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.

Fluorescence-activated nuclear sorting (FANS) of nuclei from in vitro-generated syncytiotrophoblast.

Large, multinucleated cells, like syncytiotrophoblasts (STB), are not readily analyzed by standard methods used for single cells, such as single-cell RNA-sequencing and fluorescence-activated cellular sorting (FACS). Here we have demonstrated that fluorescence-activated nuclear sorting (FANS) is suitable to analyze nuclei from STB. Human pluripotent stem cells (PSCs) can be differentiated into a mixed trophoblast populations comprising approximately 20 % STB by treatment with BMP4 (Bone Morphogenetic Protein-4), plus A83-01 and PD173074, inhibitors of activin and FGF2 signaling, respectively (the BAP model) in about a week. Here we demonstrate that FANS can be used to separate two types of STB nuclei from the nine different clusters of trophoblast nuclei previously identified in the BAP model by single nucleus RNA sequencing (snRNAseq). Rather than using cell surface markers, as in FACS, transcription factors in various combinations were employed to target specific nuclear types. Nuclei were isolated at d 8 of BAP differentiation of H1 human embryonic stem cells and fixed in 4 % paraformaldehyde. After permeabilization in 0.1 % triton X-100, nuclei were incubated for 3 and 1 h at 4 °C with primary and secondary antibodies respectively and nuclear samples were then subjected to FANS. By using markers identified by snRNA and immunohistochemistry, nuclei were first sorted into a Topoisomerase-1, or TOP1, bright population and then into the two STB subpopulations by using antibodies to JUNB (Jun B Proto-Oncogene) and TFCP2L1 (Transcription Factor CP2 Like 1). The protocol established here is simple, straightforward, and efficient and can be used on a relatively large scale to sort individual subtypes of nuclei from mixed populations of trophoblasts for further analysis.

In praise of folly: flexible goals and human cognition.

Humans often pursue idiosyncratic goals that appear remote from functional ends, including information gain. We suggest that this is valuable because goals (even prima facie foolish or unachievable ones) contain structured information that scaffolds thinking and planning. By evaluating hypotheses and plans with respect to their goals, humans can discover new ideas that go beyond prior knowledge and observable evidence. These hypotheses and plans can be transmitted independently of their original motivations, adapted across generations, and serve as an engine of cultural evolution. Here, we review recent empirical and computational research underlying goal generation and planning and discuss the ways that the flexibility of our motivational system supports cognitive gains for both individuals and societies.

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.

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 is the first application that 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.

Lower female survival from an opportunistic infection reveals progesterone-driven sex bias in trained immunity.

Immune responses differ between females and males, although such sex-based variance is incompletely understood. Observing that bacteremia of the opportunistic pathogen Burkholderia gladioli caused many more deaths of female than male mice bearing genetic deficiencies in adaptive immunity, we determined that this was associated with sex bias in the innate immune memory response called trained immunity. Female attenuation of trained immunity varies with estrous cycle stage and correlates with serum progesterone, a hormone that decreases glycolytic capacity and recall cytokine secretion induced by antigen non-specific stimuli. Progesterone receptor antagonism rescues female trained immune responses and survival from controlled B. gladioli infection to magnitudes similar to those of males. These data demonstrate progesterone-dependent sex bias in trained immunity where attenuation of female responses is associated with survival outcomes from opportunistic infection.

Methylated Septin9 identified patients with colorectal carcinoma and showed higher sensitivity than conventional biomarkers in detecting tumor.

