iScience

MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provides an exciting avenue towards antiviral therapeutics. From patient transcriptomic data, we have discovered a circulating miRNA, miR-2392, that is directly involved with SARS-CoV-2 machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia as well as promoting many symptoms associated with COVID-19 infection. We demonstrate miR-2392 is present in the blood and urine of COVID-19 positive patients, but not detected in COVID-19 negative patients. These findings indicate the potential for developing a novel, minimally invasive, COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we have developed a novel miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters and may potentially inhibit a COVID-19 disease state in humans.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causing coronavirus disease 2019 (COVID-19) has caused a global health crisis. The primary site of infection is in the respiratory tract but the virus has been associated with a variety of complications involving the gastrointestinal and cardiovascular systems. Since the virus affects a variety of tissue types, there has been interest in understanding SARS-CoV-2 infection in early development and the placenta. ACE2 and TMPRSS2, two genes that are critical for SARS-CoV-2 virus entry are expressed in placenta-specific cell types including extravillous trophoblasts (EVTs) and especially, syncytiotrophoblasts (STs). The potential of SARS-CoV-2 to infect these placental cells and its effect on placental development and function is still unclear. Furthermore, it is crucial to understand the possible mechanism of vertical transmission of SARS-CoV-2 through the placenta. Here, we developed an in vitro model of SARS-CoV-2 infection of placental cell types using induced trophoblast stem cells (iTSCs). This model allowed us to show that STs but not EVTs are infected. Importantly, infected STs lack the expression of key differentiation genes, lack typically observed differentiated morphology and produce significantly lower human chorionic gonadotropin (HCG) compared to non-infected controls. We also show that an anti-ACE2 antibody prevents SARS-CoV-2 infection and restores normal ST differentiation and function. We highlight the establishment of a platform to study SARS-CoV-2 infection in early placental cell types, which will facilitate investigation of antiviral therapy to protect the placenta during early pregnancy and development.

In their natural habitat, mice interact and communicate to regulate major functions, such as reproduction, group coordination, and protection. Nevertheless, little is currently known about their spontaneous emission of ultrasonic vocalizations (USVs), despite their broad use as a phenotypic marker in mouse models of neuropsychiatric disorders. Here, we investigated mouse spontaneous communication by coupling automatic recording, segmentation, and analysis of USVs to the tracking of complex behaviors. We continuously recorded undisturbed same-sex pairs of C57BL/6J males and females at 5 weeks and 3 and 7 months of age over three days. Males emitted only a few short USVs, mainly when isolated from their conspecific, whereas females emitted a high number of USVs, especially when engaged in intense dynamic social interactions. The context-specific use of call types and acoustic variations emerged with increasing age. The emission of USVs also reflected a high level of excitement in social interactions. Finally, mice lacking Shank3, a synaptic protein associated with autism, displayed atypical USV usage and acoustic structure, which did not appear in classical protocols, highlighting the importance of studying spontaneous communication. The methods are freely available for the research community (https://usv.pasteur.cloud).

Behavioral interactions within the nuclear family play a pivotal role in the emergence of agency: the capacity to regulate physiological, psychological and social needs. While behaviors may develop over days or weeks in line with nervous system maturation, individual behaviors can occur on sub-second time scales making it challenging to track development in lab studies with brief observation periods, or in field studies with limited temporal precision and animal identification. Here we study development in families of gerbils, a highly social rodent, collecting tens of millions of behavior time points and implementing machine learning methods to track individual subjects. We provided maturing gerbils with a large, undisturbed environment between postnatal day 15 and the age at which they would typically disperse from the family unit (day 30). We identified complex and distinct developmental trajectories for food and water acquisition, solitary exploration, and social behaviors, some of which displayed sex differences and diurnal patterns. Our work supports the emergence of well-delineated autonomous and social behavior phenotypes that correlate with specific periods and loci of neural maturation.

Autism spectrum disorder (ASD) has been increasingly associated with abnormalities in synaptic pruning. Although significant progress has been made in elucidating the genetic and immunological underpinnings of ASD, its core pathological mechanisms remain poorly understood. In this study, we developed a network model integrating the in flammatory response pathway in microglia with synaptic signaling pathway to investigate how lipopolysaccharide (LPS) and synaptic activity jointly regulate microglia-mediated synaptic pruning. Our results reveal that pro-in flammatory activation of microglia impairs pruning efficiency under reduced synaptic activity, leading to excessive synaptic accumulation particularly in the prefrontal cortex and contributing to ASD-like phenotypes. Conversely, enhanced synaptic activity partially suppresses LPS-induced synaptic apoptosis and promotes synaptic retention. These findings suggest multiple therapeutic strategies, including targeting pruningrelated molecular pathways, mitigating neuroinflammation, and modulating synaptic excitability to alleviate ASD symptoms.

