Science Advances

Iron deficiency (ID) in children caused by dietary deprivation can be alleviated in [~]40% cases with iron-fortified nutritional solutions. Devising more effective nutritional solutions requires a quantitative understanding of iron homeostasis, which is lacking. Here, we developed a physiologically-based mathematical model of paediatric iron homeostasis that recapitulates ID due to dietary deprivation and its alleviation using nutritional solutions. The model integrates key cellular and systemic iron regulatory processes, associated anatomical sites, the gut microbiota, and nutritional solutions, and shows how their complex interplay governs iron homeostasis. The model quantitatively described the alleviation of ID with nutritional solutions in a large clinical trial in Bangladesh. In virtual Indian populations, the model predicts that over-the-counter iron-fortified nutritional solutions can restore haemoglobin level to normalcy in >85% mildly anaemic infants and young children. Our study thus elucidates individual- and population-level underpinnings of ID, describes clinical observations, and informs efforts to improve intervention strategies.

Despite the accumulating evidence that increased consumption of ultra-processed food has adverse health implications, it remains difficult to decide what constitutes processed food. Indeed, the current processing-based classification of food has limited coverage and does not differentiate between degrees of processing, hindering consumer choices and slowing research on the health implications of processed food. Here we introduce a machine learning algorithm that accurately predicts the degree of processing for any food, indicating that over 73% of the U.S. food supply is ultra-processed. We show that the increased reliance of an individuals diet on ultra-processed food correlates with higher risk of metabolic syndrome, diabetes, angina, elevated blood pressure and biological age, and reduces the bio-availability of vitamins. Finally, we find that replacing foods with less processed alternatives can significantly reduce the health implications of ultra-processed food, suggesting that access to information on the degree of processing, currently unavailable to consumers, could improve population health.

The dynamics of blood sugar response to ultra-processed foods have strong parallels to the effects of addictive drugs. We hypothesize that if glycemic response is indeed an important determinant of habit formation-and hence product demand-then the largest producers of proprietary commercial foods will have formulated their products accordingly. We continuous glucose monitor (CGM) data from free-feeding adults spanning 579 meal events yielding a pooled time series dataset with more than 24,000 observations. We find strong evidence that addiction-like dynamic properties of the glycemic response (dose, rate of absorption, and withdrawal) are greater for globally branded fast food meals as compared to freshly-prepared or off-brand processed food meals. These differences are largely maintained when controlling for size of meal and nutrient content, suggesting that standard food labels may be insufficient to resolve what appears to be an important asymmetric information problem.

Chronic pain conditions are complex syndromes characterized by a mosaic of biological, psychological, and social factors. We derived predictive models for the number of co- existing pain sites in the UK Biobank and identified a common risk score that classified different chronic pain conditions in cross-sectional data, predicted the development of chronic pain in pain-free individuals, and determined the spreading of chronic pain to multiple sites or its recovery nine years later. The features with the strongest prognosis included sleeplessness, feeling fed-up, tiredness, stressful life events, and a BMI > 30. The risk score for pain was associated with an inflammatory blood marker, a polygenic risk score for pain, and a neuroimaging-based marker for sustained pain. The demonstration of a common biopsychosocial risk factor for different clinical pain conditions may help better characterize a general chronic pain syndrome, tailor research protocols, optimize patient randomization in clinical trials, and improve pain management.

The complete blood count is an important screening tool for healthy adults and is the most commonly ordered test at periodic physical exams. However, results are usually interpreted relative to one-size-fits-all reference intervals, undermining the goal of precision medicine to tailor medical care to the needs of individual patients based on their unique characteristics. Here we show that standard complete blood count indices in healthy adults have robust homeostatic setpoints that are patient-specific and stable, with the typical healthy adults set of 9 blood count setpoints distinguishable from 98% of others, and with these differences persisting for decades. These setpoints reflect a deep physiologic phenotype, enabling improved detection of both acquired and genetic determinants of hematologic regulation, including discovery of multiple novel loci via GWAS analyses. Patient-specific reference intervals derived from setpoints enable more accurate personalized risk assessment, and the setpoints themselves are significantly correlated with mortality risk, providing new opportunities to enhance patient-specific screening and early intervention. This study shows complete blood count setpoints are sufficiently stable and patient-specific to help realize the promise of precision medicine for healthy adults.

