Post-transcriptional splicing can occur in a slow-moving zone around the gene

Splicing is the stepwise molecular process by which introns are removed from pre-mRNA and exons are joined together to form mature mRNA sequences. The ordering and spatial distribution of these steps remain controversial, with opposing models suggesting splicing occurs either during or after transcription. We used single-molecule RNA FISH, expansion microscopy, and live-cell imaging to reveal the spatiotemporal distribution of nascent transcripts in mammalian cells. At super-resolution levels, we found that pre-mRNA formed clouds around the transcription site. These clouds indicate the existence of a transcription-site-proximal zone through which RNA move more slowly than in the nucleoplasm. Full-length pre-mRNA undergo continuous splicing as they move through this zone following transcription, suggesting a model in which splicing can occur post-transcriptionally but still within the proximity of the transcription site, thus seeming co-transcriptional by most assays. These results may unify conflicting reports of co-transcriptional versus post-transcriptional splicing.

Catheter ablation versus medical therapy in atrial fibrillation: an umbrella review of meta-analyses of randomized clinical trials

This umbrella review synthesizes data from 17 meta-analyses investigating the comparative outcomes of catheter ablation (CA) and medical treatment (MT) for atrial fibrillation (AF). Outcomes assessed were mortality, risk of hospitalization, AF recurrence, cardiovascular events, pulmonary vein stenosis, major bleeding, and changes in left ventricular ejection fraction (LVEF) and MLHFQ score. The findings indicate that CA significantly reduces overall mortality and cardiovascular hospitalization with high strength of evidence. The risk of AF recurrence was notably lower with CA, with moderate strength of evidence. Two associations reported an increased risk of pulmonary vein stenosis and major bleeding with CA, supported by high strength of evidence. Improved LVEF and a positive change in MLHFQ were also associated with CA. Among patients with AF and heart failure, CA appears superior to MT for reducing mortality, improving LVEF, and reducing cardiovascular rehospitalizations. In nonspecific populations, CA reduced mortality and improved LVEF but had higher complication rates. Our findings suggest that CA might offer significant benefits in managing AF, particularly in patients with heart failure. However, the risk of complications, including pulmonary vein stenosis and major bleeding, is notable. Further research in understudied populations may help refine these conclusions.

Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells

Pluripotency can be induced in somatic cells by the expression of OCT4, KLF4, SOX2, and MYC. Usually only a rare subset of cells reprogram, and the molecular characteristics of this subset remain unknown. We apply retrospective clone tracing to identify and characterize the rare human fibroblasts primed for reprogramming. These fibroblasts showed markers of increased cell cycle speed and decreased fibroblast activation. Knockdown of a fibroblast activation factor identified by our analysis increased the reprogramming efficiency. We provide evidence for a unified model in which cells can move into and out of the primed state over time, explaining how reprogramming appears deterministic at short timescales and stochastic at long timescales. Furthermore, inhibiting the activity of LSD1 enlarged the pool of cells that were primed for reprogramming. Thus, even homogeneous cell populations can exhibit heritable molecular variability that can dictate whether individual rare cells will reprogram or not.

Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning

Single-molecule RNA fluorescence in situ hybridization (RNA FISH)-based spatial transcriptomics methods have enabled the accurate quantification of gene expression at single-cell resolution by visualizing transcripts as diffraction-limited spots. While these methods generally scale to large samples, image analysis remains challenging, often requiring manual parameter tuning. We present Piscis, a fully automatic deep learning algorithm for spot detection trained using a novel loss function, the SmoothF1 loss, that approximates the F1 score to directly penalize false positives and false negatives but remains differentiable and hence usable for training by deep learning approaches. Piscis was trained and tested on a diverse dataset composed of 358 manually annotated experimental RNA FISH images representing multiple cell types and 240 additional synthetic images. Piscis outperforms other state-of-the-art spot detection methods, enabling accurate, high-throughput analysis of RNA FISH-derived imaging data without the need for manual parameter tuning.

A subpopulation of lipogenic brown adipocytes drives thermogenic memory

Sustained responses to transient environmental stimuli are important for survival. The mechanisms underlying long-term adaptations to temporary shifts in abiotic factors remain incompletely understood. Here, we find that transient cold exposure leads to sustained transcriptional and metabolic adaptations in brown adipose tissue, which improve thermogenic responses to secondary cold encounter. Primary thermogenic challenge triggers the delayed induction of a lipid biosynthesis programme even after cessation of the original stimulus, which protects from subsequent exposures. Single-nucleus RNA sequencing and spatial transcriptomics reveal that this response is driven by a lipogenic subpopulation of brown adipocytes localized along the perimeter of Ucp1hi adipocytes. This lipogenic programme is associated with the production of acylcarnitines, and supplementation of acylcarnitines is sufficient to recapitulate improved secondary cold responses. Overall, our data highlight the importance of heterogenous brown adipocyte populations for 'thermogenic memory', which may have therapeutic implications for leveraging short-term thermogenesis to counteract obesity.

23 Using visual data and teleophthalmology in paediatric ophthalmology with an app-free, browser-based, visual data platform: ISLACARE

Visual data is underutilised in ophthalmology particularly within paediatrics. Following the pandemic, virtual and remote clinics in the form of telephone and video consultations have increased but there are limitations within paediatric ophthalmology as synchronous telephone or video calls are time-consuming.Using a platform known as ISLACARE, we are able to run remote photo and video clinics that has the capability to support asynchronous or synchronous consultations. With this software, parents and clinicians do not need to create logins or download apps thus increasing compliance with the technology.In an audit of 101 consecutive cases, the following was found. Mean age: 6.67 years (0-17years). The top 4 categories used in were anterior segment (36%), Strabismus (24%), Orbit/Trauma (17%), and Oculoplastics (12%).On the use of photographs to support consultations , it was felt that 91% reduced time to treatment/supported clinical decision making and 75% improved clinician to clinician communication. We have found a 30% increase in capacity in our remote teleophthalmology clinics by utilising a pre-consultation proforma. A particular improvement has been in post-operative strabismus cases where 90% of all our first appointment checks are now done remotely.We would like to demonstrate the clinical flow of how we use ISLACARE for asynchronous consultations, remote monitoring, and visual data archiving.

Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer

Nuclear speckles are membrane-less bodies within the cell nucleus enriched in RNA biogenesis, processing, and export factors. In this study we investigated speckle phenotype variation in human cancer, finding a reproducible speckle signature, based on RNA expression of speckle-resident proteins, across >20 cancer types. Of these, clear cell renal cell carcinoma (ccRCC) exhibited a clear correlation between the presence of this speckle expression signature, imaging-based speckle phenotype, and clinical outcomes. ccRCC is typified by hyperactivation of the HIF-2α transcription factor, and we demonstrate here that HIF-2α drives physical association of a select subset of its target genes with nuclear speckles. Disruption of HIF-2α-driven speckle association via deletion of its speckle targeting motifs (STMs)-defined in this study-led to defective induction of speckle-associating HIF-2α target genes without impacting non-speckle-associating HIF-2α target genes. We further identify the RNA export complex, TREX, as being specifically altered in speckle signature, and knockdown of key TREX component, ALYREF, also compromises speckle-associated gene expression. By integrating tissue culture functional studies with tumor genomic and imaging analysis, we show that HIF-2α gene regulatory programs are impacted by specific manipulation of speckle phenotype and by abrogation of speckle targeting abilities of HIF-2α. These findings suggest that, in ccRCC, a key biological function of nuclear speckles is to modulate expression of a specific subset of HIF-2α-regulated target genes that, in turn, influence patient outcomes. We also identify STMs in other transcription factors, suggesting that DNA-speckle targeting may be a general mechanism of gene regulation.

Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells

Even among genetically identical cancer cells, resistance to therapy frequently emerges from a small subset of those cells1-7. Molecular differences in rare individual cells in the initial population enable certain cells to become resistant to therapy7-9; however, comparatively little is known about the variability in the resistance outcomes. Here we develop and apply FateMap, a framework that combines DNA barcoding with single-cell RNA sequencing, to reveal the fates of hundreds of thousands of clones exposed to anti-cancer therapies. We show that resistant clones emerging from single-cell-derived cancer cells adopt molecularly, morphologically and functionally distinct resistant types. These resistant types are largely predetermined by molecular differences between cells before drug addition and not by extrinsic factors. Changes in the dose and type of drug can switch the resistant type of an initial cell, resulting in the generation and elimination of certain resistant types. Samples from patients show evidence for the existence of these resistant types in a clinical context. We observed diversity in resistant types across several single-cell-derived cancer cell lines and cell types treated with a variety of drugs. The diversity of resistant types as a result of the variability in intrinsic cell states may be a generic feature of responses to external cues.

Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states

The ability of a virus to infect a cell type is at least in part determined by the presence of host factors required for the viral life cycle. However, even within cell types that express known factors needed for infection, not every cell is equally susceptible, suggesting that our knowledge of the full spectrum of factors that promote infection is incomplete. Profiling the most susceptible subsets of cells within a population may reveal additional factors that promote infection. However, because viral infection dramatically alters the state of the cell, new approaches are needed to reveal the state of these cells prior to infection with virus. Here, we used single-cell clone tracing to retrospectively identify and characterize lung epithelial cells that are highly susceptible to infection with SARS-CoV-2. The transcriptional state of these highly susceptible cells includes markers of retinoic acid signaling and epithelial differentiation. Loss of candidate factors identified by our approach revealed that many of these factors play roles in viral entry. Moreover, a subset of these factors exert control over the infectable cell state itself, regulating the expression of key factors associated with viral infection and entry. Analysis of patient samples revealed the heterogeneous expression of these factors across both cells and patients in vivo. Further, the expression of these factors is upregulated in particular inflammatory pathologies. Altogether, our results show that the variable expression of intrinsic cell states is a major determinant of whether a cell can be infected by SARS-CoV-2.

Choroid Plexus Calcification Correlates with Cortical Microglial Activation in Humans: A Multimodal PET, CT, MRI Study

BACKGROUND AND PURPOSE

The choroid plexus (CP) within the brain ventricles is well-known to produce cerebrospinal fluid (CSF). Recently, the CP has been recognized as critical in modulating inflammation. MRI-measured CP enlargement has been reported in neuroinflammatory disorders like MS as well as with aging and neurodegeneration. The basis of MRI-measured CP enlargement is unknown. On the basis of tissue studies demonstrating CP calcification as a common pathology associated with aging and disease, we hypothesized that previously unmeasured CP calcification contributes to MRI-measured CP volume and may be more specifically associated with neuroinflammation.

MATERIALS AND METHODS

We analyzed 60 subjects (43 healthy controls and 17 subjects with Parkinson's disease) who underwent PET/CT using 11C-PK11195, a radiotracer sensitive to the translocator protein expressed by activated microglia. Cortical inflammation was quantified as nondisplaceable binding potential. Choroid plexus calcium was measured via manual tracing on low-dose CT acquired with PET and automatically using a new CT/MRI method. Linear regression assessed the contribution of choroid plexus calcium, age, diagnosis, sex, overall volume of the choroid plexus, and ventricle volume to cortical inflammation.

RESULTS

Fully automated choroid plexus calcium quantification was accurate (intraclass correlation coefficient with manual tracing = .98). Subject age and choroid plexus calcium were the only significant predictors of neuroinflammation.

CONCLUSIONS

Choroid plexus calcification can be accurately and automatically quantified using low-dose CT and MRI. Choroid plexus calcification-but not choroid plexus volume-predicted cortical inflammation. Previously unmeasured choroid plexus calcium may explain recent reports of choroid plexus enlargement in human inflammatory and other diseases. Choroid plexus calcification may be a specific and relatively easily acquired biomarker for neuroinflammation and choroid plexus pathology in humans.

Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells

Pluripotency can be induced in somatic cells by the expression of the four "Yamanaka" factors OCT4, KLF4, SOX2, and MYC. However, even in homogeneous conditions, usually only a rare subset of cells admit reprogramming, and the molecular characteristics of this subset remain unknown. Here, we apply retrospective clone tracing to identify and characterize the individual human fibroblast cells that are primed for reprogramming. These fibroblasts showed markers of increased cell cycle speed and decreased fibroblast activation. Knockdown of a fibroblast activation factor identified by our analysis led to increased reprogramming efficiency, identifying it as a barrier to reprogramming. Changing the frequency of reprogramming by inhibiting the activity of LSD1 led to an enlarging of the pool of cells that were primed for reprogramming. Our results show that even homogeneous cell populations can exhibit heritable molecular variability that can dictate whether individual rare cells will reprogram or not.

ClonoCluster: A method for using clonal origin to inform transcriptome clustering

Clustering cells based on their high-dimensional profiles is an important data reduction process by which researchers infer distinct cellular states. The advent of cellular barcoding, however, provides an alternative means by which to group cells: by their clonal origin. We developed ClonoCluster, a computational method that combines both clone and transcriptome information to create hybrid clusters that weight both kinds of data with a tunable parameter. We generated hybrid clusters across six independent datasets and found that ClonoCluster generated qualitatively different clusters in all cases. The markers of these hybrid clusters were different but had equivalent fidelity to transcriptome-only clusters. The genes most strongly associated with the rearrangements in hybrid clusters were ribosomal function and extracellular matrix genes. We also developed the complementary tool Warp Factor that incorporates clone information in popular 2D visualization techniques like UMAP. Integrating ClonoCluster and Warp Factor revealed biologically relevant markers of cell identity.

Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks

Genetic networks should respond to signals but prevent the transmission of spontaneous fluctuations. Limited data from mammalian cells suggest that noise transmission is uncommon, but systematic claims about noise transmission have been limited by the inability to directly measure it. Here, we build a mathematical framework modeling allelic correlation and noise transmission, showing that allelic correlation and noise transmission correspond across model parameters and network architectures. Limiting noise transmission comes with the trade-off of being unresponsive to signals, and within responsive regimes, there is a further trade-off between response time and basal noise transmission. Analysis of allele-specific single-cell RNA-sequencing data revealed that genes encoding upstream factors in signaling pathways and cell-type-specific factors have higher allelic correlation than downstream factors, suggesting they are more subject to regulation. Overall, our findings suggest that some noise transmission must result from signal responsiveness, but it can be minimized by trading off for a slower response. A record of this paper's transparent peer review process is included in the supplemental information.

CTCF blocks antisense transcription initiation at divergent promoters

Transcription at most promoters is divergent, initiating at closely spaced oppositely oriented core promoters to produce sense transcripts along with often unstable upstream antisense transcripts (uasTrx). How antisense transcription is regulated and to what extent it is coordinated with sense transcription is not well understood. Here, by combining acute degradation of the multi-functional transcription factor CTCF and nascent transcription measurements, we find that CTCF specifically suppresses antisense but not sense transcription at hundreds of divergent promoters. Primary transcript RNA-FISH shows that CTCF lowers burst fraction but not burst intensity of uasTrx and that co-bursting of sense and antisense transcripts is disfavored. Genome editing, chromatin conformation studies and high-resolution transcript mapping revealed that precisely positioned CTCF directly suppresses the initiation of uasTrx, in a manner independent of its architectural function. In sum, CTCF shapes the transcriptional landscape in part by suppressing upstream antisense transcription.

CTCF blocks antisense transcription initiation at divergent promoters

Transcription at most promoters is divergent, initiating at closely spaced oppositely oriented core promoters to produce sense transcripts along with often unstable upstream antisense transcripts (uasTrx). How antisense transcription is regulated and to what extent it is coordinated with sense transcription is not well understood. Here, by combining acute degradation of the multi-functional transcription factor CTCF and nascent transcription measurements, we find that CTCF specifically suppresses antisense but not sense transcription at hundreds of divergent promoters. Primary transcript RNA-FISH shows that CTCF lowers burst fraction but not burst intensity of uasTrx and that co-bursting of sense and antisense transcripts is disfavored. Genome editing, chromatin conformation studies and high-resolution transcript mapping revealed that precisely positioned CTCF directly suppresses the initiation of uasTrx, in a manner independent of its architectural function. In sum, CTCF shapes the transcriptional landscape in part by suppressing upstream antisense transcription.

Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations

A major goal in the field of transcriptional regulation is the mapping of changes in the binding of transcription factors to the resultant changes in gene expression. Recently, methods for measuring chromatin accessibility have enabled us to measure changes in accessibility across the genome, which are thought to correspond to transcription factor‐binding events. In concert with RNA‐sequencing, these data in principle enable such mappings; however, few studies have looked at their concordance over short‐duration treatments with specific perturbations. Here, we used tandem, bulk ATAC‐seq, and RNA‐seq measurements from MCF‐7 breast carcinoma cells to systematically evaluate the concordance between changes in accessibility and changes in expression in response to retinoic acid and TGF‐β. We found two classes of genes whose expression showed a significant change: those that showed some changes in the accessibility of nearby chromatin, and those that showed virtually no change despite strong changes in expression. The peaks associated with genes in the former group had lower baseline accessibility prior to exposure to signal. Focusing the analysis specifically on peaks with motifs for transcription factors associated with retinoic acid and TGF‐β signaling did not reduce the lack of correspondence. Analysis of paired chromatin accessibility and gene expression data from distinct paths along the hematopoietic differentiation trajectory showed a much stronger correspondence, suggesting that the multifactorial biological processes associated with differentiation may lead to changes in chromatin accessibility that reflect rather than driving altered transcriptional status. Together, these results show many gene expression changes can happen independently of changes in the accessibility of local chromatin in the context of a single‐factor perturbation.

