Mutational History of a Human Cell Lineage from Somatic to Induced Pluripotent Stem Cells.

The accuracy of replicating the genetic code is fundamental. DNA repair mechanisms protect the fidelity of the genome ensuring a low error rate between generations. This sustains the similarity of individuals whilst providing a repertoire of variants for evolution. The mutation rate in the human genome has recently been measured to be 50-70 de novo single nucleotide variants (SNVs) between generations. During development mutations accumulate in somatic cells so that an organism is a mosaic. However, variation within a tissue and between tissues has not been analysed. By reprogramming somatic cells into induced pluripotent stem cells (iPSCs), their genomes and the associated mutational history are captured. By sequencing the genomes of polyclonal and monoclonal somatic cells and derived iPSCs we have determined the mutation rates and show how the patterns change from a somatic lineage in vivo through to iPSCs. Somatic cells have a mutation rate of 14 SNVs per cell per generation while iPSCs exhibited a ten-fold lower rate. Analyses of mutational signatures suggested that deamination of methylated cytosine may be the major mutagenic source in vivo, whilst oxidative DNA damage becomes dominant in vitro. Our results provide insights for better understanding of mutational processes and lineage relationships between human somatic cells. Furthermore it provides a foundation for interpretation of elevated mutation rates and patterns in cancer

Novel stem cell technologies are powerful tools to understand the impact of human factors on Plasmodium falciparum malaria

© 2023 The Author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY), https://creativecommons.org/licenses/by/4.0/Plasmodium falciparum parasites have a complex life cycle, but the most clinically relevant stage of the disease is the invasion of erythrocytes and the proliferation of the parasite in the blood. The influence of human genetic traits on malaria has been known for a long time, however understanding the role of the proteins involved is hampered by the a nuclear nature of erythrocytes that makes them inaccessible to genetic tools. Here we overcome this limitation using stem cells to generate erythroid cells with an in-vitro differentiation protocol and assess parasite invasion with an adaptation of flow cytometry to detect parasite hemozoin. We combine this strategy with reprogramming of patient cells to Induced Pluripotent Stem Cells and genome editing to understand the role of key genes and human traits in malaria infection. We show that deletion of basigin ablates invasion while deletion of ATP2B4 has a minor effect and that erythroid cells from reprogrammed patient-derived HbBart α-thalassemia samples poorly support infection. The possibility to obtain patient-secific and genetically modifed erythoid cells offers an unparalleled opportunity to study the role of human genes and polymorphisms in malaria allowing preservation of the genomic background to demonstrate their function and understand their mechanisms.Peer reviewe

Novel stem cell technologies are powerful tools to understand the impact of human factors on Plasmodium falciparum malaria

Peer reviewed: TrueAcknowledgements: The authors wish to thank Marcus Lee for his overall support and Aleš Kilpatrick for helping with imaging.Plasmodium falciparum parasites have a complex life cycle, but the most clinically relevant stage of the disease is the invasion of erythrocytes and the proliferation of the parasite in the blood. The influence of human genetic traits on malaria has been known for a long time, however understanding the role of the proteins involved is hampered by the anuclear nature of erythrocytes that makes them inaccessible to genetic tools. Here we overcome this limitation using stem cells to generate erythroid cells with an in-vitro differentiation protocol and assess parasite invasion with an adaptation of flow cytometry to detect parasite hemozoin. We combine this strategy with reprogramming of patient cells to Induced Pluripotent Stem Cells and genome editing to understand the role of key genes and human traits in malaria infection. We show that deletion of basigin ablates invasion while deletion of ATP2B4 has a minor effect and that erythroid cells from reprogrammed patient-derived HbBart α-thalassemia samples poorly support infection. The possibility to obtain patient-secific and genetically modifed erythoid cells offers an unparalleled opportunity to study the role of human genes and polymorphisms in malaria allowing preservation of the genomic background to demonstrate their function and understand their mechanisms.</jats:p

Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells

Funder: Dr Josef Steiner Cancer Research Award 2019, Medical Research Council (MRC) Grant-in-Aid to the MRC Cancer unit, CRUK Pioneer AwardAbstract: We explored human induced pluripotent stem cells (hiPSCs) derived from different tissues to gain insights into genomic integrity at single-nucleotide resolution. We used genome sequencing data from two large hiPSC repositories involving 696 hiPSCs and daughter subclones. We find ultraviolet light (UV)-related damage in ~72% of skin fibroblast-derived hiPSCs (F-hiPSCs), occasionally resulting in substantial mutagenesis (up to 15 mutations per megabase). We demonstrate remarkable genomic heterogeneity between independent F-hiPSC clones derived during the same round of reprogramming due to oligoclonal fibroblast populations. In contrast, blood-derived hiPSCs (B-hiPSCs) had fewer mutations and no UV damage but a high prevalence of acquired BCOR mutations (26.9% of lines). We reveal strong selection pressure for BCOR mutations in F-hiPSCs and B-hiPSCs and provide evidence that they arise in vitro. Directed differentiation of hiPSCs and RNA sequencing showed that BCOR mutations have functional consequences. Our work strongly suggests that detailed nucleotide-resolution characterization is essential before using hiPSCs

Mutational signatures <i>in vivo</i>, <i>in vitro</i> and through reprogramming.