Marmoset monkeys have attracted much attention as a non-human primate model for studying vocal communication, but the call pattern and its meaning in marmoset communication are largely unknown. Here, we analyze sounds produced by hundreds of marmosets either in isolation or in pairs and reveal distinct call patterns in marmoset communication. The most prominent phee calls could be categorized into multiple grades based on the number of comprising phee syllables. Call transitions exhibited non-random patterns, favoring transition to the same or adjacent grade, with long sequences limited within two adjacent grades. The interval, composition, and temporal distribution of calls were significantly different between isolated and paired marmosets. Notably, different patterns of phee calls correlated with the heart rates and emotional states of marmoset, with the higher call grade reflecting a more agitated state. Antiphonal calling also exhibited distinct patterns and phee calls directly affected the heart rate of the listener in a manner depending on the grade of phee calls. Thus, phee call patterns in marmosets could encode emotional states and transmit emotion between turn-taking marmosets. How emotional expression in animals evolves into semantic communication in humans remains a mystery. Such complex call patterns in marmoset vocalization could represent the evolutionary prelude to semantic communication in primates.

Sunlight throughout the day and seasons strongly influences our biological rhythms and activity. In recent years, it has become evident that night-time overexposure to bright light in urban environments can profoundly affect physiology and behaviour in humans and animals. In particular, the artificial emission of short-wavelength light has been shown to stimulate alertness in humans, but the mechanisms remain largely unknown. Utilising a diurnal larval zebrafish model, we identified instant, non-image-forming (NIF) responses to short-wavelength violet light (~420nm), which are activated only during light exposure, and are reminiscent of alertness, including increased heart rate, enhanced locomotor activity, and pectoral fin beating (for increased oxygen supply). We further determined that these responses are driven by sympathetic neuronal circuits and depend on the zebrafish melanopsin homologue Opn4a. We also found that these responses can be modulated by the sleep-regulatory hormone melatonin, but that melatonin is not essential. Our findings reveal a previously unknown mechanism for violet light-dependent acute alertness.

COVID-19 has impacted billions of people in the world since 2019 and unfolded a major healthcare crisis. With an increasing number of deaths and the emergence of more transmissible variants, it is crucial to better understand the biology of the disease-causing virus, the SARS-CoV-2. Peripheral neuropathies appeared as a specific COVID-19 symptom occurring at later stages of the disease. In order to understand the impact of SARS-CoV-2 on the peripheral nervous system, we generated human sensory neurons from induced pluripotent stem cells that we infected with the SARS-CoV-2 strain WA1/2020 and the variants delta and omicron. Using single cell RNA sequencing, we found that human sensory neurons can be infected by SARS-CoV-2 but are unable to produce new viruses. Our data suggests that sensory neurons can be infected by the original WA1/2020 strain of SARS-CoV-2 as well as the delta and omicron variants.

Cell fusion, a natural process occurring between similar or dissimilar cell types, often confers new or enhanced functionality, yet its impact on cellular communication and gene regulation remains poorly understood. Here, we used recent analytical frameworks to investigate accidental cell fusion between murine cardiomyocytes (mHL1) and murine mesenchymal stromal/stem cells (mMSC) leveraging previously published single-cell RNA sequencing data. After fusion, we observed a biased distribution of gene expression and acquired phenotypes in fused hybrids. Trajectory inference showed that hybrids with a more mMSC-like transcriptome diverged more significantly from parental cells relative to hybrids with a more mHL1-like transcriptome. We also observed dynamic changes in cell-cell communication, with early (Day 1) downregulation of Wnt signaling and Melanogenesis evolving into the upregulation of pathways like Endocrine resistance and Focal adhesion by Day 3. Notably, ECM (extracellular matrix)-receptor interactions were largely consistent whether annotation or unsupervised Clustree methods were used. Furthermore, our analysis indicated the emergence of various cancer-associated signaling mechanisms. Our findings highlight the remarkable plasticity of cellular identity following fusion and lay the groundwork for future research into the precise molecular mechanisms driving these transformations and the potential of cell fusion for generating novel cell types.

