The Prp19C/NTC subunit Syf2 and the Prp19C/NTC-associated protein Cwc15 function in TREX occupancy and transcription elongation.

The Prp19 complex (Prp19C), also named NineTeen Complex (NTC), is conserved from yeast to human and functions in many different processes such as genome stability, splicing, and transcription elongation. In the latter, Prp19C ensures TREX occupancy at transcribed genes. TREX, in turn, couples transcription to nuclear mRNA export by recruiting the mRNA exporter to transcribed genes and consequently to nascent mRNAs. Here, we assess the function of the nonessential Prp19C subunit Syf2 and the nonessential Prp19C-associated protein Cwc15 in the interaction of Prp19C and TREX with the transcription machinery, Prp19C and TREX occupancy, and transcription elongation. Whereas both proteins are important for Prp19C-TREX interaction, Syf2 is needed for full Prp19C occupancy, and Cwc15 is important for the interaction of Prp19C with RNA polymerase II and TREX occupancy. These partially overlapping functions are corroborated by a genetic interaction between Δcwc15 and Δsyf2 Finally, Cwc15 also interacts genetically with the transcription elongation factor Dst1 and functions in transcription elongation. In summary, we uncover novel roles of the Prp19C component Syf2 and the Prp19C-associated protein Cwc15 in Prp19C's function in transcription elongation.

Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity.

The papain-like protease PLpro is an essential coronavirus enzyme that is required for processing viral polyproteins to generate a functional replicase complex and enable viral spread1,2. PLpro is also implicated in cleaving proteinaceous post-translational modifications on host proteins as an evasion mechanism against host antiviral immune responses3-5. Here we perform biochemical, structural and functional characterization of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PLpro (SCoV2-PLpro) and outline differences with SARS-CoV PLpro (SCoV-PLpro) in regulation of host interferon and NF-κB pathways. SCoV2-PLpro and SCoV-PLpro share 83% sequence identity but exhibit different host substrate preferences; SCoV2-PLpro preferentially cleaves the ubiquitin-like interferon-stimulated gene 15 protein (ISG15), whereas SCoV-PLpro predominantly targets ubiquitin chains. The crystal structure of SCoV2-PLpro in complex with ISG15 reveals distinctive interactions with the amino-terminal ubiquitin-like domain of ISG15, highlighting the high affinity and specificity of these interactions. Furthermore, upon infection, SCoV2-PLpro contributes to the cleavage of ISG15 from interferon responsive factor 3 (IRF3) and attenuates type I interferon responses. Notably, inhibition of SCoV2-PLpro with GRL-0617 impairs the virus-induced cytopathogenic effect, maintains the antiviral interferon pathway and reduces viral replication in infected cells. These results highlight a potential dual therapeutic strategy in which targeting of SCoV2-PLpro can suppress SARS-CoV-2 infection and promote antiviral immunity.

Network medicine-based epistasis detection in complex diseases: ready for quantum computing.

Most heritable diseases are polygenic. To comprehend the underlying genetic architecture, it is crucial to discover the clinically relevant epistatic interactions (EIs) between genomic single nucleotide polymorphisms (SNPs) (1-3). Existing statistical computational methods for EI detection are mostly limited to pairs of SNPs due to the combinatorial explosion of higher-order EIs. With NeEDL (network-based epistasis detection via local search), we leverage network medicine to inform the selection of EIs that are an order of magnitude more statistically significant compared to existing tools and consist, on average, of five SNPs. We further show that this computationally demanding task can be substantially accelerated once quantum computing hardware becomes available. We apply NeEDL to eight different diseases and discover genes (affected by EIs of SNPs) that are partly known to affect the disease, additionally, these results are reproducible across independent cohorts. EIs for these eight diseases can be interactively explored in the Epistasis Disease Atlas (https://epistasis-disease-atlas.com). In summary, NeEDL demonstrates the potential of seamlessly integrated quantum computing techniques to accelerate biomedical research. Our network medicine approach detects higher-order EIs with unprecedented statistical and biological evidence, yielding unique insights into polygenic diseases and providing a basis for the development of improved risk scores and combination therapies.

The logic of universalization guides moral judgment.

To explain why an action is wrong, we sometimes say, "What if everybody did that?" In other words, even if a single person's behavior is harmless, that behavior may be wrong if it would be harmful once universalized. We formalize the process of universalization in a computational model, test its quantitative predictions in studies of human moral judgment, and distinguish it from alternative models. We show that adults spontaneously make moral judgments consistent with the logic of universalization, and report comparable patterns of judgment in children. We conclude that, alongside other well-characterized mechanisms of moral judgment, such as outcome-based and rule-based thinking, the logic of universalizing holds an important place in our moral minds.

