Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.

Genetic screens help infer gene function in mammalian cells, but it has remained difficult to assay complex phenotypes-such as transcriptional profiles-at scale. Here, we develop Perturb-seq, combining single-cell RNA sequencing (RNA-seq) and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool. We demonstrate Perturb-seq by analyzing 200,000 cells in immune cells and cell lines, focusing on transcription factors regulating the response of dendritic cells to lipopolysaccharide (LPS). Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions. We posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation. By decomposing many high content measurements into the effects of perturbations, their interactions, and diverse cell metadata, Perturb-seq dramatically increases the scope of pooled genomic assays.

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C.

We describe a Hi-C-based method, Micro-C, in which micrococcal nuclease is used instead of restriction enzymes to fragment chromatin, enabling nucleosome resolution chromosome folding maps. Analysis of Micro-C maps for budding yeast reveals abundant self-associating domains similar to those reported in other species, but not previously observed in yeast. These structures, far shorter than topologically associating domains in mammals, typically encompass one to five genes in yeast. Strong boundaries between self-associating domains occur at promoters of highly transcribed genes and regions of rapid histone turnover that are typically bound by the RSC chromatin-remodeling complex. Investigation of chromosome folding in mutants confirms roles for RSC, "gene looping" factor Ssu72, Mediator, H3K56 acetyltransferase Rtt109, and the N-terminal tail of H4 in folding of the yeast genome. This approach provides detailed structural maps of a eukaryotic genome, and our findings provide insights into the machinery underlying chromosome compaction.

Endocrine Autoimmune Disease as a Fragility of Immune Surveillance against Hypersecreting Mutants.

Some endocrine organs are frequent targets of autoimmune attack. Here, we addressed the origin of autoimmune disease from the viewpoint of feedback control. Endocrine tissues maintain mass through feedback loops that balance cell proliferation and removal according to hormone-driven regulatory signals. We hypothesized the existence of a dedicated mechanism that detects and removes mutant cells that missense the signal and therefore hyperproliferate and hypersecrete with potential to disrupt organismal homeostasis. In this mechanism, hypersecreting cells are preferentially eliminated by autoreactive T cells at the cost of a fragility to autoimmune disease. The "autoimmune surveillance of hypersecreting mutants" (ASHM) hypothesis predicts the presence of autoreactive T cells in healthy individuals and the nature of self-antigens as peptides from hormone secretion pathway. It explains why some tissues get prevalent autoimmune disease, whereas others do not and instead show prevalent mutant-expansion disease (e.g., hyperparathyroidism). The ASHM hypothesis is testable, and we discuss experimental follow-up.

Paradoxical signaling by a secreted molecule leads to homeostasis of cell levels.

A widespread feature of extracellular signaling in cell circuits is paradoxical pleiotropy: the same secreted signaling molecule can induce opposite effects in the responding cells. For example, the cytokine IL-2 can promote proliferation and death of T cells. The role of such paradoxical signaling remains unclear. To address this, we studied CD4(+) T cell expansion in culture. We found that cells with a 30-fold difference in initial concentrations reached a homeostatic concentration nearly independent of initial cell levels. Below an initial threshold, cell density decayed to extinction (OFF-state). We show that these dynamics relate to the paradoxical effect of IL-2, which increases the proliferation rate cooperatively and the death rate linearly. Mathematical modeling explained the observed cell and cytokine dynamics and predicted conditions that shifted cell fate from homeostasis to the OFF-state. We suggest that paradoxical signaling provides cell circuits with specific dynamical features that are robust to environmental perturbations.

High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies.

Cells control dynamic transitions in transcript levels by regulating transcription, processing, and/or degradation through an integrated regulatory strategy. Here, we combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the level; editing sites; and transcription, processing, and degradation rates of each transcript at a splice junction resolution during the LPS response of mouse dendritic cells. Four key regulatory strategies, dominated by RNA transcription changes, generate most temporal gene expression patterns. Noncanonical strategies that also employ dynamic posttranscriptional regulation control only a minority of genes, but provide unique signal processing features. We validate Tristetraprolin (TTP) as a major regulator of RNA degradation in one noncanonical strategy. Applying DRiLL to the regulation of noncoding RNAs and to zebrafish embryogenesis demonstrates its broad utility. Our study provides a new quantitative approach to discover transcriptional and posttranscriptional events that control dynamic changes in transcript levels using RNA sequencing data.

