ABSTRACT
Oncogenic mutations are abundant in the tissues of healthy individuals, but rarely form tumours1-3. Yet, the underlying protection mechanisms are largely unknown. To resolve these mechanisms in mouse mammary tissue, we use lineage tracing to map the fate of wild-type and Brca1-/-;Trp53-/- cells, and find that both follow a similar pattern of loss and spread within ducts. Clonal analysis reveals that ducts consist of small repetitive units of self-renewing cells that give rise to short-lived descendants. This offers a first layer of protection as any descendants, including oncogenic mutant cells, are constantly lost, thereby limiting the spread of mutations to a single stem cell-descendant unit. Local tissue remodelling during consecutive oestrous cycles leads to the cooperative and stochastic loss and replacement of self-renewing cells. This process provides a second layer of protection, leading to the elimination of most mutant clones while enabling the minority that by chance survive to expand beyond the stem cell-descendant unit. This leads to fields of mutant cells spanning large parts of the epithelial network, predisposing it for transformation. Eventually, clone expansion becomes restrained by the geometry of the ducts, providing a third layer of protection. Together, these mechanisms act to eliminate most cells that acquire somatic mutations at the expense of driving the accelerated expansion of a minority of cells, which can colonize large areas, leading to field cancerization.
Subject(s)
BRCA1 Protein , Cell Lineage , Cell Transformation, Neoplastic , Mammary Glands, Animal , Mutation , Tumor Suppressor Protein p53 , Animals , Mice , Female , Mammary Glands, Animal/cytology , Mammary Glands, Animal/pathology , Mammary Glands, Animal/metabolism , BRCA1 Protein/genetics , BRCA1 Protein/metabolism , Cell Lineage/genetics , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism , Cell Transformation, Neoplastic/genetics , Clone Cells/metabolism , Clone Cells/cytology , Carcinogenesis/genetics , Carcinogenesis/pathology , Cell Self Renewal/geneticsABSTRACT
Telomerase is intimately associated with stem cells and cancer, because it catalytically elongates telomeres-nucleoprotein caps that protect chromosome ends1. Overexpression of telomerase reverse transcriptase (TERT) enhances the proliferation of cells in a telomere-independent manner2-8, but so far, loss-of-function studies have provided no evidence that TERT has a direct role in stem cell function. In many tissues, homeostasis is shaped by stem cell competition, a process in which stem cells compete on the basis of inherent fitness. Here we show that conditional deletion of Tert in the spermatogonial stem cell (SSC)-containing population in mice markedly impairs competitive clone formation. Using lineage tracing from the Tert locus, we find that TERT-expressing SSCs yield long-lived clones, but that clonal inactivation of TERT promotes stem cell differentiation and a genome-wide reduction in open chromatin. This role for TERT in competitive clone formation occurs independently of both its reverse transcriptase activity and the canonical telomerase complex. Inactivation of TERT causes reduced activity of the MYC oncogene, and transgenic expression of MYC in the TERT-deleted pool of SSCs efficiently rescues clone formation. Together, these data reveal a catalytic-activity-independent requirement for TERT in enhancing stem cell competition, uncover a genetic connection between TERT and MYC and suggest that a selective advantage for stem cells with high levels of TERT contributes to telomere elongation in the male germline during homeostasis and ageing.