An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2.

The recognition of cis-regulatory RNA motifs in human transcripts by RNA binding proteins (RBPs) is essential for gene regulation. The molecular features that determine RBP specificity are often poorly understood. Here, we combined NMR structural biology with high-throughput iCLIP approaches to identify a regulatory mechanism for U2AF2 RNA recognition. We found that the intrinsically disordered linker region connecting the two RNA recognition motif (RRM) domains of U2AF2 mediates autoinhibitory intramolecular interactions to reduce nonproductive binding to weak Py-tract RNAs. This proofreading favors binding of U2AF2 at stronger Py-tracts, as required to define 3' splice sites at early stages of spliceosome assembly. Mutations that impair the linker autoinhibition enhance the affinity for weak Py-tracts result in promiscuous binding of U2AF2 along mRNAs and impact on splicing fidelity. Our findings highlight an important role of intrinsically disordered linkers to modulate RNA interactions of multidomain RBPs.

Conditional knockout of leptin receptor in the female reproductive tract reduces fertility due to parturition defects in mice.

Leptin is required for fertility, including initiation of estrous cycles. It is therefore challenging to assess the role of leptin signaling during pregnancy. Although neuron-specific transgene approaches suggest that leptin signaling in the central nervous system is most important, experiments with pharmacologic inhibition of leptin in the uterus or global replacement of leptin during pregnancy suggest leptin signaling in the reproductive tract may be required. Here, conditional leptin receptor knockout (Lepr cKO) with a progesterone receptor-driven Cre recombinase was used to examine the importance of leptin signaling in pregnancy. Lepr cKO mice have almost no leptin receptor in uterus or cervix, and slightly reduced leptin receptor levels in corpus luteum. Estrous cycles and progesterone concentrations were not affected by Lepr cKO. Numbers of viable embryos did not differ between primiparous control and Lepr cKO dams on Days 6.5 and 17.5 of pregnancy, despite a slight reduction in the ratio of embryos to corpora lutea, showing that uterine leptin receptor signaling is not required for embryo implantation. Placentas of Lepr cKO dams had normal weight and structure. However, over four parities, Lepr cKO mice produced 22% fewer live pups than controls, and took more time from pairing to delivery by their fourth parity. Abnormal birth outcomes of either dystocia or dead pups occurred in 33% of Lepr cKO deliveries but zero control deliveries, and the average time to deliver each pup after crouching was significantly increased. Thus, leptin receptor signaling in the reproductive tract is required for normal labor and delivery.

p63 uses a switch-like mechanism to set the threshold for induction of apoptosis.

The p53 homolog TAp63α is the transcriptional key regulator of genome integrity in oocytes. After DNA damage, TAp63α is activated by multistep phosphorylation involving multiple phosphorylation events by the kinase CK1, which triggers the transition from a dimeric and inactive conformation to an open and active tetramer that initiates apoptosis. By measuring activation kinetics in ovaries and single-site phosphorylation kinetics in vitro with peptides and full-length protein, we show that TAp63α phosphorylation follows a biphasic behavior. Although the first two CK1 phosphorylation events are fast, the third one, which constitutes the decisive step to form the active conformation, is slow. Structure determination of CK1 in complex with differently phosphorylated peptides reveals the structural mechanism for the difference in the kinetic behavior based on an unusual CK1/TAp63α substrate interaction in which the product of one phosphorylation step acts as an inhibitor for the following one.

Early onset preeclampsia in a model for human placental trophoblast.

We describe a model for early onset preeclampsia (EOPE) that uses induced pluripotent stem cells (iPSCs) generated from umbilical cords of EOPE and control (CTL) pregnancies. These iPSCs were then converted to placental trophoblast (TB) representative of early pregnancy. Marker gene analysis indicated that both sets of cells differentiated at comparable rates. The cells were tested for parameters disturbed in EOPE, including invasive potential. Under 5% O2, CTL TB and EOPE TB lines did not differ, but, under hyperoxia (20% O2), invasiveness of EOPE TB was reduced. RNA sequencing analysis disclosed no consistent differences in expression of individual genes between EOPE TB and CTL TB under 20% O2, but, a weighted correlation network analysis revealed two gene modules (CTL4 and CTL9) that, in CTL TB, were significantly linked to extent of TB invasion. CTL9, which was positively correlated with 20% O2 (P = 0.02) and negatively correlated with invasion (P = 0.03), was enriched for gene ontology terms relating to cell adhesion and migration, angiogenesis, preeclampsia, and stress. Two EOPE TB modules, EOPE1 and EOPE2, also correlated positively and negatively, respectively, with 20% O2 conditions, but only weakly with invasion; they largely contained the same sets of genes present in modules CTL4 and CTL9. Our experiments suggest that, in EOPE, the initial step precipitating disease is a reduced capacity of placental TB to invade caused by a dysregulation of O2 response mechanisms and that EOPE is a syndrome, in which unbalanced expression of various combinations of genes affecting TB invasion provoke disease onset.