Densely interconnected transcriptional circuits control cell states in human hematopoiesis.

Though many individual transcription factors are known to regulate hematopoietic differentiation, major aspects of the global architecture of hematopoiesis remain unknown. Here, we profiled gene expression in 38 distinct purified populations of human hematopoietic cells and used probabilistic models of gene expression and analysis of cis-elements in gene promoters to decipher the general organization of their regulatory circuitry. We identified modules of highly coexpressed genes, some of which are restricted to a single lineage but most of which are expressed at variable levels across multiple lineages. We found densely interconnected cis-regulatory circuits and a large number of transcription factors that are differentially expressed across hematopoietic states. These findings suggest a more complex regulatory system for hematopoiesis than previously assumed.

Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals.

Epigenetic information can be inherited through the mammalian germline and represents a plausible transgenerational carrier of environmental information. To test whether transgenerational inheritance of environmental information occurs in mammals, we carried out an expression profiling screen for genes in mice that responded to paternal diet. Offspring of males fed a low-protein diet exhibited elevated hepatic expression of many genes involved in lipid and cholesterol biosynthesis and decreased levels of cholesterol esters, relative to the offspring of males fed a control diet. Epigenomic profiling of offspring livers revealed numerous modest (∼20%) changes in cytosine methylation depending on paternal diet, including reproducible changes in methylation over a likely enhancer for the key lipid regulator Ppara. These results, in conjunction with recent human epidemiological data, indicate that parental diet can affect cholesterol and lipid metabolism in offspring and define a model system to study environmental reprogramming of the heritable epigenome.

Gene expression cartography.

Multiplexed RNA sequencing in individual cells is transforming basic and clinical life sciences1-4. Often, however, tissues must first be dissociated, and crucial information about spatial relationships and communication between cells is thus lost. Existing approaches to reconstruct tissues assign spatial positions to each cell, independently of other cells, by using spatial patterns of expression of marker genes5,6-which often do not exist. Here we reconstruct spatial positions with little or no prior knowledge, by searching for spatial arrangements of sequenced cells in which nearby cells have transcriptional profiles that are often (but not always) more similar than cells that are farther apart. We formulate this task as a generalized optimal-transport problem for probabilistic embedding and derive an efficient iterative algorithm to solve it. We reconstruct the spatial expression of genes in mammalian liver and intestinal epithelium, fly and zebrafish embryos, sections from the mammalian cerebellum and whole kidney, and use the reconstructed tissues to identify genes that are spatially informative. Thus, we identify an organization principle for the spatial expression of genes in animal tissues, which can be exploited to infer meaningful probabilities of spatial position for individual cells. Our framework ('novoSpaRc') can incorporate prior spatial information and is compatible with any single-cell technology. Additional principles that underlie the cartography of gene expression can be tested using our approach.

SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle.

RNA abundance is tightly regulated in eukaryotic cells by modulating the kinetic rates of RNA production, processing, and degradation. To date, little is known about time­dependent kinetic rates during dynamic processes. Here, we present SLAM­Drop­seq, a method that combines RNA metabolic labeling and alkylation of modified nucleotides in methanol­fixed cells with droplet­based sequencing to detect newly synthesized and preexisting mRNAs in single cells. As a first application, we sequenced 7280 HEK293 cells and calculated gene­specific kinetic rates during the cell cycle using the novel package Eskrate. Of the 377 robust­cycling genes that we identified, only a minor fraction is regulated solely by either dynamic transcription or degradation (6 and 4%, respectively). By contrast, the vast majority (89%) exhibit dynamically regulated transcription and degradation rates during the cell cycle. Our study thus shows that temporally regulated mRNA degradation is fundamental for the correct expression of a majority of cycling genes. SLAM­Drop­seq, combined with Eskrate, is a powerful approach to understanding the underlying mRNA kinetics of single­cell gene expression dynamics in continuous biological processes.

Perforin-Positive Dendritic Cells Exhibit an Immuno-regulatory Role in Metabolic Syndrome and Autoimmunity.