Subject(s)
Cell Competition , Clone Cells , Stem Cells , Telomerase , Animals , Male , Mice , Cell Differentiation , Cell Lineage , Chromatin/metabolism , Chromatin/genetics , Clone Cells/cytology , Clone Cells/enzymology , Clone Cells/metabolism , Gene Deletion , Genes, myc , Proto-Oncogene Proteins c-myc/metabolism , Proto-Oncogene Proteins c-myc/genetics , Spermatogonia/cytology , Spermatogonia/metabolism , Stem Cells/cytology , Stem Cells/enzymology , Stem Cells/metabolism , Telomerase/deficiency , Telomerase/genetics , Telomerase/metabolism , Reverse Transcription , Biocatalysis , Homeostasis , AgingABSTRACT
The tumour evolution model posits that malignant transformation is preceded by randomly distributed driver mutations in cancer genes, which cause clonal expansions in phenotypically normal tissues. Although clonal expansions can remodel entire tissues1-3, the mechanisms that result in only a small number of clones transforming into malignant tumours remain unknown. Here we develop an in vivo single-cell CRISPR strategy to systematically investigate tissue-wide clonal dynamics of the 150 most frequently mutated squamous cell carcinoma genes. We couple ultrasound-guided in utero lentiviral microinjections, single-cell RNA sequencing and guide capture to longitudinally monitor clonal expansions and document their underlying gene programmes at single-cell transcriptomic resolution. We uncover a tumour necrosis factor (TNF) signalling module, which is dependent on TNF receptor 1 and involving macrophages, that acts as a generalizable driver of clonal expansions in epithelial tissues. Conversely, during tumorigenesis, the TNF signalling module is downregulated. Instead, we identify a subpopulation of invasive cancer cells that switch to an autocrine TNF gene programme associated with epithelial-mesenchymal transition. Finally, we provide in vivo evidence that the autocrine TNF gene programme is sufficient to mediate invasive properties and show that the TNF signature correlates with shorter overall survival of patients with squamous cell carcinoma. Collectively, our study demonstrates the power of applying in vivo single-cell CRISPR screening to mammalian tissues, unveils distinct TNF programmes in tumour evolution and highlights the importance of understanding the relationship between clonal expansions in epithelia and tumorigenesis.
Subject(s)
CRISPR-Cas Systems , Carcinoma, Squamous Cell , Cell Transformation, Neoplastic , Clonal Evolution , Clone Cells , Single-Cell Analysis , Tumor Necrosis Factors , Animals , Female , Humans , Male , Mice , Carcinoma, Squamous Cell/genetics , Carcinoma, Squamous Cell/pathology , Cell Transformation, Neoplastic/genetics , Cell Transformation, Neoplastic/pathology , Clonal Evolution/genetics , Clone Cells/cytology , Clone Cells/metabolism , Clone Cells/pathology , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , CRISPR-Cas Systems/genetics , Epithelial-Mesenchymal Transition/genetics , Gene Expression Regulation, Neoplastic , Macrophages/metabolism , Mutation , Neoplasm Invasiveness/genetics , Receptors, Tumor Necrosis Factor, Type I/genetics , Receptors, Tumor Necrosis Factor, Type I/metabolism , Signal Transduction/genetics , Single-Cell Analysis/methods , Transcriptome/genetics , Tumor Necrosis Factors/genetics , Tumor Necrosis Factors/metabolism , Autocrine Communication , Survival AnalysisABSTRACT
Mosaic loss of the X chromosome (mLOX) is the most common clonal somatic alteration in leukocytes of female individuals1,2, but little is known about its genetic determinants or phenotypic consequences. Here, to address this, we used data from 883,574 female participants across 8 biobanks; 12% of participants exhibited detectable mLOX in approximately 2% of leukocytes. Female participants with mLOX had an increased risk of myeloid and lymphoid leukaemias. Genetic analyses identified 56 common variants associated with mLOX, implicating genes with roles in chromosomal missegregation, cancer predisposition and autoimmune diseases. Exome-sequence analyses identified rare missense variants in FBXO10 that confer a twofold increased risk of mLOX. Only a small fraction of associations was shared with mosaic Y chromosome loss, suggesting that distinct biological processes drive formation and clonal expansion of sex chromosome missegregation. Allelic shift analyses identified X chromosome alleles that are preferentially retained in mLOX, demonstrating variation at many loci under cellular selection. A polygenic score including 44 allelic shift loci correctly inferred the retained X chromosomes in 80.7% of mLOX cases in the top decile. Our results support a model in which germline variants predispose female individuals to acquiring mLOX, with the allelic content of the X chromosome possibly shaping the magnitude of clonal expansion.