Skeletal muscle specific mitochondrial dysfunction and altered energy metabolism in a murine model (oim/oim) of severe osteogenesis imperfecta.

Osteogenesis imperfecta (OI) is a heritable connective tissue disorder with patients exhibiting bone fragility and muscle weakness. The synergistic biochemical and biomechanical relationship between bone and muscle is a critical potential therapeutic target, such that muscle weakness should not be ignored. Previous studies demonstrated mitochondrial dysfunction in the skeletal muscle of oim/oim mice, which model a severe human type III OI. Here, we further characterize this mitochondrial dysfunction and evaluate several parameters of whole body and skeletal muscle metabolism. We demonstrate reduced mitochondrial respiration in female gastrocnemius muscle, but not in liver or heart mitochondria, suggesting that mitochondrial dysfunction is not global in the oim/oim mouse. Myosin heavy chain fiber type distributions were altered in the oim/oim soleus muscle with a decrease (-33 to 50%) in type I myofibers and an increase (+31%) in type IIa myofibers relative to their wildtype (WT) littermates. Additionally, altered body composition and increased energy expenditure were observed oim/oim mice relative to WT littermates. These results suggest that skeletal muscle mitochondrial dysfunction is linked to whole body metabolic alterations and to skeletal muscle weakness in the oim/oim mouse.

Children selectively endorse speculative conjectures.

Young children are epistemically vigilant, attending to the reliability, expertise, and confidence of their informants and the prior probability and verifiability of their claims. But the pre-eminent requirement of any hypothesis is that it provides a potential solution to the question at hand. Given questions with no known answer, the ability to selectively adopt new, unverified, speculative proposals may be critical to learning. This study explores when people might reasonably reject known facts in favor of unverified conjectures. Across four experiments, when conjectures answer questions that available facts do not, both adults (n = 48) and children (4.0-7.9 years, n = 241, of diverse race and ethnicity) prefer the conjectures, even when the conjectures are preceded by uncertainty markers or explicitly violate prior expectations.

Patients With Natural Killer (NK) Cell Chronic Active Epstein-Barr Virus Have Immature NK Cells and Hyperactivation of PI3K/Akt/mTOR and STAT1 Pathways.

BACKGROUND: Chronic active Epstein-Barr virus (CAEBV) presents with high levels of viral genomes in blood and tissue infiltration with Epstein-Barr virus (EBV)-positive lymphocytes. The pathogenesis of CAEBV is poorly understood. METHODS: We evaluated 2 patients with natural killer (NK) cell CAEBV and studied their NK cell phenotype and signaling pathways in cells. RESULTS: Both patients had increased numbers of NK cells, EBV predominantly in NK cells, and immature NK cells in the blood. Both patients had increased phosphorylation of Akt, S6, and STAT1 in NK cells, and increased total STAT1. Treatment of 1 patient with sirolimus reduced phosphorylation of S6 in T and B cells, but not in NK cells and did not reduce levels of NK cells or EBV DNA in the blood. Treatment of both patients' cells with JAK inhibitors in vitro reduced phosphorylated STAT1 to normal. Patients with T- or B-cell CAEBV had increased phosphorylation of Akt and S6 in NK cells, but no increase in total STAT1. CONCLUSIONS: The increase in phosphorylated Akt, S6, and STAT1, as well as immature NK cells describe a new phenotype for NK cell CAEBV. The reduction of STAT1 phosphorylation in their NK cells with JAK inhibitors suggests a novel approach to therapy.

Morphology and gene expression in mouse placentas lacking leptin receptors.