In addition to frequently occurring stable all-or-none responses, live cells can display more complex response dynamics, e.g., oscillations in the activity/concentration of biomolecules. While the emergence and function of oscillatory dynamics have been heavily investigated, fewer efforts have been spent on whether cells can fine-tune different aspects of an oscillatory signal (e.g., peakwidth, duty cycle, and frequency) and whether this fine-tuning can allow oscillatory signals to convey different information. In this study, we investigate glucose-induced calcium (Ca2+) oscillation in MIN6 cells, finding that the spontaneous or induced changes in the phosphatidylinositol 4,5-bisphosphate (PIP2) level during Ca2+ oscillation can modulate the peakwidth of individual Ca2+ spikes. Additionally, using a combination of optogenetics and Ca2+ imaging, we demonstrate that variation of the widths and frequencies of Ca2+ spikes can exert strong influence on coupling between neighboring MIN6 cells.

The proper balance and transition between cellular quiescence and proliferation are critical to tissue homeostasis, and their deregulations are commonly found in many human diseases, including cancer and aging. Recent studies showed that the reentry of quiescent cells to the cell cycle is subjected to circadian regulation. However, the underlying mechanisms are largely unknown. Here, we report that two circadian proteins, Cryptochrome (Cry) and Rev-erb, deepen cellular quiescence in rat embryonic fibroblasts, resulting in stronger serum stimulation required for cells to exit quiescence and reenter the cell cycle. This finding was opposite from what we expected from the literature. By modeling a library of possible regulatory topologies linking Cry and Rev-erb to a bistable Rb-E2f gene network switch that controls the quiescence-to-proliferation transition and by experimentally testing model predictions, we found Cry and Rev-erb converge to downregulate Cyclin D/Cdk4,6 activity, leading to an ultrasensitive increase of the serum threshold to activate the Rb-E2f bistable switch. Our findings suggest a mechanistic role of circadian proteins in modulating the depth of cellular quiescence, which may have implications in the varying potentials of tissue repair and regeneration at different times of the day.

In recent years, many women have delayed childbearing, thus increasing the necessity for assisted reproductive technology (ART) for older women1-3. Despite advances in ART4, its success rate in advanced-age women is still very low3,4. As time-lapse imaging became available, morphological features of the developing pre-implantation embryo, in-vitro, are heavily used to assess its potency5-9. Timing of embryo cleavage is also an important factor that correlates with blastocyst formation and pregnancy rates8,10-14. Yet, our understanding of the interplay between embryos morphology, viability, and maternal age is limited, as manual approaches to infer embryo morphokinetics are time-consuming, subjective, and prone to errors. Machine learning15-18 was recently harnessed to predict embryo developmental potential19,20, however, with limited success. Here, we develop an artificial intelligence (AI) platform that infers the embryos developmental stage and captures tens of morphological properties and developmental dynamics. We show that developmental timing is the most informative and predictive morphokinetic property, particularly for embryos from maternally aged females. Analyzing the timing distributions reveals that viable embryos are confined into an age-independent temporal corridor while non-viable embryos deviate from it towards slower transition times. Yet, the deviation of non-viable embryos from the temporal corridor is age-dependent. Furthermore, there is a significant correlation between consecutive developmental stages transition times that diminishes in maternally old embryos. Overall, our results suggest that maternally old embryos most apparent morphokinetic property is the loss of temporal regulation. Our results and platform pave the way for a more accurate, maternally-age-dependent, assisted reproductive technology.

The coronavirus disease 2019 (COVID-19) pandemic has affected tens of millions of individuals and caused hundreds of thousands of deaths worldwide. Due to its rapid surge, there is a shortage of information on viral behavior and host response after SARS-CoV-2 infection. Here we present a comprehensive, multiscale network analysis of the transcriptional response to the virus. We particularly focus on key-regulators, cell-receptors, and host-processes that are hijacked by the virus for its advantage. ACE2-controlled processes involve a key-regulator CD300e (a TYROBP receptor) and the activation of IL-2 pro-inflammatory cytokine signaling. We further investigate the age-dependency of such receptors and identify the adipose and the brain as potentially contributing tissues for the diseases severity in old patients. In contrast, several other tissues in the young population are more susceptible to SARS-CoV-2 infection. In summary, this present study provides novel insights into the gene regulatory organization during the SARS-CoV-2 infection and the tissue-specific age dependence of the cell receptors involved in COVID-19.

