CD97 negatively regulates the innate immune response against RNA viruses by promoting RNF125-mediated RIG-I degradation.

The G protein-coupled receptor ADGRE5 (CD97) binds to various metabolites that play crucial regulatory roles in metabolism. However, its function in the antiviral innate immune response remains to be determined. In this study, we report that CD97 inhibits virus-induced type-I interferon (IFN-I) release and enhances RNA virus replication in cells and mice. CD97 was identified as a new negative regulator of the innate immune receptor RIG-I, and RIG-1 degradation led to the suppression of the IFN-I signaling pathway. Furthermore, overexpression of CD97 promoted the ubiquitination of RIG-I, resulting in its degradation, but did not impact its mRNA expression. Mechanistically, CD97 upregulates RNF125 expression to induce RNF125-mediated RIG-I degradation via K48-linked ubiquitination at Lys181 after RNA virus infection. Most importantly, CD97-deficient mice are more resistant than wild-type mice to RNA virus infection. We also found that sanguinarine-mediated inhibition of CD97 effectively blocks VSV and SARS-CoV-2 replication. These findings elucidate a previously unknown mechanism through which CD97 negatively regulates RIG-I in the antiviral innate immune response and provide a molecular basis for the development of new therapeutic strategies and the design of targeted antiviral agents.

Cellular and molecular biomarkers of long COVID: a scoping review.

BACKGROUND: Long-COVID (LC) encompasses diverse symptoms lasting months after the initial SARS-CoV-2 infection. Symptoms can be debilitating and affect the quality of life of individuals with LC and their families. Although the symptoms of LC are well described, the aetiology of LC remains unclear, and consequently, patients may be underdiagnosed. Identification of LC specific biomarkers is therefore paramount for the diagnosis and clinical management of the syndrome. This scoping review describes the molecular and cellular biomarkers that have been identified to date with potential use for diagnosis or prediction of LC. METHODS: This review was conducted using the Joanna Briggs Institute (JBI) Methodology for Scoping Reviews. A search was executed in the MEDLINE and EMBASE databases, as well as in the grey literature for original studies, published until October 5th, 2022, reporting biomarkers identified in participants with LC symptoms (from all ages, ethnicities, and sex), with a previous infection of SARS-CoV-2. Non-English studies, cross-sectional studies, studies without a control group, and pre-prints were excluded. Two reviewers independently evaluated the studies, extracted population data and associated biomarkers. FINDINGS: 23 cohort studies were identified, involving 2163 LC patients [median age 51.8 years, predominantly female sex (61.10%), white (75%), and non-vaccinated (99%)]. A total of 239 candidate biomarkers were identified, consisting mainly of immune cells, immunoglobulins, cytokines, and other plasma proteins. 19 of the 239 candidate biomarkers identified were evaluated by the authors, by means of receiver operating characteristic (ROC) curves. INTERPRETATION: Diverse cellular and molecular biomarkers for LC have been proposed. Validation of candidate biomarkers in independent samples should be prioritized. Modest reported performance (particularly in larger studies) suggests LC may encompass many distinct aetiologies, which should be explored e.g., by stratifying by symptom clusters and/or sex. FUNDING: Dr. Tebbutt has received funding from the Canadian Institutes of Health Research (177747) to conduct this work. The funding source was not involved in this scoping review, or in the decision to submit this manuscript for publication.

Discovery of vaccine-like recombinant SARS-CoV-2 circulating in human.

For viral diseases, vaccination with live attenuated vaccine (LAV) is one of the most effective means for fighting the diseases. However, LAV occasionally overflows from vaccinated individuals circulate in the population with unforeseen consequences. Currently, SARS-CoV-2 LAVs are undergoing clinical trials. In this study, we found that the viruses isolated from Indian SARS CoV-2 infected persons may be candidate LAV-derived strains, indicating the risk of SARS-CoV-2 LAV spillover from vaccinated persons, increasing the complexity of SARS-CoV-2 detection. In addition, the property of frequent recombination of SARS-CoV-2 increases the chance of LAV virulence reversion. Therefore, how to distinguish the LAV viruses from the wild strain and how to avoid the recombination of the circulating vaccine strain and the wild strain are the challenges currently faced by SARS CoV-2 LAV development.

Psychometric properties of the Pregnancy-Related Anxiety Scale-Screener.