Emerging evidence suggests that immunological mechanisms underlie metabolic control of adipose tissue. Here, we have shown the regulatory impact of a rare subpopulation of dendritic cells, rich in perforin-containing granules (perf-DCs). Using bone marrow transplantation to generate animals selectively lacking perf-DCs, we found that these chimeras progressively gained weight and exhibited features of metabolic syndrome. This phenotype was associated with an altered repertoire of T cells residing in adipose tissue and could be completely prevented by T cell depletion in vivo. A similar impact of perf-DCs on inflammatory T cells was also found in a well-defined model of multiple sclerosis, experimental autoimmune encephlalomyelitis (EAE). Thus, perf-DCs probably represent a regulatory cell subpopulation critical for protection from metabolic syndrome and autoimmunity.

Elucidating Combinatorial Chromatin States at Single-Nucleosome Resolution.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has been instrumental to our current view of chromatin structure and function. It allows genome-wide mapping of histone marks, which demarcate biologically relevant domains. However, ChIP-seq is an ensemble measurement reporting the average occupancy of individual marks in a cell population. Consequently, our understanding of the combinatorial nature of chromatin states relies almost exclusively on correlation between the genomic distributions of individual marks. Here, we report the development of combinatorial-iChIP to determine the genome-wide co-occurrence of histone marks at single-nucleosome resolution. By comparing to a null model, we show that certain combinations of overlapping marks (H3K36me3 and H3K79me3) co-occur more frequently than would be expected by chance, while others (H3K4me3 and H3K36me3) do not, reflecting differences in the underlying chromatin pathways. We further use combinatorial-iChIP to illuminate aspects of the Set2-RPD3S pathway. This approach promises to improve our understanding of the combinatorial complexity of chromatin.

Mapping the Landscape of a Eukaryotic Degronome.

The ubiquitin-proteasome system (UPS) for protein degradation has been under intensive study, and yet, we have only partial understanding of mechanisms by which proteins are selected to be targeted for proteolysis. One of the obstacles in studying these recognition pathways is the limited repertoire of known degradation signals (degrons). To better understand what determines the susceptibility of intracellular proteins to degradation by the UPS, we developed an unbiased method for large-scale identification of eukaryotic degrons. Using a reporter-based high-throughput competition assay, followed by deep sequencing, we measured a degradation potency index for thousands of native polypeptides in a single experiment. We further used this method to identify protein quality control (PQC)-specific and compartment-specific degrons. Our method provides an unprecedented insight into the yeast degronome, and it can readily be modified to study protein degradation signals and pathways in other organisms and in various settings.

Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown.

In the last decade, multiple studies demonstrated that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells' total and recently-transcribed mRNA profiles immediately following an acute depletion of Xrn1-the main 5'-3' mRNA exonuclease-which was previously implicated in balancing mRNA levels. We captured the detailed dynamics of the adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in transcription and a gradual return to baseline mRNA levels. We found that this transcriptional response is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5'-3' degradation pathway are perturbed. Our data suggest that the mRNA feedback mechanism monitors the accumulation of inputs to the 5'-3' exonucleolytic pathway rather than its outputs.

Dynamic changes in tRNA modifications and abundance during T cell activation.

The tRNA pool determines the efficiency, throughput, and accuracy of translation. Previous studies have identified dynamic changes in the tRNA (transfer RNA) supply and mRNA (messenger RNA) demand during cancerous proliferation. Yet dynamic changes may also occur during physiologically normal proliferation, and these are less well characterized. We examined the tRNA and mRNA pools of T cells during their vigorous proliferation and differentiation upon triggering their antigen receptor. We observed a global signature of switch in demand for codons at the early proliferation phase of the response, accompanied by corresponding changes in tRNA expression levels. In the later phase, upon differentiation, the response of the tRNA pool relaxed back to the basal level, potentially restraining excessive proliferation. Sequencing of tRNAs allowed us to evaluate their diverse base-modifications. We found that two types of tRNA modifications, wybutosine and ms2t6A, are reduced dramatically during T cell activation. These modifications occur in the anticodon loops of two tRNAs that decode "slippery codons," which are prone to ribosomal frameshifting. Attenuation of these frameshift-protective modifications is expected to increase the potential for proteome-wide frameshifting during T cell proliferation. Indeed, human cell lines deleted of a wybutosine writer showed increased ribosomal frameshifting, as detected with an HIV gag-pol frameshifting site reporter. These results may explain HIV's specific tropism toward proliferating T cells since it requires ribosomal frameshift exactly on the corresponding codon for infection. The changes in tRNA expression and modifications uncover a layer of translation regulation during T cell proliferation and expose a potential tradeoff between cellular growth and translation fidelity.

