Single-cell transcriptional uncertainty landscape of cell differentiation

Background: Single-cell studies have demonstrated the presence of significant cell-to-cell heterogeneity in gene expression. Whether such heterogeneity is only a bystander or has a functional role in the cell differentiation process is still hotly debated. Methods: In this study, we quantified and followed single-cell transcriptional uncertainty - a measure of gene transcriptional stochasticity in single cells - in 10 cell differentiation systems of varying cell lineage progressions, from single to multi-branching trajectories, using the stochastic two-state gene transcription model. Results: By visualizing the transcriptional uncertainty as a landscape over a two-dimensional representation of the single-cell gene expression data, we observed universal features in the cell differentiation trajectories that include: (i) a peak in single-cell uncertainty during transition states, and in systems with bifurcating differentiation trajectories, each branching point represents a state of high transcriptional uncertainty; (ii) a positive correlation of transcriptional uncertainty with transcriptional burst size and frequency; (iii) an increase in RNA velocity preceding the increase in the cell transcriptional uncertainty. Conclusions: Our findings suggest a possible universal mechanism during the cell differentiation process, in which stem cells engage stochastic exploratory dynamics of gene expression at the start of the cell differentiation by increasing gene transcriptional bursts, and disengage such dynamics once cells have decided on a particular terminal cell identity. Notably, the peak of single-cell transcriptional uncertainty signifies the decision-making point in the cell differentiation process.

Constraints on Human CD34+ Cell Fate due to Lentiviral Vectors Can Be Relieved by Valproic Acid

The initial stages following the in vitro cytokine stimulation of human cord blood CD34+ cells overlap with the period when lentiviral gene transfer is typically performed. Single-cell transcriptional profiling and time-lapse microscopy were used to investigate how the vector-cell crosstalk impacts on the fate decision process. The single-cell transcription profiles were analyzed using a new algorithm, and it is shown that lentiviral transduction during the early stages of stimulation modifies the dynamics of the fate choice process of the CD34+ cells. The cells transduced with a lentiviral vector are biased toward the common myeloid progenitor lineage. Valproic acid, a histone deacetylase inhibitor known to increase the grafting potential of the CD34+ cells, improves the transduction efficiency to almost 100%. The cells transduced in the presence of valproic acid can subsequently undergo normal fate commitment. The higher gene transfer efficiency did not alter the genomic integration profile of the vector. These observations open the way to substantially improving lentiviral gene transfer protocols.

Integrated time-lapse and single-cell transcription studies highlight the variable and dynamic nature of human hematopoietic cell fate commitment

Individual cells take lineage commitment decisions in a way that is not necessarily uniform. We address this issue by characterising transcriptional changes in cord blood-derived CD34+ cells at the single-cell level and integrating data with cell division history and morphological changes determined by time-lapse microscopy. We show that major transcriptional changes leading to a multilineage-primed gene expression state occur very rapidly during the first cell cycle. One of the 2 stable lineage-primed patterns emerges gradually in each cell with variable timing. Some cells reach a stable morphology and molecular phenotype by the end of the first cell cycle and transmit it clonally. Others fluctuate between the 2 phenotypes over several cell cycles. Our analysis highlights the dynamic nature and variable timing of cell fate commitment in hematopoietic cells, links the gene expression pattern to cell morphology, and identifies a new category of cells with fluctuating phenotypic characteristics, demonstrating the complexity of the fate decision process (which is different from a simple binary switch between 2 options, as it is usually envisioned).

Hematopoietic stem cells are classically defined as a specific category of cells at the top of the hierarchy that can differentiate all blood cell types following step-by-step the instructions of a deterministic program. We have analysed this process, and our findings support a much more dynamic view than previously described. We apply time-lapse microscopy coupled to single-cell molecular analyses in human hematopoietic stem cells and find that fate decision is not a unique, programmed event but a process of spontaneous variation and selective stabilisation reminiscent of trial–error processes. We show that each cell explores (at its own pace and independently of cell division) many different possibilities before reaching a stable combination of genes to be expressed. Our results suggest, therefore, that multipotency seems to be more like a transitory state than a feature of a specific cell category.