Pregnancy-related anxiety, a distinct anxiety characterized by pregnancy-specific concerns, has consistently been associated with adverse birth outcomes and obstetric and pediatric risk factors. Despite this, widespread screening for pregnancy-related anxiety has not been integrated into routine antenatal care likely due to the absence of a psychometrically sound screener. This study reports on the initial development of a brief screener derived from the 32-item pregnancy-related anxiety scale (PrAS). Three datasets (comprising pregnant women recruited online) were utilized in the development and evaluation of the PrAS screener (PrAS-Screener). Dataset one (N = 1,084) was used to derive two potential screeners from the PrAS using principal axis factoring (PAF). The factor structure of the models was evaluated using PAF and model fit assessed with confirmatory factor analysis (CFA) using datasets two (N = 638) and three (N = 581). The model comprised 15 items and five subscales was selected as the superior model. The selected model (i.e., PrAS-Screener) was evaluated for convergent and discriminant validity demonstrating higher correlations with similar measures and lower correlations with dissimilar measures and high internal consistency reliability (α = .93). The PrAS-Screener assesses the three core areas of pregnancy-related anxiety (childbirth, body image, baby concerns) but has the advantage of also assessing anxiety symptoms and medical staff concerns, an area integral to providing optimal antenatal care through trusted relationships with clinicians. Initial evidence indicates that the PrAS-Screener is promising as a brief and easy-to-administer screener suitable for use in routine antenatal care. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

RACK1 degrades MAVS to promote bovine ephemeral fever virus replication via upregulating E3 ubiquitin ligase STUB1.

Receptors for activated C kinase 1 (RACK1) could competitively combine with mitochondrial antiviral signaling protein (MAVS) to inhibit the type I interferon (IFN) signaling pathway during viral infection in vitro. However, whether RACK1 can degrade MAVS to enhance viral replication is still unknown. In this study, we found that bovine epidemic fever virus (BEFV) infection triggered the expression of RACK1. Overexpression of RACK1 promoted BEFV replication, while knockdown of RACK1 inhibited the replication of BEFV. Further research showed that RACK1 inhibited the type I IFN signaling pathway during BEFV infection by degrading MAVS, and RACK1 degraded MAVS via the ubiquitin-proteasome system. Mechanistically, RACK1 up-regulated the expression of E3 ubiquitin ligase STIP1 homology and U-box containing protein 1 (STUB1), thereby promoting the ubiquitination and degradation of MAVS. In addition, RACK1 degraded MAVS by enhancing the interaction between STUB1 and MAVS but not via its interaction with STUB1. Overall, our study reveals a novel mechanism by which RACK1 inhibits the type I IFN signaling pathway to BEFV infection through degradation of MAVS, thereby promoting viral infection. These findings provide a new perspective for the MAVS degradation regulated by RACK1.

Combination antiretroviral therapy improves recurrent primary biliary cholangitis following liver transplantation.

Recurrent primary biliary cholangitis (rPBC) is frequent following liver transplantation and associated with increased morbidity and mortality. It has been argued that rPBC behaves like an infectious disease because more potent immunosuppression with tacrolimus is associated with earlier and more severe recurrence. Prophylactic ursodeoxycholic acid is an established therapeutic option to prevent rPBC, whereas the role of second line therapies, such as obeticholic acid and bezafibrate in rPBC, remains largely unexplored. To address the hypothesis that a human betaretrovirus plays a role in the development of PBC, we have tested antiretroviral therapy in vitro and conducted randomised controlled trials showing improvements in hepatic biochemistry. Herein, we describe the utility of combination antiretroviral therapy to manage rPBC in two patients treated with open label tenofovir/emtricitabine-based regimens in combination with either lopinavir or raltegravir. Both patients experienced sustained biochemical and histological improvement with treatment, but the antiretroviral therapy was associated with side effects.

Dynamics of Lithium Insertion in Electrochromic Titanium Dioxide Nanocrystal Ensembles.