INTRODUCTION: It is worth noting the limitations in sensitivity of the existing biomarkers carcinoembryonic antigen (CEA) and carbohydrate antigen (CA 19-9) in detection of colorectal cancer (CRC). In our study, we address the performance of the liquid biopsy biomarker "methylated septin 9" (mSEPT9) in the detection and disease surveillance of CRC. MATERIALS AND METHODS: The monocentric prospective survey encompassed 120 patients diagnosed with CRC who underwent planned curative resection between December 2018 and December 2020. Blood samples were collected from the participants preoperatively as well as at 7 days, 6 weeks, and 3 months postoperatively. The presence of mSEPT9, CEA, and CA 19-9 was detected using the pro Epi Colon® 2.0 CE test, Elecsys® CEA, and Elecsys® CA19-9 electrochemiluminescence immunoassay, respectively. RESULTS: In the preoperative setting, mSEPT9 demonstrated superior capability in identifying patients with CRC compared to CEA and CA 19-9, with detection rates of 57%, 32%, and 18% respectively. Combining all three biomarkers increased the overall sensitivity to 66% preoperatively. In considering UICC stage and T-status, mSEPT9 exhibited higher sensitivity across all stages in comparison with conventional tumor markers, and 65% of patients with metastases were identified postoperatively through mSEPT9. Tumor recognition after surgery was achieved with the sensitivity of 72% and specificity of 91%. CONCLUSIONS: We recommend using mSEPT9 as a non-invasive diagnostic tool for the ongoing monitoring of patients with CRC. The sensitivity and specificity exhibited by mSEPT9 in recognition of tumor after surgery, highlights its particular potential for monitoring of CRC patients.

Not Playing by the Rules: Exploratory Play, Rational Action, and Efficient Search.

Recent studies suggest children's exploratory play is consistent with formal accounts of rational learning. Here we focus on the tension between this view and a nearly ubiquitous feature of human play: In play, people subvert normal utility functions, incurring seemingly unnecessary costs to achieve arbitrary rewards. We show that four-and-five-year-old children not only infer playful behavior from observed violations of rational action (Experiment 1), but themselves take on unnecessary costs during both retrieval (Experiment 2) and search (Experiments 3A-B) tasks, despite acting efficiently in non-playful, instrumental contexts. We discuss the value of such apparently utility-violating behavior and why it might serve learning in the long run.

Effect of Genetically Reduced Maternal Myostatin on Late Gestation Maternal, Fetal, and Placental Metabolomes in Mice.

Myostatin (gene symbol: Mstn) is an autocrine and paracrine inhibitor of muscle growth. Pregnant mice with genetically reduced levels of myostatin give birth to offspring with greater adult muscle mass and bone biomechanical strength. However, maternal myostatin is not detectable in fetal circulations. Fetal growth is dependent on the maternal environment, and the provisioning of nutrients and growth factors by the placenta. Thus, this study examined the effect of reduced maternal myostatin on maternal and fetal serum metabolomes, as well as the placental metabolome. Fetal and maternal serum metabolomes were highly distinct, which is consistent with the role of the placenta in creating a specific fetal nutrient environment. There was no effect from myostatin on maternal glucose tolerance or fasting insulin. In comparisons between pregnant control and Mstn+/- mice, there were more significantly different metabolite concentrations in fetal serum, at 50, than in the mother's serum at 33, confirming the effect of maternal myostatin reduction on the fetal metabolic milieu. Polyamines, lysophospholipids, fatty acid oxidation, and vitamin C, in fetal serum, were all affected by maternal myostatin reduction.

The immune checkpoint molecule, VTCN1/B7-H4, guides differentiation and suppresses proinflammatory responses and MHC class I expression in an embryonic stem cell-derived model of human trophoblast.

The placenta acts as a protective barrier to pathogens and other harmful substances present in the maternal circulation throughout pregnancy. Disruption of placental development can lead to complications of pregnancy such as preeclampsia, intrauterine growth retardation and preterm birth. In previous work, we have shown that expression of the immune checkpoint regulator, B7-H4/VTCN1, is increased upon differentiation of human embryonic stem cells (hESC) to an in vitro model of primitive trophoblast (TB), that VTCN1/B7-H4 is expressed in first trimester but not term human placenta and that primitive trophoblast may be uniquely susceptible to certain pathogens. Here we report on the role of VTCN1 in trophoblast lineage development and anti-viral responses and the effects of changes in these processes on major histocompatibility complex (MHC) class I expression and peripheral NK cell phenotypes.