The constant variation: DNA methylation changes during preimplantation development

Studies on the DNA methylation changes in the mouse preimplantation embryo suggested a simple and attractive model explaining the process believed to be general in mammals. However, recent reports revealed marked differences between different species that abrogates the universal validity of the model. In order to find an explanation to the differences, we have analyzed the published mouse data and compared them to the observations available in other species. The emerging common theme is the high variability of the methylation at all scales of observation and all levels of organization. This variability is the likely consequence of a dynamic and active redistribution process of the cytosine methylation in the genome.

Paradoxical methylation of the tyrosine hydroxylase gene in mouse preimplantation embryos

The mouse tyrosine hydroxylase (Th) gene is located in an evolutionarily conserved imprinted gene cluster on distal chromosome 7. It is associated with a CpG island that spans the promoter of the gene. Using a bisulfite sequencing method we show that the Th promoter is fully methylated in both male and female mouse germ cells and in human spermatozoa, suggesting that it belongs to the newly identified category of CpG islands, the similarly methylated regions (SMRs). Contrary to other tissue-specific gene sequences, the mouse Th promoter escapes the initial wave of genome demethylation during the first few cell cycles, but becomes demethylated between the morula and the blastocyst stages. This unusual methylation ontogeny may be a characteristic of the SMRs and/or related to the localization of the Th gene in an imprinted gene cluster.

New method for culture of zona-included or zona-free embryos: the Well of the Well (WOW) system

Culture of mammalian zygotes individually and in small groups results in lower developmental rates than culture of large groups. Zona-free zygotes also have impaired developmental potential in current culture systems. This paper describes a new approach to resolve the problems, the Well of the Well (WOW) system. Small wells (WOWs) were formed in four-well dishes by melting the bottom with heated steel rods. The WOWs were then rinsed, the wells were filled with medium, and the embryos were placed into the WOWs. To test the value of the WOW system a 3 x 3 factorial experiment was performed. Bovine presumptive zygotes were cultured from day 1 to day 7 (day 0: day of insemination) using three modules (single embryos, embryo groups of five, or single zona-digested embryos) and three different culture systems (400 microl medium, 200 microl drops, or WOWs). An additional control group consisted of 40 to 50 embryos cultured in 400 microl medium. The WOW system resulted in higher blastocyst/oocyte rates for all three modules (single: 59%; group of five: 61%; single zona-digested: 53%) than the culture in drops or in wells (P < 0.05 for all). The developmental rate was independent of the number of WOWs per well. The cell number of blastocysts cultured in the WOW system did not differ from that of the controls. Apart from its theoretical value in revealing the role of different factors influencing embryo development in vitro, the WOW system may have immediate practical consequences in certain areas of mammalian embryo production.

Tissue- and developmental stage-specific imprinting of the mouse proinsulin gene, Ins2

We have investigated the imprinting status of two insulin genes using an interspecific recombinant congenic mouse strain carrying Ins1 and Ins2 alleles from Mus spretus on a C57BL/6 genetic background. At Days 12.5, 13.5, and 14.5 of gestation, expression of both parental alleles of both Ins1 and Ins2 was detected in the bodies of the embryos. In the heads, only Ins2 expression was detected, and, again, both parental alleles were expressed. In yolk sacs, only Ins2 transcripts were found. Both parental alleles were expressed on Day 12.5, but the expression of the maternal allele gradually declined with only the paternal allele remaining active by Day 14.5. Thus, Ins2 is subject to genomic imprinting in the yolk sac. This imprinting is not only tissue-specific, but appears to be a multistep process with postzygotic events likely to play an important role in repression of the maternal allele.