Nanocrystalline anatase TiO2 is a robust model anode for Li insertion in batteries. The influence of nanocrystal size on the equilibrium potential and kinetics of Li insertion is investigated with in operando spectroelectrochemistry of thin film electrodes. Distinct visible and infrared responses correlate with Li insertion and electron accumulation, respectively, and these optical signals are used to deconvolute bulk Li insertion from other electrochemical responses, such as double-layer capacitance, pseudocapacitance, and electrolyte leakage. Electrochemical titration and phase-field simulations reveal that a difference in surface energies between anatase and lithiated phases of TiO2 systematically tunes the Li-insertion potentials with the particle size. However, the particle size does not affect the kinetics of Li insertion in ensemble electrodes. Rather, the Li-insertion rates depend on the applied overpotential, electrolyte concentration, and initial state of charge. We conclude that Li diffusivity and phase propagation are not rate limiting during Li insertion in TiO2 nanocrystals. Both of these processes occur rapidly once the transformation between the low-Li anatase and high-Li orthorhombic phases begins in a particle. Instead, discontinuous kinetics of Li accumulation in TiO2 particles prior to the phase transformations limits (dis)charging rates. We demonstrate a practical means to deconvolute the nonequilibrium charging behavior in nanocrystalline electrodes through a combination of colloidal synthesis, phase field simulations, and spectroelectrochemistry.

miRNA-independent function of long noncoding pri-miRNA loci.

Among the large, diverse set of mammalian long noncoding RNAs (lncRNAs), long noncoding primary microRNAs (lnc-pri-miRNAs) are those that host miRNAs. Whether lnc-pri-miRNA loci have important biological function independent of their cognate miRNAs is poorly understood. From a genome-scale lncRNA screen, lnc-pri-miRNA loci were enriched for function in cell proliferation, and in glioblastoma (i.e., GBM) cells with DGCR8 or DROSHA knockdown, lnc-pri-miRNA screen hits still regulated cell growth. To molecularly dissect the function of a lnc-pri-miRNA locus, we studied LOC646329 (also known as MIR29HG), which hosts the miR-29a/b1 cluster. In GBM cells, LOC646329 knockdown reduced miR-29a/b1 levels, and these cells exhibited decreased growth. However, genetic deletion of the miR-29a/b1 cluster (LOC646329-miR29Δ) did not decrease cell growth, while knockdown of LOC646329-miR29Δ transcripts reduced cell proliferation. The miR-29a/b1-independent activity of LOC646329 corresponded to enhancer-like activation of a neighboring oncogene (MKLN1), regulating cell propagation. The LOC646329 locus interacts with the MKLN1 promoter, and antisense oligonucleotide knockdown of the lncRNA disrupts these interactions and reduces the enhancer-like activity. More broadly, analysis of genome-wide data from multiple human cell types showed that lnc-pri-miRNA loci are significantly enriched for DNA looping interactions with gene promoters as well as genomic and epigenetic characteristics of transcriptional enhancers. Functional studies of additional lnc-pri-miRNA loci demonstrated cognate miRNA-independent enhancer-like activity. Together, these data demonstrate that lnc-pri-miRNA loci can regulate cell biology via both miRNA-dependent and miRNA-independent mechanisms.

DDIT3 Targets Innate Immunity via the DDIT3-OTUD1-MAVS Pathway To Promote Bovine Viral Diarrhea Virus Replication.

DNA damage-inducible transcript 3 (DDIT3) plays important roles in endoplasmic reticulum (ER) stress-induced apoptosis and autophagy, but its role in innate immunity is not clear. Here, we report that DDIT3 inhibits the antiviral immune response during bovine viral diarrhea virus (BVDV) infection by targeting mitochondrial antiviral signaling (MAVS) in Madin-Darby bovine kidney (MDBK) cells and in mice. BVDV infection induced high DDIT3 mRNA and protein expression. DDIT3 overexpression inhibited type I interferon (IFN-I) and IFN-stimulated gene production, thereby promoting BVDV replication, while DDIT3 knockdown promoted the antiviral innate immune response to suppress viral replication. DDIT3 promoted NF-κB-dependent ovarian tumor (OTU) deubiquitinase 1 (OTUD1) expression. Furthermore, OTUD1 induced upregulation of the E3 ubiquitin ligase Smurf1 by deubiquitinating Smurf1, and Smurf1 degraded MAVS in MDBK cells in a ubiquitination-dependent manner, ultimately inhibiting IFN-I production. Moreover, knocking out DDIT3 promoted the antiviral innate immune response to reduce BVDV replication and pathological changes in mice. These findings provide direct insights into the molecular mechanisms by which DDIT3 inhibits IFN-I production by regulating MAVS degradation.IMPORTANCE Extensive studies have demonstrated roles of DDIT3 in apoptosis and autophagy during viral infection. However, the role of DDIT3 in innate immunity remains largely unknown. Here, we show that DDIT3 is positively regulated in bovine viral diarrhea virus (BVDV)-infected Madin-Darby bovine kidney (MDBK) cells and could significantly enhance BVDV replication. Importantly, DDIT3 induced OTU deubiquitinase 1 (OTUD1) expression by activating the NF-κB signaling pathway, thus increasing intracellular Smurf1 protein levels to degrade MAVS and inhibit IFN-I production during BVDV infection. Together, these results indicate that DDIT3 plays critical roles in host innate immunity repression and viral infection facilitation.