Subject(s)
Aneuploidy , Chromosomes, Human, X , Clone Cells , Leukocytes , Mosaicism , Adult , Female , Humans , Male , Middle Aged , Alleles , Autoimmune Diseases/genetics , Biological Specimen Banks , Chromosome Segregation/genetics , Chromosomes, Human, X/genetics , Chromosomes, Human, Y/genetics , Clone Cells/metabolism , Clone Cells/pathology , Exome/genetics , F-Box Proteins/genetics , Genetic Predisposition to Disease/genetics , Germ-Line Mutation , Leukemia/genetics , Leukocytes/metabolism , Models, Genetic , Multifactorial Inheritance/genetics , Mutation, Missense/geneticsABSTRACT
In somatic tissue differentiation, chromatin accessibility changes govern priming and precursor commitment towards cellular fates1-3. Therefore, somatic mutations are likely to alter chromatin accessibility patterns, as they disrupt differentiation topologies leading to abnormal clonal outgrowth. However, defining the impact of somatic mutations on the epigenome in human samples is challenging due to admixed mutated and wild-type cells. Here, to chart how somatic mutations disrupt epigenetic landscapes in human clonal outgrowths, we developed genotyping of targeted loci with single-cell chromatin accessibility (GoT-ChA). This high-throughput platform links genotypes to chromatin accessibility at single-cell resolution across thousands of cells within a single assay. We applied GoT-ChA to CD34+ cells from patients with myeloproliferative neoplasms with JAK2V617F-mutated haematopoiesis. Differential accessibility analysis between wild-type and JAK2V617F-mutant progenitors revealed both cell-intrinsic and cell-state-specific shifts within mutant haematopoietic precursors, including cell-intrinsic pro-inflammatory signatures in haematopoietic stem cells, and a distinct profibrotic inflammatory chromatin landscape in megakaryocytic progenitors. Integration of mitochondrial genome profiling and cell-surface protein expression measurement allowed expansion of genotyping onto DOGMA-seq through imputation, enabling single-cell capture of genotypes, chromatin accessibility, RNA expression and cell-surface protein expression. Collectively, we show that the JAK2V617F mutation leads to epigenetic rewiring in a cell-intrinsic and cell type-specific manner, influencing inflammation states and differentiation trajectories. We envision that GoT-ChA will empower broad future investigations of the critical link between somatic mutations and epigenetic alterations across clonal populations in malignant and non-malignant contexts.
Subject(s)
Chromatin , Epigenesis, Genetic , Genotype , Mutation , Single-Cell Analysis , Animals , Female , Humans , Male , Mice , Antigens, CD34/metabolism , Cell Differentiation/genetics , Chromatin/chemistry , Chromatin/genetics , Chromatin/metabolism , Epigenesis, Genetic/genetics , Epigenome/genetics , Genome, Mitochondrial/genetics , Genotyping Techniques , Hematopoiesis/genetics , Hematopoietic Stem Cells/metabolism , Hematopoietic Stem Cells/pathology , Inflammation/genetics , Inflammation/pathology , Janus Kinase 2/genetics , Janus Kinase 2/metabolism , Megakaryocytes/metabolism , Megakaryocytes/pathology , Membrane Proteins/genetics , Myeloproliferative Disorders/genetics , Myeloproliferative Disorders/metabolism , Myeloproliferative Disorders/pathology , RNA/genetics , Clone Cells/metabolismABSTRACT
Pancreatic intraepithelial neoplasias (PanINs) are the most common precursors of pancreatic cancer, but their small size and inaccessibility in humans make them challenging to study1. Critically, the number, dimensions and connectivity of human PanINs remain largely unknown, precluding important insights into early cancer development. Here, we provide a microanatomical survey of human PanINs by analysing 46 large samples of grossly normal human pancreas with a machine-learning pipeline for quantitative 3D histological reconstruction at single-cell resolution. To elucidate genetic relationships between and within PanINs, we developed a workflow in which 3D modelling guides multi-region microdissection and targeted and whole-exome sequencing. From these samples, we calculated a mean burden of 13 PanINs per cm3 and extrapolated that the normal intact adult pancreas harbours hundreds of PanINs, almost all with oncogenic KRAS hotspot mutations. We found that most PanINs originate as independent clones with distinct somatic mutation profiles. Some spatially continuous PanINs were found to contain multiple KRAS mutations; computational and in situ analyses demonstrated that different KRAS mutations localize to distinct cell subpopulations within these neoplasms, indicating their polyclonal origins. The extensive multifocality and genetic heterogeneity of PanINs raises important questions about mechanisms that drive precancer initiation and confer differential progression risk in the human pancreas. This detailed 3D genomic mapping of molecular alterations in human PanINs provides an empirical foundation for early detection and rational interception of pancreatic cancer.