Systematically quantifying morphological features reveals constraints on organoid phenotypes

Organoids recapitulate complex 3D organ structures and represent a unique opportunity to probe the principles of self-organization. While we can alter an organoid's morphology by manipulating the culture conditions, the morphology of an organoid often resembles that of its original organ, suggesting that organoid morphologies are governed by a set of tissue-specific constraints. Here, we establish a framework to identify constraints on an organoid's morphological features by quantifying them from microscopy images of organoids exposed to a range of perturbations. We apply this framework to Madin-Darby canine kidney cysts and show that they obey a number of constraints taking the form of scaling relationships or caps on certain parameters. For example, we found that the number, but not size, of cells increases with increasing cyst size. We also find that these constraints vary with cyst age and can be altered by varying the culture conditions. We observed similar sets of constraints in intestinal organoids. This quantitative framework for identifying constraints on organoid morphologies may inform future efforts to engineer organoids.

Cell type determination for cardiac differentiation occurs soon after seeding of human-induced pluripotent stem cells

Background

Cardiac differentiation of human-induced pluripotent stem (hiPS) cells consistently produces a mixed population of cardiomyocytes and non-cardiac cell types, even when using well-characterized protocols. We sought to determine whether different cell types might result from intrinsic differences in hiPS cells prior to the onset of differentiation.

Results

By associating individual differentiated cells that share a common hiPS cell precursor, we tested whether expression variability is predetermined from the hiPS cell state. In a single experiment, cells that shared a progenitor were more transcriptionally similar to each other than to other cells in the differentiated population. However, when the same hiPS cells were differentiated in parallel, we did not observe high transcriptional similarity across differentiations. Additionally, we found that substantial cell death occurs during differentiation in a manner that suggested all cells were equally likely to survive or die, suggesting that there is no intrinsic selection bias for cells descended from particular hiPS cell progenitors. We thus wondered how cells grow spatially during differentiation, so we labeled cells by expression of marker genes and found that cells expressing the same marker tended to occur in patches. Our results suggest that cell type determination across multiple cell types, once initiated, is maintained in a cell-autonomous manner for multiple divisions.

Conclusions

Altogether, our results show that while substantial heterogeneity exists in the initial hiPS cell population, it is not responsible for the variability observed in differentiated outcomes; instead, factors specifying the various cell types likely act during a window that begins shortly after the seeding of hiPS cells for differentiation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02654-6.

Image-based profiling: a powerful and challenging new data type

Software has provided cell biologists the power to quantify specific cellular features in cell images at scale. Before long, these biologists also recognized the potential to extract much more biological information from the same images. From here, the field of image-based profiling, the process of extracting unbiased representations that capture morphological cell state, was born. We are still in the early days of image-based profiling, and it is clear that the many opportunities to interrogate biological systems come with significant challenges. These challenges include building expressive and biologically-relevant representations, adjusting for technical noise, writing generalizable software infrastructure, continuing to foster a culture of open science, and promoting FAIR (findable, accessible, interoperable, and reusable) data. We present a workshop at the Pacific Symposium on Biocomputing 2022 to introduce the field of image-based profiling to the broader computational biology community. In the following document, we introduce image-based profiling, discuss current state-of-the-art methods and limitations, and provide rationale for why now is the perfect time for the field to expand. We also introduce our invited speakers and agenda, which together provide an introduction to the field complemented by in-depth application areas in industry and academia. We also include five lightning talks to complement the invited speakers on various methodological and discovery advances.

Advanced Catalytic Technologies for Compressed Natural Gas – Gasoline Fuelled Engines

The main challenges of the CNG engine fuelling in terms of methane abatement in the aftertreatment system are addressed in this study by using different loaded PGM catalysts. A dual-fuel injection strategy of methane-gasoline was implemented where methane gas was port-injected into the intake in stoichiometric conditions at levels corresponding to 20 and 40% energy density replacement of gasoline fuel. High, medium, and low loaded Pd/Rh catalysts were used and compared to study the effect of PGM loading on the catalyst light-off activity for methane. Results indicate that increasing the Pd loading led to significantly earlier light-off temperatures achieved at relatively lower temperatures of 340, 350 and 395oC respectively. However, the benefit diminishes above Pd loading >142.5 g ft-3. The study has also demonstrated that NH3 is formed over the CNG catalyst due to steam-reforming reactions from the increased levels of methane in the exhaust with the dual-fuelling. Hence aftertreatment technologies such as SCR should be adopted to remove them. This further highlights the need to regulate the harmful NH3 emissions from future passenger cars fuelled with CNG. In addition, the benefits of the dual-fuel system in terms of lower engine output CO2, non-methane hydrocarbon (NMHC) and particulate matter (PM) emissions compared to the GDI mode alone are presented.

LSPR based on-chip detection of dengue NS1 antigen in whole blood

The development of a biosensor for rapid and quantitative detection of the dengue virus continues to remain a challenge. We report a lab-on-chip device that combines membrane-based blood plasma separation and a localized surface plasmon resonance (LSPR) based biosensor for on-chip detection of dengue NS1 antigen from a few drops of blood. The LSPR effect is realized by irradiating UV-NIR light having a spectral peak at 655 nm onto nanostructures fabricated via thermal annealing of a thin metal film. We study the effect of the resulting metal nanostructures on the LSPR performance in terms of sensitivity and limit of detection, by annealing silver films at temperatures ranging from 100 to 500 °C. The effect of annealing temperature on the nanostructure size and uniformity and the resulting optical characteristics are investigated. Further, the binding between non-targeted blood plasma proteins and NS1-antibody-functionalized nanostructures on the LSPR performance is studied by considering different blocking mechanisms. Using a nanostructure annealed at 200 °C and 2X-phosphate buffer saline with 0.05% Tween-20 as the blocking buffer, from 10 μL of whole blood, the device can detect NS1 antigen at a concentration as low as 0.047 μg mL-1 within 30 min. Finally, we demonstrate the detection of NS1 in the blood samples of dengue-infected patients and validate our results with those obtained from the gold-standard ELISA test.

