Single-cell multi-omics and lineage tracing to dissect cell fate decision-making

The concept of cell fate relates to the future identity of a cell, and its daughters, which is obtained via cell differentiation and division. Understanding, predicting, and manipulating cell fate has been a long-sought goal of developmental and regenerative biology. Recent insights obtained from single-cell genomic and integrative lineage-tracing approaches have further aided to identify molecular features predictive of cell fate. In this perspective, we discuss these approaches with a focus on theoretical concepts and future directions of the field to dissect molecular mechanisms underlying cell fate

cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries

BACKGROUND: Exogenous cDNA introduced into an experimental system, either intentionally or accidentally, can appear as added read coverage over that gene in next-generation sequencing libraries derived from this system. If not properly recognized and managed, this cross-contamination with exogenous signal can lead to incorrect interpretation of research results. Yet, this problem is not routinely addressed in current sequence processing pipelines. RESULTS: We present cDNA-detector, a computational tool to identify and remove exogenous cDNA contamination in DNA sequencing experiments. We demonstrate that cDNA-detector can identify cDNAs quickly and accurately from alignment files. A source inference step attempts to separate endogenous cDNAs (retrocopied genes) from potential cloned, exogenous cDNAs. cDNA-detector provides a mechanism to decontaminate the alignment from detected cDNAs. Simulation studies show that cDNA-detector is highly sensitive and specific, outperforming existing tools. We apply cDNA-detector to several highly-cited public databases (TCGA, ENCODE, NCBI SRA) and show that contaminant genes appear in sequencing experiments where they lead to incorrect coverage peak calls. CONCLUSIONS: cDNA-detector is a user-friendly and accurate tool to detect and remove cDNA detection in NGS libraries. This two-step design reduces the risk of true variant removal since it allows for manual review of candidates. We find that contamination with intentionally and accidentally introduced cDNAs is an underappreciated problem even in widely-used consortium datasets, where it can lead to spurious results. Our findings highlight the importance of sensitive detection and removal of contaminant cDNA from NGS libraries before downstream analysis

Clonal expansion and epigenetic inheritance of long-lasting NK cell memory

Clonal expansion of cells with somatically diversified receptors and their long-term maintenance as memory cells is a hallmark of adaptive immunity. Here, we studied pathogen-specific adaptation within the innate immune system, tracking natural killer (NK) cell memory to human cytomegalovirus (HCMV) infection. Leveraging single-cell multiomic maps of ex vivo NK cells and somatic mitochondrial DNA mutations as endogenous barcodes, we reveal substantial clonal expansion of adaptive NK cells in HCMV(+) individuals. NK cell clonotypes were characterized by a convergent inflammatory memory signature enriched for AP1 motifs superimposed on a private set of clone-specific accessible chromatin regions. NK cell clones were stably maintained in specific epigenetic states over time, revealing that clonal inheritance of chromatin accessibility shapes the epigenetic memory repertoire. Together, we identify clonal expansion and persistence within the human innate immune system, suggesting that these mechanisms have evolved independent of antigen-receptor diversification

Multifractality of Hamiltonians with power-law transfer terms

Finite-size effects in the generalized fractal dimensions $d_q$ are investigated numerically. We concentrate on a one-dimensional disordered model with long-range random hopping amplitudes in both the strong- and the weak-coupling regime. At the macroscopic limit, a linear dependence of $d_q$ on $q$ is found in both regimes for values of q \alt 4g^{-1}, where $g$ is the coupling constant of the model.Comment: RevTex4, 5 two-column pages, 5 .eps figures, to be published in Phys. Rev.