Subject(s)
Genetic Heterogeneity , Genomics , Imaging, Three-Dimensional , Pancreatic Neoplasms , Precancerous Conditions , Single-Cell Analysis , Adult , Female , Humans , Male , Clone Cells/metabolism , Clone Cells/pathology , Exome Sequencing , Machine Learning , Mutation , Pancreas/anatomy & histology , Pancreas/cytology , Pancreas/metabolism , Pancreas/pathology , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/pathology , Precancerous Conditions/genetics , Precancerous Conditions/pathology , Workflow , Disease Progression , Early Detection of Cancer , Oncogenes/geneticsABSTRACT
Debate remains around the anatomical origins of specific brain cell subtypes and lineage relationships within the human forebrain1-7. Thus, direct observation in the mature human brain is critical for a complete understanding of its structural organization and cellular origins. Here we utilize brain mosaic variation within specific cell types as distinct indicators for clonal dynamics, denoted as cell-type-specific mosaic variant barcode analysis. From four hemispheres and two different human neurotypical donors, we identified 287 and 780 mosaic variants, respectively, that were used to deconvolve clonal dynamics. Clonal spread and allele fractions within the brain reveal that local hippocampal excitatory neurons are more lineage-restricted than resident neocortical excitatory neurons or resident basal ganglia GABAergic inhibitory neurons. Furthermore, simultaneous genome transcriptome analysis at both a cell-type-specific and a single-cell level suggests a dorsal neocortical origin for a subgroup of DLX1+ inhibitory neurons that disperse radially from an origin shared with excitatory neurons. Finally, the distribution of mosaic variants across 17 locations within one parietal lobe reveals that restriction of clonal spread in the anterior-posterior axis precedes restriction in the dorsal-ventral axis for both excitatory and inhibitory neurons. Thus, cell-type-resolved somatic mosaicism can uncover lineage relationships governing the development of the human forebrain.
Subject(s)
Cell Lineage , Clone Cells , Mosaicism , Neurons , Prosencephalon , Aged , Female , Humans , Alleles , Cell Lineage/genetics , Clone Cells/cytology , Clone Cells/metabolism , GABAergic Neurons/cytology , GABAergic Neurons/metabolism , Hippocampus/cytology , Homeodomain Proteins/metabolism , Neocortex/cytology , Neural Inhibition , Neurons/cytology , Neurons/metabolism , Parietal Lobe/cytology , Prosencephalon/anatomy & histology , Prosencephalon/cytology , Prosencephalon/metabolism , Single-Cell Analysis , Transcriptome/geneticsABSTRACT
The evolutionary processes that underlie the marked sensitivity of small cell lung cancer (SCLC) to chemotherapy and rapid relapse are unknown1-3. Here we determined tumour phylogenies at diagnosis and throughout chemotherapy and immunotherapy by multiregion sequencing of 160 tumours from 65 patients. Treatment-naive SCLC exhibited clonal homogeneity at distinct tumour sites, whereas first-line platinum-based chemotherapy led to a burst in genomic intratumour heterogeneity and spatial clonal diversity. We observed branched evolution and a shift to ancestral clones underlying tumour relapse. Effective radio- or immunotherapy induced a re-expansion of founder clones with acquired genomic damage from first-line chemotherapy. Whereas TP53 and RB1 alterations were exclusively part of the common ancestor, MYC family amplifications were frequently not constituents of the founder clone. At relapse, emerging subclonal mutations affected key genes associated with SCLC biology, and tumours harbouring clonal CREBBP/EP300 alterations underwent genome duplications. Gene-damaging TP53 alterations and co-alterations of TP53 missense mutations with TP73, CREBBP/EP300 or FMN2 were significantly associated with shorter disease relapse following chemotherapy. In summary, we uncover key processes of the genomic evolution of SCLC under therapy, identify the common ancestor as the source of clonal diversity at relapse and show central genomic patterns associated with sensitivity and resistance to chemotherapy.