Nucleotide-derived cofactors could function as a missing link between the informational and the metabolic part at lifes emergence. One well-known example is nicotinamide dinucleotide (NAD), one of the evolutionarily most conserved redox cofactors found in metabolism. Here, we propose that the role of these cofactors could even extend to missing links between geo- and biochemistry. We show NAD+ can be reduced under close-to nature conditions with nickel-iron-alloys found in water-rock-interaction settings rich in hydrogen (serpentinizing systems) and that nicotinamide mononucleotide (NMN), a precursor molecule to NAD, has different properties regarding reduction specificity and sensitivity than NAD. The additional adenosine monophosphate (AMP) "tail" of the dinucleotide, a shared trait between many organic cofactors, seems to play a crucial mechanistic role in preventing overreduction of the nicotinamide-bearing nucleotide. This specificity is also connected to the used transition metals. While the combination of nickel and iron promotes the reduction of NAD+ to 1,4-NADH most efficiently, in the case of NMN, the presence of nickel leads to the accumulation of overreduction products. Testing the reducing abilities of both NADH and NMNH under abiotic conditions showed that both molecules act as equally effective, soluble hydride donors in non-enzymatic, proto-metabolic stages of lifes emergence.

Chronic pain is attributable to both local and systemic pathology. To investigate the latter, we focused on genetic risk shared among 24 chronic pain conditions in the UK Biobank. We conducted genome-wide association studies (GWAS) on all conditions and estimated genetic correlations among them, using these to model a factor structure in Genomic SEM. This revealed a general factor explaining most of the shared genetic variance in all conditions and an additional musculoskeletal pain-selective factor. Network analyses revealed a large cluster of highly genetically inter-connected conditions, with arthropathic, back, and neck pain showing the highest centrality. Functional annotation (FUMA) showed organogenesis, metabolism, transcription, and DNA repair as associated pathways, with enrichment for associated genes exclusively in brain tissues. Cross-reference with previous GWAS showed genetic overlap with cognition, mood, and brain structure. In sum, our results identify common genetic risks and suggest neurobiological and psychosocial mechanisms of vulnerability to chronic pain.

Brains come in various sizes and shapes, yet how neuronal position constrains the type of circuits that they can form remains largely unknown. The spatial layout of anatomical structures with corresponding functions varies widely across species (J-4). Also, during evolution, anatomical structures have duplicated and then diverged to generate new circuits and functions (5, 6). Thus, it is critical to understand how the position of neurons constrains their integration into circuits and, ultimately, their function. To address this question, we studied EmlJ knockout mice in which subsets of neocortical neurons form a new structure below the neocortex termed heterotopia (Ht). We examined how this new location affects the molecular identity, topography, input-output circuit connectivity, electrophysiology, and functional properties of these neurons. Our results reveal a striking conservation of the cellular features and circuit properties of Ht neurons, despite their abnormal location and misorientation. Supporting this observation, these neurons were able to functionally substitute for overlying neocortical neurons in a behaviorally relevant task when the latter were optogenetically silenced. Hence, specific neuronal identities and associated function can be reproduced in altered anatomical settings, revealing a remarkable level of self-organization and adaptability of neocortical circuits.