Single cell biology-a Keystone Symposia report

Single cell biology has the potential to elucidate many critical biological processes and diseases, from development and regeneration to cancer. Single cell analyses are uncovering the molecular diversity of cells, revealing a clearer picture of the variation among and between different cell types. New techniques are beginning to unravel how differences in cell state-transcriptional, epigenetic, and other characteristics-can lead to different cell fates among genetically identical cells, which underlies complex processes such as embryonic development, drug resistance, response to injury, and cellular reprogramming. Single cell technologies also pose significant challenges relating to processing and analyzing vast amounts of data collected. To realize the potential of single cell technologies, new computational approaches are needed. On March 17-19, 2021, experts in single cell biology met virtually for the Keystone eSymposium "Single Cell Biology" to discuss advances both in single cell applications and technologies.

Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro

Identifying the particular transcription factors that maintain cell type in vitro is important for manipulating cell type. Identifying such transcription factors by their cell-type-specific expression or their involvement in developmental regulation has had limited success. We hypothesized that because cell type is often resilient to perturbations, the transcriptional response to perturbations would reveal identity-maintaining transcription factors. We developed perturbation panel profiling (P³) as a framework for perturbing cells across many conditions and measuring gene expression responsiveness transcriptome-wide. In human iPSC-derived cardiac myocytes, P³ showed that transcription factors important for cardiac myocyte differentiation and maintenance were among the most frequently upregulated (most responsive). We reasoned that one function of responsive genes may be to maintain cellular identity. We identified responsive transcription factors in fibroblasts using P³ and found that suppressing their expression led to enhanced reprogramming. We propose that responsiveness to perturbations is a property of transcription factors that help maintain cellular identity in vitro. A record of this paper's transparent peer review process is included in the supplemental information.

Variability within rare cell states enables multiple paths toward drug resistance

Molecular differences between individual cells can lead to dramatic differences in cell fate, such as death versus survival of cancer cells upon drug treatment. These originating differences remain largely hidden due to difficulties in determining precisely what variable molecular features lead to which cellular fates. Thus, we developed Rewind, a methodology that combines genetic barcoding with RNA FISH to directly capture rare cells that give rise to cellular behaviors of interest. Applied to BRAF^V600E melanoma, we trace drug-resistant cell fates back to single-cell gene expression differences in their drug-naive precursors (initial frequency of ~1:1000–1:10,000 cells) and relative persistence of MAP-kinase signaling soon after drug treatment. Within this rare subpopulation, we uncover a rich substructure in which molecular differences between several distinct subpopulations predict future differences in phenotypic behavior, such as proliferative capacity of distinct resistant clones following drug treatment. Our results reveal hidden, rare-cell variability that underlies a range of latent phenotypic outcomes upon drug exposure.

A new methodology, Rewind, traces vemurafenib-resistant melanoma back to their initial cell state before drug treatment, creating, effectively, a cellular time machine.

Genetic screening for single-cell variability modulators driving therapy resistance

Cellular plasticity describes the ability of cells to transition from one set of phenotypes to another. In melanoma, transient fluctuations in the molecular state of tumor cells mark the formation of rare cells primed to survive BRAF inhibition and reprogram into a stably drug-resistant fate. However, the biological processes governing cellular priming remain unknown. We used CRISPR-Cas9 genetic screens to identify genes that affect cell fate decisions by altering cellular plasticity. We found that many factors can independently affect cellular priming and fate decisions. We discovered a new plasticity-based mode of increasing resistance to BRAF inhibition that pushes cells towards a more differentiated state. Manipulating cellular plasticity through inhibition of DOT1L before the addition of the BRAF inhibitor resulted in more therapy resistance than concurrent administration. Our results indicate that modulating cellular plasticity can alter cell fate decisions and may prove useful for treating drug resistance in other cancers.

Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals

Two different cell signals often affect transcription of the same gene. In such cases, it is natural to ask how the combined transcriptional response compares to the individual responses. The most commonly used mechanistic models predict additive or multiplicative combined responses, but a systematic genome-wide evaluation of these predictions is not available. Here, we analyzed the transcriptional response of human MCF-7 cells to retinoic acid and TGF-β, applied individually and in combination. The combined transcriptional responses of induced genes exhibited a range of behaviors, but clearly favored both additive and multiplicative outcomes. We performed paired chromatin accessibility measurements and found that increases in accessibility were largely additive. There was some association between super-additivity of accessibility and multiplicative or super-multiplicative combined transcriptional responses, while sub-additivity of accessibility associated with additive transcriptional responses. Our findings suggest that mechanistic models of combined transcriptional regulation must be able to reproduce a range of behaviors.

Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors

Non-genetic factors can cause individual cells to fluctuate substantially in gene expression levels over time. It remains unclear whether these fluctuations can persist for much longer than the time of one cell division. Current methods for measuring gene expression in single cells mostly rely on single time point measurements, making the duration of gene expression fluctuations or cellular memory difficult to measure. Here, we combined Luria and Delbrück's fluctuation analysis with population-based RNA sequencing (MemorySeq) for identifying genes transcriptome-wide whose fluctuations persist for several divisions. MemorySeq revealed multiple gene modules that expressed together in rare cells within otherwise homogeneous clonal populations. These rare cell subpopulations were associated with biologically distinct behaviors like proliferation in the face of anti-cancer therapeutics. The identification of non-genetic, multigenerational fluctuations can reveal new forms of biological memory in single cells and suggests that non-genetic heritability of cellular state may be a quantitative property.

Social reprogramming in ants induces longevity-associated glia remodeling

In social insects, workers and queens arise from the same genome but display profound differences in behavior and longevity. In Harpegnathos saltator ants, adult workers can transition to a queen-like state called gamergate, which results in reprogramming of social behavior and life-span extension. Using single-cell RNA sequencing, we compared the distribution of neuronal and glial populations before and after the social transition. We found that the conversion of workers into gamergates resulted in the expansion of neuroprotective ensheathing glia. Brain injury assays revealed that activation of the damage response gene Mmp1 was weaker in old workers, where the relative frequency of ensheathing glia also declined. On the other hand, long-lived gamergates retained a larger fraction of ensheathing glia and the ability to mount a strong Mmp1 response to brain injury into old age. We also observed molecular and cellular changes suggestive of age-associated decline in ensheathing glia in Drosophila.