Subject(s)
Evolution, Molecular , Immunotherapy , Lung Neoplasms , Platinum , Small Cell Lung Carcinoma , Animals , Female , Humans , Male , Mice , Middle Aged , Clone Cells/drug effects , Clone Cells/metabolism , Clone Cells/pathology , Drug Resistance, Neoplasm/drug effects , Drug Resistance, Neoplasm/genetics , Genes, myc/genetics , Lung Neoplasms/genetics , Lung Neoplasms/immunology , Lung Neoplasms/pathology , Lung Neoplasms/therapy , Mutation , Neoplasm Recurrence, Local/genetics , Neoplasm Recurrence, Local/pathology , Platinum/pharmacology , Platinum/therapeutic use , Recurrence , Small Cell Lung Carcinoma/genetics , Small Cell Lung Carcinoma/immunology , Small Cell Lung Carcinoma/pathology , Small Cell Lung Carcinoma/therapyABSTRACT
Plants possess different degrees of tolerance to abiotic stress, which can mitigate the detrimental effect of environmental inputs affecting carbon balance. Less is known about the functions of osmoprotectants in scavenging of reactive oxygen species (ROS), generated at different sites depending on leaf age. This study aimed to clarify the osmotic adjustments adopted by old and young leaves of Oxford and I-214 poplar clones [differing in ozone (O3) sensitivity] to cope with three levels of O3 [ambient (AA), and two elevated O3 levels]. In both clones, the impact of intermediate O3 concentrations (1.5 × AA) on ROS production appeared to be leaf age-specific, given the accumulation of hydrogen peroxide (H2O2) observed only in old leaves of the Oxford plants and in young leaves of the I-214 ones (2- fold higher than AA and +79%, respectively). The induction of an oxidative burst was associated with membrane injury, indicating an inadequate response of the antioxidative systems [decrease of lutein and ß-carotene (-37 and -85% in the old leaves of the Oxford plants), accumulation of proline and tocopherols (+60 and +12% in the young leaves of the I-214 ones)]. Intermediate O3 concentrations reacted with unsaturated lipids of the plasma membrane in old and young leaves of the Oxford plants, leading to an increase of malondialdehyde by-products (more than 2- fold higher than AA), while no effect was recorded for I-214. The impact of the highest O3 concentrations (2.0 × AA) on ROS production did not appear clone-specific, which may react with cell wall components by leading to oxidative pressure. Outcomes demonstrated the ability of young leaves of I-214 plants in contain O3 phytotoxic effects.
Subject(s)
Ozone , Populus , Antioxidants/metabolism , Ozone/toxicity , Hydrogen Peroxide/metabolism , Reactive Oxygen Species/metabolism , Plant Leaves/metabolism , Populus/metabolism , Clone Cells/metabolism , PhotosynthesisABSTRACT
Site-specific integration (SSI) via recombinase mediated cassette exchange (RMCE) has shown advantages over random integration methods for expression of biotherapeutics. As an extension of our previous work developing SSI host cells, we developed a dual-site SSI system having two independent integration sites at different genomic loci, each containing a unique landing pad (LP). This system was leveraged to generate and compare two RMCE hosts, one (dFRT) compatible with the Flp recombinase, the other (dBxb1) compatible with the Bxb1 recombinase. Our comparison demonstrated that the dBxb1 host was able to generate stable transfectant pools in a shorter time frame, and cells within the dBxb1 transfectant pools were more phenotypically and genotypically stable. We further improved process performance of the dBxb1 host, resulting in desired fed batch performance attributes. Clones derived from this improved host (referred as 41L-11) maintained stable expression profiles over extended generations. While the data represents a significant improvement in the efficiency of our cell line development process, the dual LP architecture also affords a high degree of flexibility for development of complex protein modalities.
Subject(s)
Genomics , Recombinases , Cricetinae , Animals , CHO Cells , Cricetulus , Recombinases/genetics , Clone Cells/metabolism , Genomics/methods , TransgenesABSTRACT
The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived haematopoietic stem cells (HSCs)1. Perturbations to this process underlie diverse diseases, but the clonal contributions to human haematopoiesis and how this changes with age remain incompletely understood. Although recent insights have emerged from barcoding studies in model systems2-5, simultaneous detection of cell states and phylogenies from natural barcodes in humans remains challenging. Here we introduce an improved, single-cell lineage-tracing system based on deep detection of naturally occurring mitochondrial DNA mutations with simultaneous readout of transcriptional states and chromatin accessibility. We use this system to define the clonal architecture of HSCs and map the physiological state and output of clones. We uncover functional heterogeneity in HSC clones, which is stable over months and manifests as both differences in total HSC output and biases towards the production of different mature cell types. We also find that the diversity of HSC clones decreases markedly with age, leading to an oligoclonal structure with multiple distinct clonal expansions. Our study thus provides a clonally resolved and cell-state-aware atlas of human haematopoiesis at single-cell resolution, showing an unappreciated functional diversity of human HSC clones and, more broadly, paving the way for refined studies of clonal dynamics across a range of tissues in human health and disease.