High-resolution chromatin dynamics during a yeast stress response.

Covalent histone modifications are highly conserved and play multiple roles in eukaryotic transcription regulation. Here, we mapped 26 histone modifications genome-wide in exponentially growing yeast and during a dramatic transcriptional reprogramming-the response to diamide stress. We extend prior studies showing that steady-state histone modification patterns reflect genomic processes, especially transcription, and display limited combinatorial complexity. Interestingly, during the stress response we document a modest increase in the combinatorial complexity of histone modification space, resulting from roughly 3% of all nucleosomes transiently populating rare histone modification states. Most of these rare histone states result from differences in the kinetics of histone modification that transiently uncouple highly correlated marks, with slow histone methylation changes often lagging behind the more rapid acetylation changes. Explicit analysis of modification dynamics uncovers ordered sequences of events in gene activation and repression. Together, our results provide a comprehensive view of chromatin dynamics during a massive transcriptional upheaval.

Pediatric Hospitalizations After School Reopening During the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Alpha (B.1.1.7) Variant Spread: A Multicenter Cross-sectional Study in Israel.

This multicenter, cross-sectional study provides evidence on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-associated emergency department visits and hospitalizations in pediatric wards and intensive care units after school reopening during the SARS-CoV-2 Alpha (B.1.1.7) variant spread in Israel. Study findings suggest that school reopening was not followed by an increase in SARS-CoV-2-related pediatric morbidity.

Avidity optimization of a MAGE-A1-specific TCR with somatic hypermutation.

A T-cell receptor (TCR) with optimal avidity to a tumor antigen can be used to redirect T cells to eradicate cancer cells via adoptive cell transfer. Cancer testis antigens (CTAs) are attractive targets because they are expressed in the testis, which is immune-privileged, and in the tumor. However, CTAs are self-antigens and natural TCRs to CTAs have low affinity/avidity due to central tolerance. We previously described a method of directed evolution of TCR avidity using somatic hypermutation. In this study, we made several improvements to this method and enhanced the avidity of the hT27 TCR, which is specific for the cancer testis antigen HLA-A2-MAGE-A1278-286 . We identified eight point mutations with varying degrees of improved avidity. Human T cells transduced with TCRs containing these mutations displayed enhanced tetramer binding, IFN-γ and IL2 production, and cytotoxicity. Most of the mutations have retained specificity, except for one mutant with extremely high avidity. We demonstrate that somatic hypermutation is capable of optimizing avidity of clinically relevant TCRs for immunotherapy.

Triage performance in adolescent patients with SARS-CoV-2 infection in Israel.

OBJECTIVE: The aim of this study was to assess the performance of the Pediatric Canadian Triage and Acuity Scale (PaedCTAS) in adolescent patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. METHODS: A time-series study was conducted in the Emergency Departments (EDs) of 17 public hospitals during the Delta (B.1.617.2) variant spread in Israel. Data were collected prospectively from June 11, 2021 to August 15, 2021. Multivariate regression analyses were performed to identify independent variables associated with hospital admission and with admission to an Intensive Care Unit (ICU). RESULTS: During the study period, 305 SARS-CoV-2 patients ages 12-18 years presenting to the ED were included, and 267 (87.5%) were unvaccinated. Sixty-seven (22.0%) and 12 (3.9%) patients were admitted to pediatric wards and ICUs, respectively. PaedCTAS level 1-2 and the presence of chronic disease increased the odds of hospital admission (adjusted odds ratio (aOR) 5.74, 95% CI, 2.30-14.35, p < 0.0001), and (aOR 2.9, 95% CI, 1.48-5.67, p < 0.02), respectively. PaedCTAS level 1-2 and respiratory symptoms on presentation to ED increased the odds of ICU admission (aOR 27.79; 95% CI, 3.85-176.91, p < 0.001), and (aOR 26.10; 95% CI, 4.47-172.63, p < 0.0001), respectively. PaedCTAS level 3-5 was found in 217/226 (96%) of the patients who were discharged home from the ED. CONCLUSIONS: The findings suggest that PaedCTAS level 1-2 was the strongest factor associated with hospital and ICU admission. Almost all the patients who were discharged home had PaedCTAS level 3-5. Study findings suggest good performance of the PaedCTAS in this cohort.