The zonal expression of chicken cartilage matrix protein gene in the developing skeleton of transgenic mice

Cartilage matrix protein (CMP) is a major noncollagenous glycoprotein of hyaline cartilage with a molecular mass of about 148 kDa. It has been proposed to be involved in matrix organization by its interactions with proteoglycan and type II collagen. The 54-kDa monomers form homotrimers stabilized by disulfide bonds. The gene for chicken cartilage matrix protein was isolated, and its regulation has been studied recently in transient expression experiments. To learn more about the spatial and temporal expression of the gene during ontogenic development, we created transgenic mice via microinjection of a 21.8-kb genomic fragment, encoding the chicken cartilage matrix protein. None of the founder animals exhibited any abnormal phenotype. The developmental stage-specific expression of the transgene was examined by immunostaining with a chicken CMP specific antiserum at different stages of embryonic development in cartilage from different sources: lower and upper limb, vertebrae, ribs and nasal septum. The level of transgene expression showed marked differences in various zones of cartilage. Briefly, high levels were found in the zones of proliferating chondrocytes, while little if any transgene product was detected in the very early and hypertrophic stage of chondrogenesis. The expression pattern of the transgene correlated with the endogenous mouse CMP and did not cause any morphological changes detectable by microscopic analysis of cartilage. These data indicate that the injected CMP gene with its flanking sequences contained all the information necessary for cell type-specific expression in transgenic mice.

Biopsy and sex determination by PCR of IVF bovine embryos

Sex of early bovine embryos was determined by polymerase chain reaction (PCR) using a single blastomere removed at the 16-32 cell stage. Embryos were produced in vitro and biopsied on the fifth day after in vitro fertilization. Biopsied embryos were cultured on a cumulus cell monolayer until embryo transfer. For the PCR, one pair of bovine-specific and one pair of Y-chromosome-specific primers were used. Definite signals following PCR amplification were obtained in 95.4% of cases indicating that one blastomere from a preimplantation bovine embryo is sufficient for sex determination by PCR. Nineteen biopsied embryos of predetermined sex were transferred into synchronized recipient females to examine their developmental potential in vivo. Ten of the recipients (52.6%) were found to be pregnant by ultrasonography 25 days after transfer. This result did not differ significantly from that achieved with the use of the control non-manipulated IVF embryos (54.1%; P > 0.1).

Prenatal fate of parthenogenetic cells in mouse aggregation chimaeras

Parthenogenetically activated BCF1 and fertilized BALB/c embryos were aggregated to form chimaeras. The fate of the parthenogenetic component was followed in the conceptus during the second half of gestation. The results indicate an early strong selection against parthenogenetic cells in the extra-embryonal part, which is presumably complete by term, and a weaker selective process in the embryo. During early development, parthenogenetic cells have nearly normal developmental potency in the embryo, which allows their balanced contribution in the chimaeras on day 12. Later, this contribution declines significantly resulting in an unbalanced relation to the advantage of the fertilized counterpart. From the results, we suggest that gametic imprinting may play a role not only in the key steps of preimplantation and early postimplantation development, but later in cell and tissue differentiation.

Inhibition of angiotensin-converting enzyme by angiotensin I analogue peptide inhibitors. A kinetic study

Angiotensin I analogues with a phosphonic acid group replacing the C-terminal carboxyl group were shown to be competitive inhibitors of angiotensin-converting enzyme. This new class of inhibitors was used to study the binding requirements of the angiotensin I-like ligands to the enzyme's active site. These studies indicate that angiotensin-converting enzyme recognizes at least five amino acid residues at the C-terminus of the peptide. The effect of pH on the binding of the most potent inhibitor peptide was compared to Captopril. The two inhibitors showed similar Ki-pH profiles despite their structural differences. Chloride enhanced the binding of the peptide inhibitor at both pH 9.0 and pH 6.5. At pH 9.0 the inhibitor peptide and the anion bind randomly to the enzyme, while at pH 6.5 the mechanism is ordered. In the latter case, the anion binds first to the enzyme.

Action of neutral metalloendopeptidase ("enkephalinase") on beta-endorphin

Human beta-endorphin was digested by neutral metalloendopeptidase from rabbit kidney and the products were isolated and identified. Based on the structure and yield of the fragments, the major cleavage sites were identified with the Leu17-Phe18, Gly3-Phe4, Pro13-Leu14 and Ile22-Ile23 peptide bonds of the beta-endorphin structure. The cleavage of the Leu17-Phe18 bond appears to be the rate-limiting step of the enzymic conversion similarly to the previously proposed pathways of beta-endorphin degradation by brain homogenates and synaptic membranes.