Subject(s)
Cell Lineage , Hematopoiesis , Hematopoietic Stem Cells , Humans , Chromatin/genetics , Chromatin/metabolism , Clone Cells/classification , Clone Cells/cytology , Clone Cells/metabolism , DNA, Mitochondrial/genetics , Hematopoietic Stem Cells/classification , Hematopoietic Stem Cells/cytology , Hematopoietic Stem Cells/metabolism , Mutation , Single-Cell Analysis , Transcription, Genetic , AgingABSTRACT
Bone mesenchymal stem cell (BMSC)-derived exosome (BMSC-Exo) could be a treatment method for ischemic injury. In ischemic cerebrovascular disease (IC), microglia is pivotal in neuronal damage and remodeling. This study explores the mechanisms of BMSC-Exo miR-148b-3p in regulating oxygen-glucose deprivation/reoxygenation (OGD/R)-induced human microglial clone 3 (HMC3) cell activation. Transmission electron microscopy (TEM) and qNano were used to assess BMSC-Exo features. The functions of BMSC-Exo miR-148 b-3p in OGD/R-induced HMC3 cell activation were explored via MTT assay, flow cytometry, scratch, transwell, and enzyme-linked immunosorbent assay (ELISA) assays. A dual-luciferase reporter assay was performed to determine the relationship between miR-148b-3p and Delta-like ligand 4(DDL4) or neurogenic locus notch homolog protein 1 (Notch1). OGD/R decreased miR-148b-3p expression in HMC3 cells. After BMSC-Exo treatment, miR-148b-3p expression was upregulated, cell viability and migration were inhibited, cell cycles remained in the G0/G1 phase, and proinflammatory cytokines were decreased in OGD/R-induced HMC3 cells. More importantly, BMSC-Exo miR-148b-3p could further strengthen BMSC-Exo effects. DDL4 and Notch1 are direct targets of miR-148b-3p, respectively. Moreover, the knockdown of DLL4 or Notch1 could inhibit OGD/R-induced HMC3 cell activation. BMSC-Exo miR-148b-3p inhibited OGD/R-induced HMC3 cell activation via inhibiting DLL4 and Notch1 expression, which provided a new strategy for treating cerebral ischemia.
Subject(s)
Mesenchymal Stem Cells , MicroRNAs , Humans , MicroRNAs/metabolism , Oxygen/pharmacology , Glucose/pharmacology , Mesenchymal Stem Cells/metabolism , Clone Cells/metabolism , Apoptosis , Calcium-Binding Proteins/metabolism , Adaptor Proteins, Signal Transducing/metabolismABSTRACT
Raman spectroscopy is widely used in monitoring and controlling cell cultivations for biopharmaceutical drug manufacturing. However, its implementation for culture monitoring in the cell line development stage has received little attention. Therefore, the impact of clonal differences, such as productivity and growth, on the prediction accuracy and transferability of Raman calibration models is not yet well described. Raman OPLS models were developed for predicting titer, glucose and lactate using eleven CHO clones from a single cell line. These clones exhibited diverse productivity and growth rates. The calibration models were evaluated for clone-related biases using clone-wise linear regression analysis on cross validated predictions. The results revealed that clonal differences did not affect the prediction of glucose and lactate, but titer models showed a significant clone-related bias, which remained even after applying variable selection methods. The bias was associated with clonal productivity and lead to increased prediction errors when titer models were transferred to cultivations with productivity levels outside the range of their training data. The findings demonstrate the feasibility of Raman-based monitoring of glucose and lactate in cell line development with high accuracy. However, accurate titer prediction requires careful consideration of clonal characteristics during model development.