Geospatial analysis of severe road traffic accidents in Singapore in 2013-2014.

INTRODUCTION: Injury is a significant cause of mortality and morbidity. We aimed to investigate which areas in Singapore have a significantly higher incidence of road traffic accidents (RTA) resulting in severe injuries (Tier 1), which is defined as an Injury Severity Score (ISS) greater than 15, and to develop a spatiotemporal model. METHODS: Data was obtained from the National Trauma Registry. The RTA locations were geomapped onto the Singapore map, and spatial statistical techniques were used to identify hotspots with the Getis-Ord Gi* algorithm. RESULTS: From 1 January 2013 to 31 December 2014, there were 35,673 people who were injured as a result of RTAs and 976 Tier 1 RTA victims. A total of 920 people were included in the geospatial analysis. Another 56 were involved in RTAs that did not occur within Singapore or had missing location data and thus were not included. 745 (81.0%) were discharged alive, whereas 175 (19.0%) did not survive to discharge (median ISS 38.00, interquartile range 30.00-48.00). Most of the Tier 1 RTA victims were motorcycle riders (50.1%, n = 461), pedestrians (21.8%, n = 201) and cyclists (9.9%, n = 91). The majority were male and aged 20-40 years, and there was a peak occurrence at 0600-0759 hours. Nine hotspots were identified (p < 0.01). CONCLUSION: Information from studying hotspots of RTAs, especially those resulting in severe injuries, can be used by multiple agencies to direct resources efficiently.

Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults.

Conventional vaccine design has been based on trial-and-error approaches, which have been generally successful. However, there have been some major failures in vaccine development and we still do not have highly effective licensed vaccines for tuberculosis, HIV, respiratory syncytial virus, and other major infections of global significance. Approaches at rational vaccine design have been limited by our understanding of the immune response to vaccination at the molecular level. Tools now exist to undertake in-depth analysis using systems biology approaches, but to be fully realized, studies are required in humans with intensive blood and tissue sampling. Methods that support this intensive sampling need to be developed and validated as feasible. To this end, we describe here a detailed approach that was applied in a study of 15 healthy adults, who were immunized with hepatitis B vaccine. Sampling included ~350 mL of blood, 12 microbiome samples, and lymph node fine needle aspirates obtained over a ~7-month period, enabling comprehensive analysis of the immune response at the molecular level, including single cell and tissue sample analysis. Samples were collected for analysis of immune phenotyping, whole blood and single cell gene expression, proteomics, lipidomics, epigenetics, whole blood response to key immune stimuli, cytokine responses, in vitro T cell responses, antibody repertoire analysis and the microbiome. Data integration was undertaken using different approaches-NetworkAnalyst and DIABLO. Our results demonstrate that such intensive sampling studies are feasible in healthy adults, and data integration tools exist to analyze the vast amount of data generated from a multi-omics systems biology approach. This will provide the basis for a better understanding of vaccine-induced immunity and accelerate future rational vaccine design.

BCG vaccination-induced emergency granulopoiesis provides rapid protection from neonatal sepsis.

Death from sepsis in the neonatal period remains a serious threat for millions. Within 3 days of administration, bacille Calmette-Guérin (BCG) vaccination can reduce mortality from neonatal sepsis in human newborns, but the underlying mechanism for this rapid protection is unknown. We found that BCG was also protective in a mouse model of neonatal polymicrobial sepsis, where it induced granulocyte colony-stimulating factor (G-CSF) within hours of administration. This was necessary and sufficient to drive emergency granulopoiesis (EG), resulting in a marked increase in neutrophils. This increase in neutrophils was directly and quantitatively responsible for protection from sepsis. Rapid induction of EG after BCG administration also occurred in three independent cohorts of human neonates.

CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma.