The disease caused by SARS-CoV-2 is a global pandemic that threatens to bring long-term changes worldwide. Approximately 80% of infected patients are asymptomatic or have mild symptoms such as fever or cough, while rest of the patients have varying degrees of severity of symptoms, with 3-4% mortality rate. Severe symptoms such as pneumonia and Acute Respiratory Distress Syndrome can be caused by tissue damage mostly due to aggravated and unresolved innate and adaptive immune response, often resulting from a cytokine storm. However, the mechanistic underpinnings of such responses remain elusive, with an incomplete understanding of how an intricate interplay among infected cells and cells of innate and adaptive immune system can lead to such diverse clinicopathological outcomes. Here, we use a dynamical systems approach to dissect the emergent nonlinear intra-host dynamics among virally infected cells, the immune response to it and the consequent immunopathology. By mechanistic analysis of cell-cell interactions, we have identified key parameters affecting the diverse clinical phenotypes associated with COVID-19. This minimalistic yet rigorous model can explain the various phenotypes observed across the clinical spectrum of COVID-19, various co-morbidity risk factors such as age and obesity, and the effect of antiviral drugs on different phenotypes. It also reveals how a fine-tuned balance of infected cell killing and resolution of inflammation can lead to infection clearance, while disruptions can drive different severe phenotypes. These results will help further the case of rational selection of drug combinations that can effectively balance viral clearance and minimize tissue damage simultaneously. Significance StatementThe SARS-CoV-2 pandemic has already infected millions of people, and thousands of lives have been lost to it. The pandemic has already tested the limits of our public healthcare systems with a wide spectrum of clinicopathological symptoms and outcomes. The mechanistic underpinnings of the resultant immunopathology caused by the viral infection still remains to be elucidated. Here we propose a minimalistic but rigorous description of the interactions of the virus infected cells and the core components of the immune system that can potentially explain such diversity in the observed clinical outcomes. Our proposed framework could enable a platform to determine the efficacy of various treatment combinations and can contributes a conceptual understanding of dynamics of disease pathogenesis in SARS-CoV-2 infections.

Benthic animals live on or in the seafloor, a habitat known as the benthic zone. These bottom-dwelling organisms account for the largest fraction of animal diversity in our seas, playing vital roles in nutrient cycling, sediment stabilization and the broader food webs. Historically, the behavioral repertoire of benthic animals attached permanently to the sea floor has been considered as extremely limited (if at all present), reflecting an evolutionary adaptation to their sessile lifestyle and simplified nervous systems. Here, we overturn this view by studying the spontaneous and stimulus evoked behavioral repertoire of the basal chordate Ciona intestinalis which has a benthic sessile adult stage. We found that Ciona adults transition between three main postural engagement behavioral states. These are defined by different body part kinematics and postural dynamics characterised by changes in body shape configuration as opposed to locomotion. Transitions between states can occur probabilistically in spontaneously behaving animals suggesting that they can be internally generated by the simple brain of an adult Ciona. Importantly, using spatiotemporal embedding of postural features, we constructed a behavioral space for Ciona adults, which was divided into 18 stereotyped behavioral modes revealing the unappreciated richness of adult Ciona behaviors. Our analysis showed that Ciona adults can deploy in a selective manner these behavioral modules to elicit distinct responses to different mechanical stimuli, suggesting the presence of a sensory context dependent regulation of behavior in these benthic organisms. Our study raises the possibility that embodied postures is underlie the evolution of behavioral repertoires in sessile benthic animals.

Despite the large diversity of the proteins involved in cellular signaling, many intracellular signaling pathways converge onto one of only dozens of small molecule second messengers. Cyclic adenosine monophosphate (cAMP), one of these second messengers, is known to regulate activity of both Protein Kinase A (PKA) and the Extracellular Regulated Kinase (ERK), among other signaling pathways. In its role as an important cellular signaling hub, intracellular cAMP concentration has long been assumed to monotonically regulate its known effectors. Using an optogenetictool that can introduce precise amounts of cAMP in MDCKI cells, we identify genes whose expression changes biphasically with monotonically increasing cAMP levels. By examining the behavior of PKA and ERK1/2 in the same dose regime, we find that these kinases also respond biphasically to increasing cAMP levels, with opposite phases. We reveal that this behavior results from an elaborate integration by PKA of many cellular signals triggered by cAMP. In addition to the direct activation of PKA, cAMP also modulates the activity of p38 and ERK, which then converge to inhibit PKA. These interactions and their ensuing biphasic PKA profile have important physiological repercussions, influencing the ability of MDCKI cells to proliferate and form acini. Our data, supported by computational modeling, synthesize a set of network interconnections involving PKA and other important signaling pathways into a model that demonstrates how cells can capitalize on signal integration to create a diverse set of responses to cAMP concentration and produce complex input-output relationships.