Subject(s)
Lactic Acid , Spectrum Analysis, Raman , Cricetinae , Animals , CHO Cells , Cricetulus , Calibration , Feasibility Studies , Lactic Acid/metabolism , Spectrum Analysis, Raman/methods , Glucose/metabolism , Clone Cells/metabolismABSTRACT
How individual T cells compete for and respond to IL-2 at the molecular level, and, as a consequence, how this shapes population dynamics and the selection of high-affinity clones is still poorly understood. Here we describe how the RNA binding protein ZFP36L1, acts as a sensor of TCR affinity to promote clonal expansion of high-affinity CD8 T cells. As part of an incoherent feed-forward loop, ZFP36L1 has a nonredundant role in suppressing multiple negative regulators of cytokine signaling and mediating a selection mechanism based on competition for IL-2. We suggest that ZFP36L1 acts as a sensor of antigen affinity and establishes the dominance of high-affinity T cells by installing a hierarchical response to IL-2.
Subject(s)
Cytokines , Receptors, Antigen, T-Cell , Interleukin-2 , CD8-Positive T-Lymphocytes , Clone Cells/metabolismABSTRACT
Parkinson's disease is the second most common neurodegenerative disorder and is pathologically characterized by synuclein-rich aggregations (Lewy bodies) in neurons. Multiplication of the synuclein gene (SNCA) increases the mRNA and protein levels of synuclein, resulting in autosomal dominant hereditary Parkinson's disease. In the present study, we established three isogenic induced pluripotent stem cells (iPSCs) from a patient harboring SNCA duplication, which showed pluripotency, three-germ layer differentiation capacity, and normal karyotypes.
Subject(s)
Induced Pluripotent Stem Cells , Parkinson Disease , Humans , Parkinson Disease/genetics , Parkinson Disease/metabolism , alpha-Synuclein/genetics , alpha-Synuclein/metabolism , Induced Pluripotent Stem Cells/metabolism , Clone Cells/metabolism , Cell DifferentiationABSTRACT
The type and strength of effector functions mediated by immunoglobulin G (IgG) antibodies rely on the subclass and the composition of the N297 glycan. Glycosylation analysis of both bulk and antigen-specific human IgG has revealed a marked diversity of the glycosylation signatures, including highly dynamic patterns as well as long-term stability of profiles, yet information on how individual B cell clones would contribute to this diversity has hitherto been lacking. Here, we assessed whether clonally related B cells share N297 glycosylation patterns of their secreted IgG. We differentiated single antigen-specific peripheral IgG+ memory B cells into antibody-secreting cells and analysed Fc glycosylation of secreted IgG. Furthermore, we sequenced the variable region of their heavy chain, which allowed the grouping of the clones into clonotypes. We found highly diverse glycosylation patterns of culture-derived IgG, which, to some degree, mimicked the glycosylation of plasma IgG. Each B cell clone secreted IgG with a mixture of different Fc glycosylation patterns. The majority of clones produced fully fucosylated IgG. B cells producing afucosylated IgG were scattered across different clonotypes. In contrast, the remaining glycosylation traits were, in general, more uniform. These results indicate IgG-Fc fucosylation to be regulated at the single-clone level, whereas the regulation of other glycosylation traits most likely occurs at a clonotypic or systemic level. The discrepancies between plasma IgG and culture-derived IgG, could be caused by the origin of the B cells analysed, clonal dominance or factors from the culture system, which need to be addressed in future studies.
Subject(s)
Immunoglobulin Fc Fragments , Immunoglobulin G , Humans , Glycosylation , Immunoglobulin Fc Fragments/genetics , B-Lymphocytes/metabolism , Clone Cells/metabolismABSTRACT
The spatial distribution of lymphocyte clones within tissues is critical to their development, selection, and expansion. We have developed spatial transcriptomics of variable, diversity, and joining (VDJ) sequences (Spatial VDJ), a method that maps B cell and T cell receptor sequences in human tissue sections. Spatial VDJ captures lymphocyte clones that match canonical B and T cell distributions and amplifies clonal sequences confirmed by orthogonal methods. We found spatial congruency between paired receptor chains, developed a computational framework to predict receptor pairs, and linked the expansion of distinct B cell clones to different tumor-associated gene expression programs. Spatial VDJ delineates B cell clonal diversity and lineage trajectories within their anatomical niche. Thus, Spatial VDJ captures lymphocyte spatial clonal architecture across tissues, providing a platform to harness clonal sequences for therapy.