Dissemination and Use of Point-of-Care Ultrasound by Pediatricians in Europe: A Research in European Pediatric Emergency Medicine Network Collaborative Survey.

OBJECTIVE: We surveyed the dissemination and use of point-of-care ultrasound (POCUS), physician training levels, and barriers and limitations to use of POCUS among pediatricians and pediatric emergency medicine (PEM) physicians across Europe and Israel. METHODS: A questionnaire was distributed through the PEM section of the European Society for Emergency Medicine and the Research in European Pediatric Emergency Medicine Network. RESULTS: A total of 581 physicians from 22 countries fully completed the questionnaire. Participants were primarily pediatric attending physicians (34.9% [203 of 581]) and PEM attending physicians (28.6% [166 of 581]). Most of the respondents, 58.5% (340 of 581), reported using POCUS in their practice, and 61.9% (359/581) had undergone POCUS training. Point-of-care ultrasound courses represented the most common method of becoming proficient in POCUS. Overall, the Focused Assessment with Sonography in Trauma scan was the mostly taught application, with 76.3% (274 of 359). Resuscitative, diagnostic, and procedural POCUS were rated as very useful or useful by the most of respondents.The lack of qualified personnel to train (76.9% [447 of 581]), and the insufficient time for physicians to learn, POCUS (63.7% [370 of 581]) were identified as the main limitations to POCUS implementation. CONCLUSIONS: The dissemination of pediatric POCUS in the European and Israeli centers we surveyed is limited, and its applications are largely restricted to the Focused Assessment with Sonography in Trauma examination. This is likely related to lack of training programs. In contrast, the potential value of use of POCUS in PEM practice is recognized by the majority of respondents.

Diagnostic Accuracy of Point-of-Care Ultrasound for Intussusception: A Multicenter, Noninferiority Study of Paired Diagnostic Tests.

STUDY OBJECTIVE: To determine the diagnostic accuracy of point-of-care ultrasound (POCUS) performed by experienced clinician sonologists compared to radiology-performed ultrasound (RADUS) for detection of clinically important intussusception, defined as intussusception requiring radiographic or surgical reduction. METHODS: We conducted a multicenter, noninferiority, observational study among a convenience sample of children aged 3 months to 6 years treated in tertiary care emergency departments across North and Central America, Europe, and Australia. The primary outcome was diagnostic accuracy of POCUS and RADUS with respect to clinically important intussusception. Sample size was determined using a 4-percentage-point noninferiority margin for the absolute difference in accuracy. Secondary outcomes included agreement between POCUS and RADUS for identification of secondary sonographic findings. RESULTS: The analysis included 256 children across 17 sites (35 sonologists). Of the 256 children, 58 (22.7%) had clinically important intussusception. POCUS identified 60 (23.4%) children with clinically important intussusception. The diagnostic accuracy of POCUS was 97.7% (95% confidence interval [CI] 94.9% to 99.0%), compared to 99.3% (95% CI 96.8% to 99.9%) for RADUS. The absolute difference between the accuracy of RADUS and that of POCUS was 1.5 percentage points (95% CI -0.6 to 3.6). Sensitivity for POCUS was 96.6% (95% CI 87.2% to 99.1%), and specificity was 98.0% (95% CI 94.7% to 99.2%). Agreement was high between POCUS and RADUS for identification of trapped free fluid (83.3%, n=40/48) and decreased color Doppler signal (95.7%, n=22/23). CONCLUSION: Our findings suggest that the diagnostic accuracy of POCUS performed by experienced clinician sonologists may be noninferior to that of RADUS for detection of clinically important intussusception. Given the limitations of convenience sampling and spectrum bias, a larger randomized controlled trial is warranted.