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

2020 ◽  
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.

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

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.

scholarly journals The mutational landscape of human somatic and germline cells

2020 ◽  
Author(s):  
Luiza Moore ◽  
Alex Cagan ◽  
Tim H.H. Coorens ◽  
Matthew D.C. Neville ◽  
Rashesh Sanghvi ◽  
...  
Keyword(s):  
Human Population ◽  
Cell Types ◽  
Mutational Signatures ◽  
Division Rate ◽  
Anatomical Structures ◽  
Mutational Landscape ◽  
Cell Division Rate ◽  
Normal Human ◽  
Multiple Samples ◽  
Mutational Processes

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.

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

1994 ◽  
Vol 107 (4) ◽  
pp. 983-992 ◽  
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.

Mechanistic Comparison of High-Fidelity and Error-Prone DNA Polymerases and Ligases Involved in DNA Repair

ChemInform ◽  
2006 ◽  
Vol 37 (21) ◽  
Author(s):  
Alexander K. Showalter ◽  
Brandon J. Lamarche ◽  
Marina Bakhtina ◽  
Mei-I Su ◽  
Kuo-Hsiang Tang ◽  
...  
Keyword(s):  
Dna Repair ◽  
Dna Polymerases ◽  
High Fidelity

scholarly journals Hairpin structure facilitates high-fidelity DNA amplification reactions in both qPCR and high-throughput sequencing

2021 ◽  
Author(s):  
Kerou Zhang ◽  
Alessandro Pinto ◽  
Peng Dai ◽  
Michael Wang ◽  
Lauren Yuxuan Cheng ◽  
...  
Keyword(s):  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Limit Of Detection ◽  
Dna Polymerases ◽  
Dna Amplification ◽  
Cost Effective ◽  
High Fidelity ◽  
Resistance Mutations ◽  
Chain Reactions ◽  
Early Cancer Diagnosis

Effective polymerase chain reactions (PCR) are important in bio-laboratories. It is essential to detect rare DNA-sequence variants for early cancer diagnosis or for drug-resistance mutations identification. Some of the common detection quantitative PCR (qPCR) methods are restricted in the limit of detection (LoD) because of the high polymerase misincorporation rate in Taq DNA polymerases. High-fidelity (HiFi) DNA polymerases have a 50- to 250-fold higher fidelity. Yet, there are currently no proper designs for multiplexed HiFi qPCR reactions. Moreover, the popularity of targeting highly multiplex DNA sequences requires minimizing PCR side products, as the potential of dimerization grows quadratically as the plexes of primers increases. Efforts tried before were either an add-on step, or technology-specific, or requiring high-level computing skills. There lacks an easy-to-apply and cost-effective method for dimerization reduction. Here, we presented the Occlusion System, composed of a 5'-overhanged primer and a probe with a short-stem hairpin. We demonstrated that it allowed multiplexing high-fidelity qPCR reaction, it was also compatible with the current variant-enrichment method to improve the LoD by 10-fold. Further, we found that the Occlusion System reduced the dimerization up to 10-fold in highly multiplexed PCR. Thus, the Occlusion System satisfactorily improved both qPCR sensitivity and PCR efficiency.

Mechanistic Comparison of High-Fidelity and Error-Prone DNA Polymerases and Ligases Involved in DNA Repair

2006 ◽  
Vol 106 (2) ◽  
pp. 340-360 ◽  
Author(s):  
Alexander K. Showalter ◽  
Brandon J. Lamarche ◽  
Marina Bakhtina ◽  
Mei-I Su ◽  
Kuo-Hsiang Tang ◽  
...  
Keyword(s):  
Dna Repair ◽  
Dna Polymerases ◽  
High Fidelity

scholarly journals Alterations of Glycosphingolipid Glycans and Chondrogenic Markers during Differentiation of Human Induced Pluripotent Stem Cells into Chondrocytes

Biomolecules ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1622
Author(s):  
Liang Xu ◽  
Hisatoshi Hanamatsu ◽  
Kentaro Homan ◽  
Tomohiro Onodera ◽  
Takuji Miyazaki ◽  
...  
Keyword(s):  
Stem Cells ◽  
Induced Pluripotent Stem Cells ◽  
Pluripotent Stem Cells ◽  
Chondrogenic Differentiation ◽  
Cell Types ◽  
Human Cartilage ◽  
Human Ipscs ◽  
Normal Human ◽  
Induced Pluripotent ◽  
Promising Source

Due to the limited intrinsic healing potential of cartilage, injury to this tissue may lead to osteoarthritis. Human induced pluripotent stem cells (iPSCs), which can be differentiated into chondrocytes, are a promising source of cells for cartilage regenerative therapy. Currently, however, the methods for evaluating chondrogenic differentiation of iPSCs are very limited; the main techniques are based on the detection of chondrogenic genes and histological analysis of the extracellular matrix. The cell surface is coated with glycocalyx, a layer of glycoconjugates including glycosphingolipids (GSLs) and glycoproteins. The glycans in glycoconjugates play important roles in biological events, and their expression and structure vary widely depending on cell types and conditions. In this study, we performed a quantitative GSL-glycan analysis of human iPSCs, iPSC-derived mesenchymal stem cell like cells (iPS-MSC like cells), iPS-MSC-derived chondrocytes (iPS-MSC-CDs), bone marrow-derived mesenchymal stem cells (BMSCs), and BMSC-derived chondrocytes (BMSC-CDs) using glycoblotting technology. We found that GSL-glycan profiles differed among cell types, and that the GSL-glycome underwent a characteristic alteration during the process of chondrogenic differentiation. Furthermore, we analyzed the GSL-glycome of normal human cartilage and found that it was quite similar to that of iPS-MSC-CDs. This is the first study to evaluate GSL-glycan structures on human iPS-derived cartilaginous particles under micromass culture conditions and those of normal human cartilage. Our results indicate that GSL-glycome analysis is useful for evaluating target cell differentiation and can thus support safe regenerative medicine.