<p><b>a</b>. Schematic showing the longitudinal progression from <i>in vivo</i> development, <i>in vitro</i> culture of somatic cells through reprogramming and finally through to the experimental set-up used to calculate the mutation rate in iPSC maintenance culture. <b>b</b>. Mutational spectrum of SNVs found in the EPCs (top), and primary (middle) and sub-cloned (bottom) S7-RE14 iPSC lines. Clonal (left) and sub-clonal (right) mutations were shown separately. <b>c</b>. Contribution of mutational processes identified by the NNMF analysis. The germ line mutations described in ref 18 were analysed [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005932#pgen.1005932.ref018" target="_blank">18</a>]. The NNMF analysis was not performed for the mutations in sub-clonal S7-EPC due to the limited number of mutations available.</p

Mutation rate of human pluripotent cells in culture.

<p><b>a</b>. The mean numbers of SNVs accumulated during 60 cell divisions in 2 iPSC lines, S7-RE14 (<i>n</i> = 3) and S4-SF6 (<i>n</i> = 2) and a human ESC line H9 (<i>n</i> = 3). Data are shown as mean ± SD. <b>b</b>. Mutation rate per cell per division in each pluripotent cell line.</p

Summary of WGS and deep sequence analysis.

<p>Summary of WGS and deep sequence analysis.</p

Comparing acquired SNVs in iPSCs derived from a polyclonal or a monoclonal origin.

<p><b>a</b>. Schematic comparing the reprogramming of polyclonal and monoclonal cells. Polyclonal cells such as fibroblasts (left panel) give rise to iPSCs which do not share a majority of mutations since they are derived from different progenitors. In contrast, iPSCs derived from monoclonal cells (right panel) such as EPCs share a proportion of their mutations and carry private mutations specific to each line. <b>b, c</b>. Exome sequencing of iPSCs generated using fibroblasts from two different individuals, a 65-year-old alpha-1 antitrypsin deficiency patient (AATD) (<b>b</b>) and a healthy subject, S2 (<b>c</b>). The data for iPSC-B were taken from our previous work [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005932#pgen.1005932.ref011" target="_blank">11</a>]. Each column represents one SNV in the indicated gene. Duplicated genes indicate two adjacent SNVs. Green, mutation absent; pink, mutation present. See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005932#pgen.1005932.s004" target="_blank">S2</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005932#pgen.1005932.s005" target="_blank">S3</a> Tables for the complete description. <b>d, e</b>. Exome sequencing of iPSC lines generated using monoclonal EPCs from the same AATD patient in <b>b</b> as well as a healthy subject, S7 (<b>e</b>). Orange, mutation detected by amplicon resequencing. See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005932#pgen.1005932.s006" target="_blank">S4</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005932#pgen.1005932.s007" target="_blank">S5</a> Tables for the complete description.</p

Acquisition of epithelial plasticity in human chronic liver disease.

For many adult human organs, tissue regeneration during chronic disease remains a controversial subject. Regenerative processes are easily observed in animal models, and their underlying mechanisms are becoming well characterized1-4, but technical challenges and ethical aspects are limiting the validation of these results in humans. We decided to address this difficulty with respect to the liver. This organ displays the remarkable ability to regenerate after acute injury, although liver regeneration in the context of recurring injury remains to be fully demonstrated. Here we performed single-nucleus RNA sequencing (snRNA-seq) on 47 liver biopsies from patients with different stages of metabolic dysfunction-associated steatotic liver disease to establish a cellular map of the liver during disease progression. We then combined these single-cell-level data with advanced 3D imaging to reveal profound changes in the liver architecture. Hepatocytes lose their zonation and considerable reorganization of the biliary tree takes place. More importantly, our study uncovers transdifferentiation events that occur between hepatocytes and cholangiocytes without the presence of adult stem cells or developmental progenitor activation. Detailed analyses and functional validations using cholangiocyte organoids confirm the importance of the PI3K-AKT-mTOR pathway in this process, thereby connecting this acquisition of plasticity to insulin signalling. Together, our data indicate that chronic injury creates an environment that induces cellular plasticity in human organs, and understanding the underlying mechanisms of this process could open new therapeutic avenues in the management of chronic diseases