1214 Higher Bedroom Temperature Associated With Poorer Sleep: Data From Over 3.75 Million Nights

Introduction

Bedroom temperature can influence nocturnal thermoregulation and sleep. To date, limited, small experimental studies have shown that bedroom temperatures outside the recommended range of 65 and 70°F can negatively impact sleep. However, this association has not been studied in a large-scale data set. Using over 3.75 million nights of objectively measured data, we analyzed the associations between habitual bedroom temperatures and sleep.

Methods

Over 3.75 million nights of sleep and bedroom temperature data were collected using S+ by ResMed technology from 34,096 Individuals (57% male, 20-90 years, mean age 48.7 +/-14.5 years, all US residents). Multilevel regression analyses were used to analyze associations between bedroom temperature and sleep. A stricter alpha level of 0.001 was used to account for the large number of observations in the dataset.

Results

Bedroom temperature was above 70°F for 69% of nights, with the average temperature ranging between 68.8 and 76.2°F. For each 1°F increase in bedroom temperature between 60-85°F, sleep efficiency decreased by 0.06%. Likewise, higher bedroom temperatures were linked to shorter Total Sleep Time duration (-0.45 mins/°F), longer Sleep Onset Latency (+0.04 mins/°F), and longer Wake After Sleep Onset (+0.11 mins/°F), all ps<0.001.

Conclusion

Analyzing data from over 3.75 million nights, we found that many people sleep in a bedroom warmer than the optimal temperature. Further, higher bedroom temperatures - even within the recommended range for optimal sleep - are associated with poorer sleep and higher wakefulness. Bedroom thermostats and cooling options should be considered to achieve optimal sleeping temperature conditions.

Support

N/A

0412 Parents Sleep Longer When School is Out for the Summer: Associations Among Parenthood, Gender, and Season

Introduction

Seasonal effects in sleep are often attributed to day length; however, change in obligatory daily activities might also have an impact on sleep behavior. Longitudinal measurement using consumer sleep technology enables the observation of patterns in sleep behavior in the home environment. We analyzed the impact of parenthood and gender on total sleep time (TST) over the summer break period using data collected in the home.

Methods

Sleep data were collected using the SleepScore mobile application from October 2018 through October 2019, with the summer break period defined as June 25th - August 5th. U.S. age and gender matched samples of parents and non-parents were selected using Mahalanobis distance from a pool of users more likely to have school-aged children. The final samples included n=345 parents (38.7 +/- 4.5 years) and n=345 non-parents (37.8 +/- 4.7 years); both groups were 46% female. Only weeknights (n=34,323) were analyzed to maximize impact of school schedule. Linear regression and independent t-tests were used to analyze main and interaction effects for gender, parenthood, and summer break.

Results

Male gender, parenthood, and summer break were associated with decreased sleep duration (ps < .01). However, during summer break, parents exhibited an increase in TST, with mothers (+5.6 mins) having a greater increase than fathers (+1.1 mins). In contrast, adults without children showed a decrease in TST during summer break, with males having a greater reduction (-8.8 mins) than females (-6.5 mins).

Conclusion

These results suggest that parental status may play a part in seasonal sleep patterns. Contrary to the typical trend of shorter TST during summer, being a parent is associated with longer TST during summer break, with a greater increase for females. This change may be attributed to parents following a less rigid schedule when their children are not in school.

Support

N/A

0443 Intra Week Sleep Patterns Analyzed Using Consumer Sleep Tracker Data

Introduction

Big data collected using consumer sleep technology can provide objectively measured insights on sleep behavior in the real-life environment. It has the advantage over self-report data of being less prone to bias. Here we used a non-contact bio-motion sensor to remotely capture objective sleep data. We analyzed 168432 nights of sleep data to test if differences between weekday versus weekend sleep behavior, known from self-report, would still hold using objective data in a large population.

Methods

Sleep data was acquired using the SleepScore Max remote sleep sensor and included 168432 nights (2730 users, mean age: 46.6 +/- 11.8 years, 33% female, all resident in the USA). Analysis was restricted to those of working age; adults between 20-65. Any sleep which ended from Monday to Friday was considered weekday sleep, and any ending on Saturday or Sunday as weekend sleep. Data records were inspected and cleaned before analyzing. Descriptive statistics and independent t-tests were used to analyze the data.

Results

Total Sleep Time, Time In Bed and Sleep Onset Latencies were longer during weekend (TST: + 20.6 mins, TIB: +22.9 mins, SOL: +1.1 min, all p <0.001), resulting in a slightly poorer Sleep Efficiency (-.016%, p<0.01) for weekend nights. Time to bed and final awakening were both delayed in weekends as compared to weekdays (Time to bed +30.0 mins, and final awakening +53.4 mins, both p<0.001).

Conclusion

This big data analysis confirms the earlier observed difference in sleep and sleep behavior between weekdays and weekends. This should be considered for optimizing (automated) sleep interventions, that may not normally take the weekend effect into consideration.

Support

 

Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer

Non-genetic transcriptional variability is a potential mechanism for therapy resistance in melanoma. Specifically, rare subpopulations of cells occupy a transient pre-resistant state characterized by coordinated high expression of several genes and survive therapy. How might these rare states arise and disappear within the population? It is unclear whether the canonical models of probabilistic transcriptional pulsing can explain this behavior, or if it requires special, hitherto unidentified mechanisms. We show that a minimal model of transcriptional bursting and gene interactions can give rise to rare coordinated high expression states. These states occur more frequently in networks with low connectivity and depend on three parameters. While entry into these states is initiated by a long transcriptional burst that also triggers entry of other genes, the exit occurs through independent inactivation of individual genes. Together, we demonstrate that established principles of gene regulation are sufficient to describe this behavior and argue for its more general existence. A record of this paper's transparent peer review process is included in the Supplemental Information.

Outcome of pregnancies in women with pulmonary hypertension: a single-centre experience from South India

OBJECTIVE

To study maternal complications and pregnancy outcome in women with pulmonary hypertension, attending a tertiary centre in south India.

STUDY DESIGN

Retrospective observational study.