scholarly journals Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Irene Franco ◽  
Hafdis T. Helgadottir ◽  
Aldo Moggio ◽  
Malin Larsson ◽  
Peter Vrtačnik ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Somatic Mutation ◽  
Somatic Mutations ◽  
Adult Life ◽  
Cell Types ◽  
Human Cells ◽  
Specific Cell ◽  
Whole Genome ◽  
Cell Type ◽  
Healthy Human

Abstract Background The lifelong accumulation of somatic mutations underlies age-related phenotypes and cancer. Mutagenic forces are thought to shape the genome of aging cells in a tissue-specific way. Whole genome analyses of somatic mutation patterns, based on both types and genomic distribution of variants, can shed light on specific processes active in different human tissues and their effect on the transition to cancer. Results To analyze somatic mutation patterns, we compile a comprehensive genetic atlas of somatic mutations in healthy human cells. High-confidence variants are obtained from newly generated and publicly available whole genome DNA sequencing data from single non-cancer cells, clonally expanded in vitro. To enable a well-controlled comparison of different cell types, we obtain single genome data (92% mean coverage) from multi-organ biopsies from the same donors. These data show multiple cell types that are protected from mutagens and display a stereotyped mutation profile, despite their origin from different tissues. Conversely, the same tissue harbors cells with distinct mutation profiles associated to different differentiation states. Analyses of mutation rate in the coding and non-coding portions of the genome identify a cell type bearing a unique mutation pattern characterized by mutation enrichment in active chromatin, regulatory, and transcribed regions. Conclusions Our analysis of normal cells from healthy donors identifies a somatic mutation landscape that enhances the risk of tumor transformation in a specific cell population from the kidney proximal tubule. This unique pattern is characterized by high rate of mutation accumulation during adult life and specific targeting of expressed genes and regulatory regions.

scholarly journals Synthesis of a peroxidase activity by the cells of hairy cell leukemia: a study by ultrastructural cytochemistry

Blood ◽  
1978 ◽  
Vol 52 (3) ◽  
pp. 537-550 ◽  
Author(s):  
F Reyes ◽  
MF Gourdin ◽  
JP Farcet ◽  
B Dreyfus ◽  
J Breton-Gorius
Keyword(s):  
Peroxidase Activity ◽  
Hairy Cell Leukemia ◽  
Cell Types ◽  
Human Monocytes ◽  
Hairy Cell ◽  
Blood Monocytes ◽  
Cell Leukemia ◽  
Data Points ◽  
Normal Human ◽  
Hairy Cells

Abstract The nature of cells present in the blood, marrow, and spleen of patients with hairy cell leukemia is largely debated. These cells have been tentatively categorized on the basis of either monocytic or lymphocytic markers, and the accumulating data points to the fact that they share some characteristics of both cell types. Although hairy cells are known to lack myeloperoxidase-positive granules, present in normal human monocytes, we investigated the possible presence of other peroxidase activities differing from the granule-bound myeloperoxidase. The study was carried out with several methods based on the incubation of fixed and unfixed cells in the presence of diaminobenzidine and hydrogen peroxide. A peroxidase activity was found in hairy cells, located always in the endoplasmic reticulum but not in the Golgi apparatus or in any granule. By its cytochemical characteristics it appears to be closely related to that of tissue macrophages, activated blood monocytes, and other nonlymphocytic hematopoietic cells. This peroxidase is not found in lymphocytes with B or T phenotypes.

scholarly journals Expression of TAL-1 proteins in human tissues

Blood ◽  
1995 ◽  
Vol 85 (3) ◽  
pp. 675-684 ◽  
Author(s):  
K Pulford ◽  
N Lecointe ◽  
K Leroy-Viard ◽  
M Jones ◽  
D Mathieu-Mahul ◽  
...  
Keyword(s):  
Molecular Weight ◽  
T Cell ◽  
Cell Lines ◽  
Fetal Liver ◽  
Cell Types ◽  
Human Tissues ◽  
Aberrant Expression ◽  
Erythroid Precursor ◽  
Normal Human

Rearrangement of the tal-1 gene (also known as SCL or TCL-5) occurs in at least 25% of T-cell acute lymphoblastic leukemias (T-ALLs) and results in the aberrant expression of tal-1 mRNA in the neoplastic cells. Also, tal-1 mRNA is constitutively expressed in erythroid precursors and megakaryocytes. This report describes a direct immunocytochemical study of the distribution and localization of TAL-1 protein in normal human tissues and cell lines using four monoclonal antibodies raised against recombinant TAL-1 proteins. One of these reagents recognizes a protein of 41 kD molecular weight in in vitro- translated TAL-1 proteins, two others recognize proteins of 39 and 41 kD molecular weight, and the fourth antibody also recognizes a TAL-1 protein of 22 kD in addition to the 39- and 41-kD proteins. These anti- TAL-1 antibodies label the nuclei of erythroid precursor cells and megakaryocytes in fetal liver and adult bone marrow. The punctate pattern of nuclear labeling suggests that TAL-1 may comprise part of a novel nuclear structure, similar to that recently found for the PML protein. The nuclei of T cell lines known to express mRNA encoding the full-length TAL-1 protein (eg, CCRF-CEM, RPMI 8402, and Jurkat) are also labeled. A study of normal human tissues (including thymus) showed labeling of smooth muscle, some tissue macrophages, and endothelial cells. TAL-1 protein is undetectable in other cell types. These reagents may play an important role in the diagnosis of T-ALL and could also be used in the context of lymphoma diagnosis on routinely fixed material.

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