Projection Postulate and Atomic Quantum Zeno Effect

The projection postulate has been used to predict a slow-down of the time evolution of the state of a system under rapidly repeated measurements, and ultimately a freezing of the state. To test this so-called quantum Zeno effect an experiment was performed by Itano et al. (Phys. Rev. A 41, 2295 (1990)) in which an atomic-level measurement was realized by means of a short laser pulse. The relevance of the results has given rise to controversies in the literature. In particular the projection postulate and its applicability in this experiment have been cast into doubt. In this paper we show analytically that for a wide range of parameters such a short laser pulse acts as an effective level measurement to which the usual projection postulate applies with high accuracy. The corrections to the ideal reductions and their accumulation over n pulses are calculated. Our conclusion is that the projection postulate is an excellent pragmatic tool for a quick and simple understanding of the slow-down of time evolution in experiments of this type. However, corrections have to be included, and an actual freezing does not seem possible because of the finite duration of measurements.Comment: 25 pages, LaTeX, no figures; to appear in Phys. Rev.

Mitochondrial variant enrichment from high-throughput single-cell RNA-seq resolves clonal populations

Reconstructing lineage relationships in complex tissues can reveal mechanisms underlying development and disease. Recent methods combine single-cell transcriptomics with mitochondrial DNA variant detection to establish lineage relationships in primary human cells, but are not scalable to interrogate complex tissues. To overcome this limitation, here we develop a technology for high-confidence detection of mitochondrial mutations from high-throughput single-cell RNA-sequencing. We use the new method to identify skewed immune cell expansions in primary human clonal hematopoiesis

Transcriptional states and chromatin accessibility underlying human erythropoiesis

Human erythropoiesis serves as a paradigm of physiologic cellular differentiation. This process is also of considerable interest for better understanding anemias and identifying new therapies. Here, we apply deep transcriptomic and accessible chromatin profiling to characterize a faithful ex vivo human erythroid differentiation system from hematopoietic stem and progenitor cells. We reveal stage-specific transcriptional states and chromatin accessibility during various stages of erythropoiesis, including 14,260 differentially expressed genes and 63,659 variably accessible chromatin peaks. Our analysis suggests differentiation stage-predominant roles for specific master regulators, including GATA1 and KLF1. We integrate chromatin profiles with common and rare genetic variants associated with erythroid cell traits and diseases, finding that variants regulating different erythroid phenotypes likely act at variable points during differentiation. In addition, we identify a regulator of terminal erythropoiesis, TMCC2, more broadly illustrating the value of this comprehensive analysis to improve our understanding of erythropoiesis in health and disease

Automatizability and Simple Stochastic Games

The complexity of simple stochastic games (SSGs) has been open since they were dened by Condon in 1992. Despite intensive eort, the complexity of this problem is still unresolved. In this paper, building on the results of [4], we establish a connection between the complexity of SSGs and the complexity of an important problem in proof complexity{the proof search problem for low depth Frege systems. We prove that if depth-3 Frege systems are weakly automatizable, then SSGs are solvable in polynomial-time. Moreover we identify a natural combinatorial principle, which is a version of the well-known Graph Ordering Principle (GOP), that we call the integer-valued GOP (IGOP). This principle states that for any graph G with nonnegative integer weights associated with each node, there exists a locally maximal vertex (a vertex whose weight is at least as large as its neighbors). We prove that if depth-2 Frege plus IGOP is weakly automatizable, then SSG is in P. Supported by NSERC.

Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis

Genome-wide association studies (GWAS) have identified thousands of variants associated with human diseases and traits. However, the majority of GWAS-implicated variants are in non-coding regions of the genome and require in depth follow-up to identify target genes and decipher biological mechanisms. Here, rather than focusing on causal variants, we have undertaken a pooled loss-of-function screen in primary hematopoietic cells to interrogate 389 candidate genes contained in 75 loci associated with red blood cell traits. Using this approach, we identify 77 genes at 38 GWAS loci, with most loci harboring 1-2 candidate genes. Importantly, the hit set was strongly enriched for genes validated through orthogonal genetic approaches. Genes identified by this approach are enriched in specific and relevant biological pathways, allowing regulators of human erythropoiesis and modifiers of blood diseases to be defined. More generally, this functional screen provides a paradigm for gene-centric follow up of GWAS for a variety of human diseases and traits