SETTING

Tertiary centre in south India.

POPULATION

Pregnant women with pulmonary hypertension.

METHOD

Data regarding demographics, clinical course, medication received, and echocardiographic diagnosis regarding pulmonary hypertension and antenatal care received were collected from the records. Details of labour and delivery, and postpartum follow up were retrieved. We compared the outcome based on the presence or absence of cyanosis and right ventricular systolic pressure levels.

MAIN OUTCOME MEASURES

Maternal mortality, occurrence of complications such as heart failure, fetal growth restriction.

RESULTS

There were 81 pregnancies in 73 women with pulmonary hypertension. The majority of them had pulmonary hypertension secondary to congenital heart disease (80.8%); 17.8% had Eisenmenger syndrome. An advanced pulmonary artery hypertension (PAH) medication, sildenafil, was administered in 25 (31.3%) pregnancies. There were four maternal deaths, of which three had Eisenmenger syndrome. Heart failure complicated 6.3% and fetal growth restriction 26.3% of pregnancies. Morbidity was significantly increased in women with pulmonary hypertension associated with a cyanotic cardiac lesion or with right ventricular systolic pressure >70 mmHg.

CONCLUSION

Despite advances in care, mortality in pregnant women with pulmonary hypertension is a matter of concern, especially in those with Eisenmenger syndrome. Multidisciplinary team management in tertiary centres and the use of advanced PAH medications even in low- to middle-income countries with limited resources, could lead to a reduction in morbidity and mortality related to pulmonary hypertension.

TWEETABLE ABSTRACT

Multidisciplinary care and use of new medication may improve outcomes in pregnant women with pulmonary hypertension.

Abstract SY18-03: Single cells and therapy resistance in cancer

Cancer is a disease that originates from single cells, and the treatment of cancer also is a problem of single cells: anti-cancer therapies can often kill the vast majority of tumor cells but a few rare cells remain and grow despite treatment. Often, it is thought that the underlying basis for the behavior of these rare cells is a genetic difference. However, we and others have shown that non-genetic differences may be a key driver of rare, drug resistant cells, yet the precise molecular nature of these differences often remains mysterious. We here describe the development of a cellular “time machine” that allows us to link the ultimate cellular fate to the initial cellular state on a single cell basis, thus revealing markers for pre-resistant cells in the population. Further, we use genetic screening technologies to elucidate the pathways that control the formation of these rare cells and discuss their therapeutic implications.

Citation Format: Arjun Raj. Single cells and therapy resistance in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr SY18-03.

Abstract LB-050: Memory sequencing reveals heritable single cell gene expression programs associated with therapy resistance

Single cancer cells can have substantial fluctuations in gene expression from non-genetic factors. However, it is unclear how long these fluctuations exist and whether they extend beyond the length of a single-cell division. Current technologies for gene expression measurements in single cells provide just one measurement of each cells’ transcriptome and fail to capture how these gene expression fluctuations change with time. We developed a new method combining Luria and Delbruck's fluctuation analysis with population-based RNA sequencing (MemorySeq) for identifying genes transcriptome-wide whose fluctuations persist for several cell divisions. MemorySeq revealed multiple gene modules that express together in rare cells within otherwise homogeneous clonal populations. Further, we found that these rare cell subpopulations are associated with biologically distinct phenotypes in multiple different cancer cell lines. In melanoma, we identified a rare subpopulation of cells expressing EGFR, NGFR, and AXL, and demonstrated that these cells are resistant to BRAF and MEK inhibitors. In triple-negative breast cancer cells, we identified a different gene expression signature consisting of CA9, and found that this subpopulation is resistant to paclitaxol. We validated these findings in melanoma cell lines by tagging the endogenous locus of MemorySeq gene, NGFR, with a fluorescent protein to directly visualize gene expression fluctuations in individual cells. Broadly, we believe that memory is an essential property of variability that will have phenotypic consequences for cancer cells. Thus, we anticipate that MemorySeq can be extended to uncover the transcriptional states of rare cells driving many phenotypes in cancer including drug resistance, differentiation, invasion, and metastasis.

Citation Format: Sydney Shaffer, Benjamin Emert, Eduardo Torre, Arjun Raj. Memory sequencing reveals heritable single cell gene expression programs associated with therapy resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-050.

LADL: light-activated dynamic looping for endogenous gene expression control

Mammalian genomes are folded into tens of thousands of long-range looping interactions. The cause-and-effect relationship between looping and genome function is poorly understood, and the extent to which loops are dynamic on short time scales remains an unanswered question. Here, we engineer a new class of synthetic architectural proteins for directed rearrangement of the three-dimensional genome using blue light. We target our light-activated-dynamic-looping (LADL) system to two genomic anchors with CRISPR guide RNAs and induce their spatial colocalization via light-induced heterodimerization of cryptochrome 2 and a dCas9-CIBN fusion protein. We apply LADL to redirect a stretch enhancer (SE) away from its endogenous Klf4 target gene and to the Zfp462 promoter. Using single-molecule RNA-FISH, we demonstrate that de novo formation of the Zfp462-SE loop correlates with a modest increase in Zfp462 expression. LADL facilitates colocalization of genomic loci without exogenous chemical cofactors and will enable future efforts to engineer reversible and oscillatory loops on short time scales.