BACKGROUND: Long non-coding RNAs (lncRNAs) exhibit highly cell type-specific expression and function, making this class of transcript attractive for targeted cancer therapy. However, the vast majority of lncRNAs have not been tested as potential therapeutic targets, particularly in the context of currently used cancer treatments. Malignant glioma is rapidly fatal, and ionizing radiation is part of the current standard-of-care used to slow tumor growth in both adult and pediatric patients. RESULTS: We use CRISPR interference (CRISPRi) to screen 5689 lncRNA loci in human glioblastoma (GBM) cells, identifying 467 hits that modify cell growth in the presence of clinically relevant doses of fractionated radiation. Thirty-three of these lncRNA hits sensitize cells to radiation, and based on their expression in adult and pediatric gliomas, nine of these hits are prioritized as lncRNA Glioma Radiation Sensitizers (lncGRS). Knockdown of lncGRS-1, a primate-conserved, nuclear-enriched lncRNA, inhibits the growth and proliferation of primary adult and pediatric glioma cells, but not the viability of normal brain cells. Using human brain organoids comprised of mature neural cell types as a three-dimensional tissue substrate to model the invasive growth of glioma, we find that antisense oligonucleotides targeting lncGRS-1 selectively decrease tumor growth and sensitize glioma cells to radiation therapy. CONCLUSIONS: These studies identify lncGRS-1 as a glioma-specific therapeutic target and establish a generalizable approach to rapidly identify novel therapeutic targets in the vast non-coding genome to enhance radiation therapy.

Whole blood vs PBMC: compartmental differences in gene expression profiling exemplified in asthma.

BACKGROUND: Blood has proven to be a useful resource for molecular analysis in numerous biomedical studies, with peripheral blood mononuclear cells (PBMCs) and whole blood being the major specimen types. However, comparative analyses between these two major compartments (PBMCs and whole blood) are few and far between. In this study, we compared gene expression profiles of PBMCs and whole blood samples obtained from research subjects with or without mild allergic asthma. METHODS: Whole blood (PAXgene) and PBMC samples were obtained from 5 mild allergic asthmatics and 5 healthy controls. RNA from both sample types was measured for expression of 730 immune-related genes using the NanoString nCounter platform. RESULTS: We identified 64 uniquely expressed transcripts in whole blood that reflected a variety of innate, humoral, and adaptive immune processes, and 13 uniquely expressed transcripts in PBMCs which were representative of T-cell and monocyte-mediated processes. Furthermore, analysis of mild allergic asthmatics versus non-asthmatics revealed 47 differentially expressed transcripts in whole blood compared to 1 differentially expressed transcript in PBMCs (FDR < 0.25). Finally, through simultaneous measurement of PBMC proteins on the nCounter assay, we identified CD28 and OX40 (TNFRSF4), both of which are critical co-stimulatory molecules during T-cell activation, as significantly upregulated in asthmatics. CONCLUSIONS: Whole blood RNA preserved in PAXgene tubes is excellent for producing gene expression data with minimal variability and good sensitivity, suggesting its utility in multi-centre studies requiring measurement of blood gene expression.

Cholinergic synapse pathway gene polymorphisms associated with allergen-induced late asthmatic responses.

Cholinergic synapse pathway gene polymorphisms may play a role in regulating a type of asthmatic airway response triggered upon allergen challenge http://bit.ly/2lJx1VG.

Free-Wilson Analysis of Comprehensive Data on Phosphoinositide-3-kinase (PI3K) Inhibitors Reveals Importance of N-Methylation for PI3Kδ Activity.

Phosphoinositide-3-kinase δ (PI3Kδ) is a critical regulator of cell growth and transformation and has been explored as a therapeutic target for a range of diseases. Through the exploration of the thienopyrimidine scaffold, we have identified a ligand-efficient methylation that leads to remarkable selectivity for PI3Kδ over the closely related isoforms. Interrogation through the Free-Wilson analysis highlights the innate selectivity the thienopyrimidine scaffold has for PI3Kδ and provides a predictive model for the activity against the PI3K isoforms.

Dynamic molecular changes during the first week of human life follow a robust developmental trajectory.