RISING STARS: Approaches to modeling placental function in preeclampsia in vitro and in vivo.

Modeling preeclampsia remains difficult due to the nature of the disease and the unique characteristics of the human placenta. Members of the Hominidae superfamily have a villous hemochorial placenta that is different in structure from those of other therian mammals, including the mouse hemochorial placenta, making this common animal model less ideal for studying this disease. Human placental tissues delivered from pregnancies complicated by preeclampsia are excellent for assessing the damage the disease causes but cannot answer how or when the disease begins. Symptoms of preeclampsia manifest halfway through pregnancy or later, making it currently impossible to identify preeclampsia in human tissues obtained from an early stage of pregnancy. Many animal and cell culture models recapitulate various aspects of preeclampsia, though none can on its own completely capture the complexity of human preeclampsia. It is particularly difficult to uncover the cause of the disease using models in which the disease is induced in the lab. However, the many ways by which preeclampsia-like features can be induced in a variety of laboratory animals are consistent with the idea that preeclampsia is a two-stage disease, in which a variety of initial insults may lead to placental ischemia, and ultimately systemic symptoms. The recent development of stem cell-based models, organoids, and various coculture systems have brought in vitro systems with human cells ever closer to recapitulating in vivo events that lead to placental ischemia.

Foundations of intuitive power analyses in children and adults.

Decades of research indicate that some of the epistemic practices that support scientific enquiry emerge as part of intuitive reasoning in early childhood. Here, we ask whether adults and young children can use intuitive statistical reasoning and metacognitive strategies to estimate how much information they might need to solve different discrimination problems, suggesting that they have some of the foundations for 'intuitive power analyses'. Across five experiments, both adults (N = 290) and children (N = 48, 6-8 years) were able to precisely represent the relative difficulty of discriminating populations and recognized that larger samples were required for populations with greater overlap. Participants were sensitive to the cost of sampling, as well as the perceptual nature of the stimuli. These findings indicate that both young children and adults metacognitively represent their own ability to make discriminations even in the absence of data, and can use this to guide efficient and effective exploration.

High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance.

Following CART-19 immunotherapy for B-cell acute lymphoblastic leukaemia (B-ALL), many patients relapse due to loss of the cognate CD19 epitope. Since epitope loss can be caused by aberrant CD19 exon 2 processing, we herein investigate the regulatory code that controls CD19 splicing. We combine high-throughput mutagenesis with mathematical modelling to quantitatively disentangle the effects of all mutations in the region comprising CD19 exons 1-3. Thereupon, we identify ~200 single point mutations that alter CD19 splicing and thus could predispose B-ALL patients to developing CART-19 resistance. Furthermore, we report almost 100 previously unknown splice isoforms that emerge from cryptic splice sites and likely encode non-functional CD19 proteins. We further identify cis-regulatory elements and trans-acting RNA-binding proteins that control CD19 splicing (e.g., PTBP1 and SF3B4) and validate that loss of these factors leads to pervasive CD19 mis-splicing. Our dataset represents a comprehensive resource for identifying predictive biomarkers for CART-19 therapy.

Association of serum leptin at 24-28 weeks gestation with initiation and progression of labor in women.