Predictive model of spread of Parkinson's pathology using network diffusion

Growing evidence suggests that a "prion-like" mechanism underlies the pathogenesis of many neurodegenerative disorders, including Parkinson's disease (PD). We extend and tailor previously developed quantitative and predictive network diffusion model (NDM) to PD, by specifically modeling the trans-neuronal spread of alpha-synuclein outward from the substantia nigra (SN). The model demonstrated the spatial and temporal patterns of PD from neuropathological and neuroimaging studies and was statistically validated using MRI deformation of 232 Parkinson's patients. After repeated seeding simulations, the SN was found to be the most likely seed region, supporting its unique lynchpin role in Parkinson's pathology spread. Other alternative spread models were also evaluated for comparison, specifically, random spread and distance-based spread; the latter tests for Braak's original caudorostral transmission theory. We showed that the distance-based spread model is not as well supported as the connectivity-based model. Intriguingly, the temporal sequencing of affected regions predicted by the model was in close agreement with Braak stages III-VI, providing what we consider a "computational Braak" staging system. Finally, we investigated whether the regional expression patterns of implicated genes contribute to regional atrophy. Despite robust evidence for genetic factors in PD pathogenesis, NDM outperformed regional genetic expression predictors, suggesting that network processes are far stronger mediators of regional vulnerability than innate or cell-autonomous factors. This is the first finding yet of the ramification of prion-like pathology propagation in Parkinson's, as gleaned from in vivo human imaging data. The NDM is potentially a promising robust and clinically useful tool for diagnosis, prognosis and staging of PD.

Learning from UJAMBO: Perspectives on Gynecologic Care in African Immigrant and Refugee Women in Boston, Massachusetts

African-born immigrant women, and particularly refugees and asylum seekers, are at risk for reproductive health disparities but inadequately use relevant gynecologic services. We sought to elucidate perspectives on gynecologic care in a population of Congolese and Somali immigrants. We conducted a secondary qualitative analysis of focus group data using a grounded theory approach and the Integrated Behavioral Model as our theoretical framework. Thirty one women participated in six focus groups. Participant beliefs included the states of pregnancy and/or pain as triggers for care, preferences included having female providers and those with familiarity with female genital cutting. Barriers included stigma, lack of partner support, and lack of resources to access care. Experiential attitudes, normative beliefs, and environmental constraints significantly mediated care preferences for/barriers to gynecologic health service utilization in this population. Centering of patient perspectives to adapt delivery of gynecologic care to immigrants and refugees may improve utilization and reduce disparities.

Illuminating Genomic Dark Matter with RNA Imaging

In the postgenomic era, it is clear that the human genome encodes thousands of long noncoding RNAs (lncRNAs). Along the way, RNA imaging (e.g., RNA fluorescence in situ hybridization [RNA-FISH]) has been instrumental in identifying powerful roles for lncRNAs based on their subcellular localization patterns. Here, we explore how RNA imaging technologies have shed new light on how, when, and where lncRNAs may play functional roles. Specifically, we will synthesize the underlying principles of RNA imaging techniques by exploring several landmark lncRNA imaging studies that have illuminated key insights into lncRNA biology.

Weak correlation of bleeding scores to platelet electron microscopy: A retrospective chart review of pediatric patients with delta-storage pool disorder

BACKGROUND

Delta granule storage pool deficiency (δ-SPD) is a rare platelet disorder in which a deficiency of platelet granules leads to poor aggregation, resulting in varying clinical bleeding phenotypes. Children with δ-SPD have variable laboratory results, making the proper diagnosis and evaluation controversial.

OBJECTIVES

To describe the demographic and laboratory trends of this population and to assess the value of electron microscopy in diagnostic evaluation and its correlation to bleeding symptoms.

METHODS

We performed a retrospective review of 109 pediatric patients diagnosed with δ-SPD. We collected demographic information and bleeding scores using a validated bleeding assessment tool. A descriptive and exploratory analysis was performed.

RESULTS

The majority of patients were female, with an average age at diagnosis of 11.61 years. Females were diagnosed at a significantly older age presenting most often with menorrhagia, while males presented most commonly with epistaxis. The majority showed normal lumiaggregometry, the mean platelet electron microscopy (PEM) value was 2.37, and the mean bleeding score was 6. Bleeding assessment tool and PEM had a significantly weak correlation.

CONCLUSIONS

Patients with more dense granules per platelet had higher bleeding scores than those with fewer dense granules per platelet. The current body of evidence does not favor the use of PEM in routine clinical practice, and results are difficult to interpret. In patients with severe mucocutaneous bleeding symptoms and normal platelet aggregation studies, consideration should be given to an alternative diagnosis and further evaluation is warranted.

Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation

Transcriptional regulation occurs via changes to rates of different biochemical steps of transcription, but it remains unclear which rates are subject to change upon biological perturbation. Biochemical studies have suggested that stimuli predominantly affect the rates of RNA polymerase II (Pol II) recruitment and polymerase release from promoter-proximal pausing. Single-cell studies revealed that transcription occurs in discontinuous bursts, suggesting that features of such bursts like frequency and intensity could also be regulated. We combined Pol II chromatin immunoprecipitation sequencing (ChIP-seq) and single-cell transcriptional measurements to show that an independently regulated burst initiation step is required before polymerase recruitment can occur. Using a number of global and targeted transcriptional regulatory perturbations, we showed that biological perturbations regulated both burst initiation and polymerase pause release rates but seemed not to regulate polymerase recruitment rate. Our results suggest that transcriptional regulation primarily acts by changing the rates of burst initiation and polymerase pause release.

Non-inertial lift induced migration for label-free sorting of cells in a co-flowing aqueous two-phase system

We present a novel label-free passive microfluidic technique for isolation of cancer cells (EpCAM+ and CD45−) from peripheral blood mononuclear cells (PBMCs) (CD45+ and EpCAM−) in aqueous two-phase system (ATPS).

ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification

Methods for detecting single nucleic acids in cell and tissues, such as fluorescence in situ hybridization (FISH), are limited by relatively low signal intensity and nonspecific probe binding. Here we present click-amplifying FISH (clampFISH), a method for fluorescence detection of nucleic acids that achieves high specificity and high-gain (>400-fold) signal amplification. ClampFISH probes form a 'C' configuration upon hybridization to the sequence of interest in a double helical manner. The ends of the probes are ligated together using bio-orthogonal click chemistry, effectively locking the probes around the target. Iterative rounds of hybridization and click amplify the fluorescence intensity. We show that clampFISH enables the detection of RNA species with low-magnification microscopy and in RNA-based flow cytometry. Additionally, we show that the modular design of clampFISH probes allows multiplexing of RNA and DNA detection, that the locking mechanism prevents probe detachment in expansion microscopy, and that clampFISH can be applied in tissue samples.