Systems biology can unravel complex biology but has not been extensively applied to human newborns, a group highly vulnerable to a wide range of diseases. We optimized methods to extract transcriptomic, proteomic, metabolomic, cytokine/chemokine, and single cell immune phenotyping data from <1 ml of blood, a volume readily obtained from newborns. Indexing to baseline and applying innovative integrative computational methods reveals dramatic changes along a remarkably stable developmental trajectory over the first week of life. This is most evident in changes of interferon and complement pathways, as well as neutrophil-associated signaling. Validated across two independent cohorts of newborns from West Africa and Australasia, a robust and common trajectory emerges, suggesting a purposeful rather than random developmental path. Systems biology and innovative data integration can provide fresh insights into the molecular ontogeny of the first week of life, a dynamic developmental phase that is key for health and disease.

The spike onset zone: The region where epileptic spikes start and from where they propagate.

OBJECTIVE: To determine whether the maximum hemodynamic response to scalp interictal epileptic discharges (IEDs) corresponds to the region where IEDs originate and from where they propagate. METHODS: We studied 19 patients who underwent first an EEG-fMRI showing responses in the gray matter, and then intracranial EEG (iEEG). We coregistered the hemodynamic responses to the iEEG electrode contacts and analyzed IEDs in the iEEG channel adjacent to a maximum response (labeled the main channel), in relation to IEDs in other channels during a widespread intracranial IED event. IEDs in the main channel were aligned at their peak, and IEDs in each channel were averaged time-locked to these instants. The beginning and peak of IEDs in the averaged trace were identified, blinded to the identity of the main channel. The latency of IEDs was computed between the earliest and all other channels. RESULTS: The median latency of IEDs in the main channel was significantly smaller than in other channels for either the peak (15.5 vs 67.5 milliseconds, p = 0.00037) or the beginning (46.5 vs 118.4 milliseconds, p = 0.000048). The latency of IED was significantly correlated to the distance from the maximum hemodynamic response (p < 0.0001 for either the peak or the beginning). CONCLUSION: IED adjacent to a maximum hemodynamic response, which often corresponds to the seizure onset zone, is more likely to precede IEDs in remote locations during a widespread intracranial discharge. Thus, EEG-fMRI is a unique noninvasive method to reveal the origin of IEDs, which we propose to label the spike onset zone.

Switching Cyclic Nucleotide-Selective Activation of Cyclic Adenosine Monophosphate-Dependent Protein Kinase Holoenzyme Reveals Distinct Roles of Tandem Cyclic Nucleotide-Binding Domains.

The cyclic adenosine monophosphate (cAMP)- and cyclic guanosine monophosphate (cGMP)-dependent protein kinases (PKA and PKG) are key effectors of cyclic nucleotide signaling. Both share structural features that include tandem cyclic nucleotide-binding (CNB) domains, CNB-A and CNB-B, yet their functions are separated through preferential activation by either cAMP or cGMP. Based on structural studies and modeling, key CNB contact residues have been identified for both kinases. In this study, we explored the requirements for conversion of PKA activation from cAMP-dependent to cGMP-dependent. The consequences of the residue substitutions T192R/A212T within CNB-A or G316R/A336T within CNB-B of PKA-RIα on cyclic nucleotide binding and holoenzyme activation were assessed in vitro using purified recombinant proteins, and ex vivo using RIα-deficient mouse embryonic fibroblasts genetically reconstituted with wild-type or mutant PKA-RIα. In vitro, a loss of binding and activation selectivity was observed when residues in either one of the CNB domains were mutated, while mutations in both CNB domains resulted in a complete switch of selectivity from cAMP to cGMP. The switch in selectivity was also recapitulated ex vivo, confirming their functional roles in cells. Our results highlight the importance of key cyclic nucleotide contacts within each CNB domain and suggest that these domains may have evolved from an ancestral gene product to yield two distinct cyclic nucleotide-dependent protein kinases.

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells.

The human genome produces thousands of long noncoding RNAs (lncRNAs)-transcripts >200 nucleotides long that do not encode proteins. Although critical roles in normal biology and disease have been revealed for a subset of lncRNAs, the function of the vast majority remains untested. We developed a CRISPR interference (CRISPRi) platform targeting 16,401 lncRNA loci in seven diverse cell lines, including six transformed cell lines and human induced pluripotent stem cells (iPSCs). Large-scale screening identified 499 lncRNA loci required for robust cellular growth, of which 89% showed growth-modifying function exclusively in one cell type. We further found that lncRNA knockdown can perturb complex transcriptional networks in a cell type-specific manner. These data underscore the functional importance and cell type specificity of many lncRNAs.