In the pregnant mouse, the hormone leptin is primarily produced by adipose tissue and does not significantly cross the placenta into fetal circulation. Nonetheless, leptin treatment during gestation affects offspring phenotypes. Leptin treatment also affects placental trophoblast cells in vitro, by altering proliferation, invasion and nutrient transport. The goal of the present study was to determine whether the absence of placental leptin receptors alters placental development and gene expression. Leprdb-3j+ mice possessing only one functional copy of the leptin receptor were mated to obtain wildtype, Leprdb-3j+ and Leprdb-3j/db-3j conceptuses, which were then transferred to wildtype recipient dams. Placentas were collected at gestational d18.5 to examine placental morphology and gene expression. Placentas lacking functional leptin receptor had reduced weights, but were otherwise morphologically indistinguishable from control placentas. Relative mRNA levels, however, were altered in Leprdb-3j/db-3j placentas, particularly transcripts related to amino acid and lipid metabolism and transport. Consistent with a previous in vitro study, leptin was found to promote expression of stathmin, a positive regulator of trophoblast invasion, and of serotonin receptors, potential mediators of offspring neurological development. Overall placental leptin receptor was found not to play a significant role in morphological development of the placenta, but to regulate placental gene expression, including in metabolic pathways that affect fetal growth.

Use of a human embryonic stem cell model to discover GABRP, WFDC2, VTCN1 and ACTC1 as markers of early first trimester human trophoblast.

Human placental development during early pregnancy is poorly understood. Many conceptuses are lost at this stage. It is thought that preeclampsia, intrauterine growth restriction and other placental syndromes that manifest later in pregnancy may originate early in placentation. Thus, there is a need for models of early human placental development. Treating human embryonic stem cells (hESCs) with BMP4 (bone morphogenic protein 4) plus A83-01 (ACTIVIN/NODAL signaling inhibitor) and PD173074 (fibroblast growth factor 2 or FGF2 signaling inhibitor) (BAP conditions) induces differentiation to the trophoblast lineage (hESCBAP), but it is not clear which stage of trophoblast differentiation these cells resemble. Here, comparison of the hESCBAP transcriptome to those of trophoblasts from human blastocysts, trophoblast stem cells and placentas collected in the first-third trimester of pregnancy by principal component analysis suggests that hESC after 8 days BAP treatment most resemble first trimester syncytiotrophoblasts. To further test this hypothesis, transcripts were identified that are expressed in hESCBAP but not in cultures of trophoblasts isolated from term placentas. Proteins encoded by four genes, GABRP (gamma-aminobutyric acid type A receptor subunit Pi), WFDC2 (WAP four-disulfide core domain 2), VTCN1 (V-set domain containing T-cell activation inhibitor 1) and ACTC1 (actin alpha cardiac muscle 1), immunolocalized to placentas at 4-9 weeks gestation, and their expression declined with gestational age (R2 = 0.61-0.83). None are present at term. Expression was largely localized to syncytiotrophoblast of both hESCBAP cells and placental material from early pregnancy. WFDC2, VTCN1 and ACTC1 have not previously been described in placenta. These results support the hypothesis that hESCBAP represent human trophoblast analogous to that of early first trimester and are a tool for discovery of factors important to this stage of placentation.

Pediatric Cancers among Alaska Native People.

OBJECTIVE: To evaluate the descriptive epidemiology of pediatric cancers among Alaska Native people. STUDY DESIGN: We used data from the Alaska Native Tumor Registry, a population-based registry capturing cancer information among Alaska Native people 1969-present. Specifically, we examined all cases of cancer diagnosed among individuals ages 0-19 years. Cases were classified according to the International Classification of Childhood Cancers, 3rd edition (ICCC-3). We estimated incidence and distribution of cases by ICCC-3 cancer site, comparing between the time periods 1969-1996 and 1997-2016. We assessed 12-month and 5-year cause-specific survival, and examined differences over the time period, adjusted for age, sex, and ICCC-3 site. RESULTS: Incidence rates of pediatric cancers increased between 1969 and 1996 (n = 134) and 1997 and 2016 (n = 186) among Alaska Native people, from 139.8 in 1 000 000 (95% CI, 116.99-165.7) to 197.54 in 1 000 000 (95% CI, 170.1-228.1). Distribution of ICCC-3 sites differed between time periods (P < .0001). Finally, cancer survival was high; the 12-month survival probability from all ICCC-3 sites combined was 0.88 (95% CI, 0.84-0.92) and the 5-year survival probability was 0.76 (95% CI, 0.70-0.81) for 1969-2016. After adjusting for age, sex, and ICCC-3 site, we observed a 57% decrease in the risk of death when comparing Alaska Native pediatric cancer cases diagnosed in 1997-2016 with those diagnosed in 1969-1996. CONCLUSIONS: This information will be of value for our understanding of pediatric cancers among Indigenous peoples of the US, and will also be informative for clinicians providing care to this population.

