase Activity in Maize Leaves Grown at Contrasting Temperatures and Soil Water Conditions

PLANT PHYSIOLOGY ◽

10.1104/pp.124.3.1393 ◽

2000 ◽

Vol 124 (3) ◽

pp. 1393-1402 ◽

Cited By ~ 75

Author(s):

Christine Granier ◽

Dirk Inzé ◽

François Tardieu

Keyword(s):

Spatial Distribution ◽

Cell Division ◽

Soil Water ◽

Kinase Activity ◽

Division Rate ◽

Cell Division Rate ◽

Water Conditions ◽

Maize Leaves ◽

Soil Water Conditions

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E-cadherin is the major mediator of human melanocyte adhesion to keratinocytes in vitro

Journal of Cell Science ◽

10.1242/jcs.107.4.983 ◽

1994 ◽

Vol 107 (4) ◽

pp. 983-992 ◽

Cited By ~ 9

Author(s):

A. Tang ◽

M.S. Eller ◽

M. Hara ◽

M. Yaar ◽

S. Hirohashi ◽

...

Keyword(s):

Cell Types ◽

Melanoma Metastasis ◽

Normal Keratinocytes ◽

Human Melanocyte ◽

Human Melanocytes ◽

Dependent Cell ◽

Normal Human ◽

Pre Treatment ◽

E Cadherin

E- and P-cadherin are calcium (Ca2+)-dependent cell adhesion molecules important in the morphogenesis and maintenance of skin structure. By use of flow cytometry and specific antibodies, we now show that cultured human melanocytes express E- and P-cadherin on their surfaces, and that these molecules have the same characteristics as reported for other cell types. Specifically, melanocyte cadherins are sensitive to trypsin digestion in the absence of Ca2+ and are protected from trypsin degradation by Ca2+, and are functional at 37 degrees C but not at 4 degrees C. We further show that melanocytes contain mRNA transcripts encoding both E- and P-cadherin. Adhesion of cultured melanocytes to keratinocyte monolayers is abolished by pre-treatment of the melanocytes with trypsin/EDTA, which degrades E- and P-cadherins, is greatly reduced by anti-E-cadherin antibodies and is slightly reduced by antibodies to P-cadherin, alpha 2, alpha 3 and beta 1 integrins. In contrast to normal melanocytes, eight of nine melanoma cell lines lacked E-cadherin (or expressed markedly reduced levels) and five were negative for P-cadherin. Melanoma cells also failed to adhere to keratinocyte monolayers. These results demonstrate that normal human melanocytes express functional E- and P-cadherin and that E-cadherin is primarily responsible for adhesion of human melanocytes to keratinocytes in vitro. In addition, transformed melanocytes express markedly reduced levels of E- and P-cadherin, and exhibit decreased affinity for normal keratinocytes in vitro, suggesting that loss of cadherins may play a role in melanoma metastasis.

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