Space travel is becoming accessible, yet our understanding of how space environment and microgravity ({micro}G) affect biology, physiology, and health remains incomplete. We investigated {micro}G effects on neuromuscular development and aging in Caenorhabditis elegans. Nematodes in {micro}G showed downregulation of genes related to synaptic signaling, dopamine response, locomotion, and cuticle development, with impaired synaptic vesicle dynamics, reduced motility, and shorter body lengths. Aged worms in {micro}G showed decreased collagen gene expression, increased motor neuron defects, synaptic vesicle accumulation and decreased release, and mitochondrial morphology collapse in body wall muscles, indicating accelerated aging. MEC-4 mechanoreceptor was identified as a key mediator of {micro}G-induced body length reduction and changes in extracellular matrix gene expression. {micro}G conditions suppressed mechanoreceptor genes, suggesting multiple mechanosensory systems are affected. Physical stimulation through culture medium with small beads in space mitigated many {micro}G-induced expression changes, including mechanoreceptors, neuromuscular defects, and aging-related phenotypes. These results highlight mechanical stimulis role in maintaining neuromuscular integrity during spaceflight and suggest restoring tactile input could counter health risks from reduced stimulation in long-term space missions. SIGNIFICACEWe found that microgravity ({micro}G) conditions suppress the expression of multiple mechanoreceptor genes in Caenorhabditis elegans, indicating that several mechanosensory systems are affected during spaceflight. Importantly, reintroducing physical stimulation by adding small beads to the culture medium in space partially reversed many of these {micro}G-induced gene expression changes. This intervention also mitigated neuromuscular defects and aging-related phenotypes observed under {micro}G conditions. Collectively, these findings underscore the essential role of mechanical stimuli in preserving neuromuscular integrity during space missions and suggest that restoring tactile input may be a promising strategy to counteract the health risks associated with reduced tactile stimulation during prolonged spaceflights.

A minority of people infected with SARS-CoV-2 will develop severe COVID-19 disease. To help physicians predict who is more likely to require admission to ICU, we conducted an unsupervised stratification of the circulating proteome that identified six endophenotypes (EPs) among 731 SARS-CoV-2 PCR-positive hospitalized participants in the Biobanque Quebecoise de la COVID-19, with varying degrees of disease severity and times to intensive care unit (ICU) admission. One endophenotype, EP6, was associated with a greater proportion of ICU admission, ventilation support, acute respiratory distress syndrome (ARDS) and death. Clinical features of EP6 included increased levels of C-reactive protein, D-dimers, interleukin-6, ferritin, soluble fms-like tyrosine kinase-1, elevated neutrophils, and depleted lymphocytes, whereas another endophenotype (EP5) was associated with cardiovascular complications, congruent with elevated blood biomarkers of cardiovascular disease like N-terminal pro B-type natriuretic peptide (NT-proBNP), Growth Differentiation Factor-15 (GDF-15), and Troponin T. Importantly, a prognostic model solely based on clinical laboratory measurements was developed and validated on 903 patients that generalizes the EPs to new patients recruited across all pandemic waves (2020-2022) and create new opportunities for automated identification of high-risk groups in the clinic. Thus, this novel way to address pathogenesis that leverages detailed phenotypic information but relies on routinely available information in the clinic to favor translation may find applications in other diseases beyond COVID-19.

Despite its popularity as an index of self-recognition, the mark test has not been used for assessing representations of the bodily self. This study combines the mark test and cross-reality task, to demonstrate novel aspects of childrens body representation and its development. Participants real-time skeletal data was captured, and virtual marks were displayed on 30 body parts for participants to interact through touch. The accuracy and trajectory of the first touch and reaction time were analyzed. Thirty Japanese 2- and 3-year-olds participated. Localization error could be predicted by dynamical body part coordination. Three-year-olds displayed fast and predictive reaching instead of visually guided reaching. Analyzing hand-reaching strategies in the XR mark test revealed aspects of the development of sensorimotor body representations.

Retinoblastoma (RB) represents one of the most prevalent intraocular cancers in children. Understanding the tumor heterogeneity in RB is important to design better targeted therapies. Here we used spatial transcriptomic to profile human retina and RB tumor to comprehensively dissect the spatial cell-cell communication networks. We found high intratumoral heterogeneity in RB, consisting of 10 transcriptionally distinct subpopulations with varying levels of proliferation capacity. Our results uncovered a complex architecture of the tumor microenvironment that predominantly consisted of cone precursors, as well as glial cells and cancer-associated fibroblasts. We delineated the cell trajectory underlying malignant progression of RB, and identified key signaling pathways driving genetic regulation across RB progression. We also explored the signaling pathways mediating cell-cell communications in RB subpopulations, and mapped the spatial networks of RB subpopulations and region neighbors. Altogether, we constructed the first spatial gene atlas for RB, which allowed us to characterize the transcriptomic landscape in spatially-resolved RB subpopulations, providing novel insights into the complex spatial communications involved in RB progression.