Fecundity is impaired in a mouse model of osteogenesis imperfecta.

Osteogenesis imperfecta (OI), or brittle bone disease, is most often caused by mutations in genes encoding type I collagen or proteins that process it. Women with OI have a small, but significant increase in risk of serious pregnancy complications including uterine rupture. Here, the OI mouse, Col1a2oim/oim , was used to examine the effects of collagen mutation on establishment and maintenance of pregnancy. Picrosirius birefringence was faint in Col1a2oim/oim uteri, indicating diminished collagen in the myometrium and endometrium. There was some evidence of increased uterine gland number (p = .055) and size (p = .12) in (p = .055) virgin uteri, though the they were not significantly different than controls. There were no differences in the number of corpora lutea, or the time from pairing to delivery of pups between Col1a2oim/oim and control dams, suggesting that ovulation and conception occur normally. However, when examined at Gestation Day 6.5 (postimplantation), gestation Day 10.5 (midpregnancy), and Postnatal Days 1-2, Col1a2oim/oim dams had significantly fewer viable pups than controls overall. In pairwise comparisons, the loss was only significant in the postnatal group, suggesting the gradual loss of pups over time. Overall, the Col1a2oim/oim mouse data suggest that OI impairs uterine function in pregnancy in a way that affects a small but significant number of fetuses.

The Naïve Utility Calculus as a unified, quantitative framework for action understanding.

The human ability to reason about the causes behind other people' behavior is critical for navigating the social world. Recent empirical research with both children and adults suggests that this ability is structured around an assumption that other agents act to maximize some notion of subjective utility. In this paper, we present a formal theory of this Naïve Utility Calculus as a probabilistic generative model, which highlights the role of cost and reward tradeoffs in a Bayesian framework for action-understanding. Our model predicts with quantitative accuracy how people infer agents' subjective costs and rewards based on their observable actions. By distinguishing between desires, goals, and intentions, the model extends to complex action scenarios unfolding over space and time in scenes with multiple objects and multiple action episodes. We contrast our account with simpler model variants and a set of special-case heuristics across a wide range of action-understanding tasks: inferring costs and rewards, making confidence judgments about relative costs and rewards, combining inferences from multiple events, predicting future behavior, inferring knowledge or ignorance, and reasoning about social goals. Our work sheds light on the basic representations and computations that structure our everyday ability to make sense of and navigate the social world.

Understanding Social Display Rules: Using One Person's Emotional Expressions to Infer the Desires of Another.

In social contexts, people's emotional expressions may disguise their true feelings but still be revealing about the probable desires of their intended audience. This study investigates whether children can use emotional expressions in social contexts to recover the desires of the person observing, rather than displaying the emotion. Children (7.0-10.9 years, N = 211 across five experiments) saw a protagonist express one emotional expression in front of her social partner, and a different expression behind her partner's back. Although the protagonist expressed contradictory emotions (and the partner expressed none), even 7-year-olds inferred both the protagonist's and social partner's desires. These results suggest that children can recover not only the desire of the person displaying emotion but also of the person observing it.

How Adults' Actions, Outcomes, and Testimony Affect Preschoolers' Persistence.

Across four experiments, we looked at how 4- and 5-year-olds' (n = 520) task persistence was affected by observations of adult actions (high or low effort), outcomes (success or failure), and testimony (setting expectations-"This will be hard," pep talks-"You can do this," value statements-"Trying hard is important," and baseline). Across experiments, outcomes had the biggest impact: preschoolers consistently tried harder after seeing the adult succeed than fail. Additionally, adult effort affected children's persistence, but only when the adult succeeded. Finally, children's persistence was highest when the adult both succeeded and practiced what she preached: exerting effort while testifying to its value.

Social Pragmatics: Preschoolers Rely on Commonsense Psychology to Resolve Referential Underspecification.

Four experiments show that 4- and 5-year-olds (total N = 112) can identify the referent of underdetermined utterances through their Naïve Utility Calculus-an intuitive theory of people's behavior structured around an assumption that agents maximize utilities. In Experiments 1-2, a puppet asked for help without specifying to whom she was talking ("Can you help me?"). In Experiments 3-4, a puppet asked the child to pass an object without specifying what she wanted ("Can you pass me that one?"). Children's responses suggest that they considered cost trade-offs between the members in the interaction. These findings add to a body of work showing that reference resolution is informed by commonsense psychology from early in childhood.