Subject(s)
B-Lymphocytes , Pre-B Cell Receptors , Receptors, Antigen, T-Cell , T-Lymphocytes , Humans , B-Lymphocytes/metabolism , Clone Cells/metabolism , Gene Expression Profiling/methods , Pre-B Cell Receptors/genetics , Receptors, Antigen, T-Cell/genetics , T-Lymphocytes/metabolismABSTRACT
BACKGROUND AND AIMS: Smooth muscle cell (SMC) lineage cells in atherosclerosis and flow cessation-induced neointima are oligoclonal, being recruited from a tiny fraction of medial SMCs that modulate and proliferate. The present study aimed to investigate the clonal structure of SMC lineage cells healing more severe arterial injury. METHODS: Arterial injury (wire, stretch, and partial ligation) was inflicted on the right carotid artery in mice with homozygous, SMC-restricted, stochastically recombining reporter transgenes that produced mosaic expression of 10 distinguishable fluorescent phenotypes for clonal tracking. Healed arteries and contra-lateral controls were analyzed after 3 weeks. Additional analysis of cell death and proliferation after injury was performed in wildtype mice. RESULTS: The total number of SMC lineage cells in healed arteries was comparable to normal arteries but comprised significantly fewer fluorescent phenotypes. The population had a complex, intermixed, clonal structure. By statistical analysis of expected versus observed fractions of fluorescent phenotypes and visual inspection of coherent groups of same-colored cells, we concluded that >98% of SMC lineage cells in healed arteries belonged to a detectable clone, indicating that nearly all surviving SMCs after severe injury at some point undergo proliferation. This was consistent with serial observations in the first week after injury, which showed severe loss of medial cells followed by widespread proliferation. CONCLUSIONS: After severe arterial injury, many surviving SMCs proliferate to repair the media and form a neointima. This indicates that the fraction of medial SMCs that are mobilized to repair arteries increases with the level of injury.
Subject(s)
Neointima , Vascular System Injuries , Mice , Animals , Neointima/metabolism , Cell Proliferation , Muscle, Smooth, Vascular/metabolism , Clone Cells/metabolism , Vascular System Injuries/metabolism , Myocytes, Smooth Muscle/metabolism , Cells, CulturedABSTRACT
Pseudomonas aeruginosa high-risk clones pose severe threats to public health. Here, we characterize the imipenem/relebactam (IR) resistance mechanisms in P. aeruginosa high-risk clones sequence type 235 (ST235) and ST463 in China. Minimum inhibitory concentrations (MICs) were determined, and Illumina short-read sequencing was performed for 1,168 clinical carbapenem-resistant P. aeruginosa (CRPA) isolates. The gene copy number and expression level were analyzed by Illumina sequencing depth and reverse transcription-quantitative PCR, respectively. Resistance conferred by bla GES-5 was evaluated by cloning experiments. ST463 and ST235 accounted for 9.8% (115/1,168) and 4.5% (53/1,168) of total isolates, respectively, and showed high frequencies of extensively drug-resistant and difficult-to-treat resistant phenotypes. The overall IR-resistant rate in CRPA was 21.0% (245/1,168). However, the IR resistance rate was 81.7% (94/115) in ST463-PA and 52.8% (28/53) in ST235-PA. Of the ST463 isolates, 92.2% (106/115) were Klebsiella pneumoniae carbapenemase-producing P. aeruginosa (KPC-PA), and all 94 IR-resistant ST463-PA produced KPC-2. Compared to IR-susceptible ST463 KPC-2-PA, IR-resistant ST463 KPC-2-PA exhibited significantly higher bla KPC-2 copy numbers and expression levels. In ST463 KPC-2-PA, 16 mg/L relebactam resulted in additional fourfold reductions in imipenem MIC50/90 values compared to 4 mg/L relebactam. In ST235, 1.9% (1/53) carried bla IMP carbapenemase and 54.7% (29/53) carried bla GES carbapenemase. Other than the IMP producer, all 27 IR-resistant ST235-PA produced GES-5. Cloning experiments revealed that imipenem resistance in bla GES-5-carrying PAO1 transformants was generally unaffected by relebactam. In conclusion, IR-resistant CRPA isolates in China were mainly distributed in P. aeruginosa high-risk clones ST463 and ST235. The major underlying IR resistance mechanisms were bla KPC-2 overexpression and bla GES-5 carriage.