Single-Cell Sequencing: With the rapid progress in sequencing technologies, single-cell sequencing is now possible, promising insight into how cell-to-cell heterogeneity affects biological behavior. Achieving adequate genome coverage remains a challenge because single-cell sequencing relies on genome amplification that is prone to sequence bias. Zong et al. (p. 1622 ) report a new amplification method: multiple annealing and looping-based amplification cycles that allowed 93% genome coverage for a human cell. This coverage facilitated accurate detection of point mutations and copy number variations. Lu et al. (p. 1627 ) used the method to sequence 99 sperm cells from a single individual. Mapping the meiotic crossovers revealed a nonrandom distribution with a reduced recombination rate near transcription start sites.

The cross-talk between immune cells and blood vessel endothelial cells promotes pericyte coverage and decreases hypoxia in mouse tumour models, and correlative evidence suggests that these processes influence cancer prognosis in humans. Tumours often develop with abnormal vasculature, characterized among other things by lower pericyte coverage of blood vessels, as well as leaky vessels that result in a hypoxic environment. Abnormal vessels limit immune infiltration and CD4 T cells can regulate angiogenesis. Using mouse models, the authors further dissect this crosstalk between immune cells and blood vessels in cancer, and describe a role for immune cells in normalizing the vasculature of tumours. The crosstalk between CD4 T cells and endothelial cells promotes pericyte coverage and decreases hypoxia, and correlative evidence suggests that these processes influence cancer prognosis in humans. The authors postulate that interventions that foster CD4 T-cell function, such as immune checkpoint blockade, also have a beneficial effect by normalizing the tumour vasculature. Blockade of angiogenesis can retard tumour growth, but may also paradoxically increase metastasis1,2. This paradox may be resolved by vessel normalization3, which involves increased pericyte coverage, improved tumour vessel perfusion, reduced vascular permeability, and consequently mitigated hypoxia3. Although these processes alter tumour progression, their regulation is poorly understood. Here we show that type 1 T helper (TH1) cells play a crucial role in vessel normalization. Bioinformatic analyses revealed that gene expression features related to vessel normalization correlate with immunostimulatory pathways, especially T lymphocyte infiltration or activity. To delineate the causal relationship, we used various mouse models with vessel normalization or T lymphocyte deficiencies. Although disruption of vessel normalization reduced T lymphocyte infiltration as expected4, reciprocal depletion or inactivation of CD4+ T lymphocytes decreased vessel normalization, indicating a mutually regulatory loop. In addition, activation of CD4+ T lymphocytes by immune checkpoint blockade increased vessel normalization. TH1 cells that secrete interferon-γ are a major population of cells associated with vessel normalization. Patient-derived xenograft tumours growing in immunodeficient mice exhibited enhanced hypoxia compared to the original tumours in immunocompetent humans, and hypoxia was reduced by adoptive TH1 transfer. Our findings elucidate an unexpected role of TH1 cells in vasculature and immune reprogramming. TH1 cells may be a marker and a determinant of both immune checkpoint blockade and anti-angiogenesis efficacy.

Ido Golding and colleagues examine transcriptional time series in Escherichia coli, characterizing mRNA copy number statistics for 20 promoters at single transcript resolution. They find that the degree of burstiness depends primarily on the level of gene expression. Gene activity is described by the time series of discrete, stochastic mRNA production events. This transcriptional time series shows intermittent, bursty behavior. One consequence of this temporal intricacy is that gene expression can be tuned by varying different features of the time series. Here we quantify copy-number statistics of mRNA from 20 Escherichia coli promoters using single-molecule fluorescence in situ hybridization in order to characterize the general properties of these transcriptional time series. We find that the degree of burstiness is correlated with gene expression level but is largely independent of other parameters of gene regulation. The observed behavior can be explained by the underlying variation in the duration of bursting events. Using Shannon's mutual information function, we estimate the mutual information transmitted between an outside stimulus, such as the extracellular concentration of inducer molecules, and intracellular levels of mRNA. This suggests that the outside stimulus transmits information reflected in the properties of transcriptional time series.

Significance: In a few milliliters of blood from a cancer patient, one can isolate a few circulating tumor cells (CTCs). Originating from the primary tumor, CTCs seed metastases, which account for the majority of cancer-related deaths. We demonstrate the analyses of the whole genome of single CTCs, which are highly needed for personalized treatment. We discovered that copy number variations (CNVs), one of the major genomic variations, are specific to cancer types, reproducible from cell to cell, and even from patient to patient. We hypothesize that CNVs at certain genomic loci are selected for and lead to metastasis. Our work shows the prospect of noninvasive CTC-based cancer diagnostics.

Single-Cell Sequencing: With the rapid progress in sequencing technologies, single-cell sequencing is now possible, promising insight into how cell-to-cell heterogeneity affects biological behavior. Achieving adequate genome coverage remains a challenge because single-cell sequencing relies on genome amplification that is prone to sequence bias. Zong et al. (p. 1622 ) report a new amplification method: multiple annealing and looping-based amplification cycles that allowed 93% genome coverage for a human cell. This coverage facilitated accurate detection of point mutations and copy number variations. Lu et al. (p. 1627 ) used the method to sequence 99 sperm cells from a single individual. Mapping the meiotic crossovers revealed a nonrandom distribution with a reduced recombination rate near transcription start sites.