Concentrations of the hormone leptin, which is produced by adipose tissue, increase with increasing BMI, whereas leptin sensitivity often declines with higher BMI. Thus, altered leptin signaling may play a role in reproductive health risks observed with increasing BMI, which include later onset and slow progression of labor. Conflicting evidence from clinical, animal and in vitro studies have suggested that leptin either promotes or inhibits labor. We hypothesized that serum leptin concentrations or serum leptin: body mass index (BMI) ratios in women may be associated with the initiation and progression of labor. Following informed consent, serum samples were collected from 90 women with singleton pregnancies at the time of routine glucose-challenge testing, for measurement of leptin. The potential influence of leptin on gestation length and cervical dilation timing were examined by multiple linear regression. Data were analyzed from 63 participants who met exclusion and inclusion criteria. Leptin concentrations (log-transformed) at 24-28 weeks gestation were not significantly correlated with first trimester BMI . Log serum leptin and leptin: BMI ratio each were significantly associated with shorter total gestation length in uncomplicated, term pregnancies. In contrast, the mid-pregnancy leptin concentrations were not associated with progression of labor, assessed by cervical dilation over time. The association between higher serum leptin and shorter gestation length is consistent with the hypothesis that leptin promotes, or is permissive for, the onset of labor.

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.

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.

Children's exploratory play tracks the discriminability of hypotheses.

Effective curiosity-driven learning requires recognizing that the value of evidence for testing hypotheses depends on what other hypotheses are under consideration. Do we intuitively represent the discriminability of hypotheses? Here we show children alternative hypotheses for the contents of a box and then shake the box (or allow children to shake it themselves) so they can hear the sound of the contents. We find that children are able to compare the evidence they hear with imagined evidence they do not hear but might have heard under alternative hypotheses. Children (N = 160; mean: 5 years and 4 months) prefer easier discriminations (Experiments 1-3) and explore longer given harder ones (Experiments 4-7). Across 16 contrasts, children's exploration time quantitatively tracks the discriminability of heard evidence from an unheard alternative. The results are consistent with the idea that children have an "intuitive psychophysics": children represent their own perceptual abilities and explore longer when hypotheses are harder to distinguish.

Leveraging cognitive science to foster children's persistence.

Persistence is crucial for overcoming academic and interpersonal challenges. However, there has been little progress in developing effective interventions to improve persistence in childhood. Here we outline how recent insights from cognitive science can be leveraged to promote young children's persistence and highlight future directions to bridge research with practice.

Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts.

Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrant CD19 pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded within CD19 exon 2. While "exitrons" are known to exist in hundreds of human transcripts, we discovered, using reporter assays and direct long-read RNA sequencing (dRNA-seq), that the CD19 exitron is an artifact of reverse transcription. Extending our analysis to publicly available datasets, we identified dozens of questionable exitrons, dubbed "falsitrons," that appear only in cDNA-seq, but never in dRNA-seq. Our results highlight the importance of dRNA-seq for transcript isoform validation.

Placental structural abnormalities in gestational diabetes and when they develop: A scoping review.

Gestational diabetes mellitus (GDM) is defined as diabetes with onset or first recognition during gestation. It is a common complication of pregnancy that has become more prevalent over the past few decades. Abnormalities in fetal growth, including increased incidence of both large and small for gestational age babies, suggest placental dysfunction. The major goal of this scoping review is to determine what is known about abnormalities in placentas delivered from GDM pregnancies, and how early in gestation these abnormalities arise. A secondary goal is to review to what extent other selected factors, in particular obesity, have been found to influence or modify the reported effects of GDM on placental development, and whether these are considered in the study of GDM placentas. PubMed and Scopus databases were searched using the key terms: "gestational diabetes AND (woman OR human) AND placenta AND (ultrasound OR ultrastructure OR imaging OR histology OR pathology). Studies of gross morphology and histoarchitecture in placentas delivered from GDM pregnancies consistently report increased placental size, villous immaturity and a range of vascular lesions when compared to uncomplicated pregnancies. In contrast, a small number of ultrasound studies have examined placental development in GDM pregnancies in the second, and especially, the first trimester. Relatively few studies have analyzed interactions with maternal BMI, but these do suggest that it may play a role in placental abnormalities. Further examination of placental development early in pregnancy is needed to understand when it becomes disrupted in GDM, as a first step to identifying the underlying causes.