Why some surgical participants experience pain that extends beyond the original site of injury while others do not remains poorly understood. Both pain intensity and widespread pain contribute to recovery and quality of life, yet their psychosocial correlates are often examined separately. Using data from two large pre-surgical cohorts--participants preparing for knee replacement or thoracic surgery--we examined associations between sociodemographic and psychosocial factors, pain intensity at surgical and non-surgical sites, and widespread chronic pain. Across cohorts and outcomes, fatigue showed the strongest and most consistent associations with pain intensity and widespread pain, independent of other measured factors. Fatigue also occupied a central position in statistical association networks and accounted for substantial shared variance among multiple psychosocial variables, including sleep disturbance, depression, stress, and socioeconomic disadvantage. Pain at non-surgical sites was strongly associated with widespread pain and frequently accounted for observed associations between surgical-site pain and widespread pain. Together, these findings highlight robust patterns of association linking fatigue, pain intensity, and widespread pain in pre-surgical populations. One Sentence SummaryFatigue is the strongest and most consistent factor linked to how pain intensifies and spreads before surgery.

Despite the ongoing epidemic of opioid use disorder and death by fentanyl overdose, opioids remain the gold standard for analgesics. Pharmacokinetics (PK) dictates the individuals experience and utility of drugs; however, PK and behavioral outcomes have been conventionally studied in separate groups, even in preclinical models. To bridge this gap, we developed the first class of sensitive, selective, and genetically encodable fluorescent opioid biosensors, iOpioidSnFRs, including the fentanyl sensor, iFentanylSnFR. We expressed iFentanylSnFR in the ventral tegmental area of mice and recorded [fentanyl] alongside videos of behaviors before and after administration. We developed a machine vision routine to quantify the effects of the behavior on locomotor activity. We found that mice receiving fentanyl exhibited a repetitive locomotor pattern that paralleled the [fentanyl] time course. In a separate experiment, mice navigating a complex maze for water showed a dose-dependent impairment in navigation, in which animals repeated incorrect paths to the exclusion of most of the unexplored maze for the duration of the average fentanyl time course. This approach complements classical operant conditioning experiments and introduces a key feature of human addiction, the ability to carry out an ethologically relevant survival task, only now quantified in rodents. Finally, we demonstrate the utility of iFentanylSnFR in detecting fentanyl spiked into human biofluids and the generalizability of engineering methods to evolve selective biosensors of other opioids, such as tapentadol and levorphanol. These results encourage diagnostic and continuous monitoring approaches to personalizing opioid regimens for humans.

Emerging evidence has challenged the traditional view of a single-region origin for Homo sapiens, suggesting instead that our species arose and diversified across multiple geographically distinct populations in Africa, which intermittently exchanged genes and culture. However, our understanding of how this Pan-African metapopulation would have changed through time is still limited. Further, the drivers of such changes are uncertain, and quantitative models of the respective contribution of different African regions are lacking. Here we provide a complete reconstruction of the meta-population dynamics over the last 200,000 years by quantitatively integrating an environmental niche model based on archaeological sites within a spatially explicit population genetic framework. The inferred metapopulation dynamics not only fully explains the divergence among all available contemporary and ancient genomes of African hunter-gatherers, which were used to calibrate the model, but also accurately predicts the patterns of craniometric diversification across the continent from the Middle Pleistocene to the present. Furthermore, we show how the climate-driven changes in population sizes and connectivity predict major patterns of archaeological and phenotypic diversification over the last 200,000 years across the African continent.

Cells grow their boundaries by incorporating newly synthesized lipids into their membranes as well as through fusion of intracellular vesicles. As these processes yield trans-bilayer imbalances in lipid numbers, cells must actively flip lipid molecules across the bilayer to enable growth. Using giant and small unilamellar vesicles (GUVs and SUVs, respectively), we here recapitulate cellular growth and division under various conditions of transmembrane flip flop of lipids. By dynamically monitoring the changes in reduced volume and spontaneous curvature of GUVs that grow by fusion of many small SUVs, the morphology of these growing synthetic cells is quantified. We demonstrate that lipid flip flop relaxes curvature stresses and yields more symmetrically sized buds. Further increasing the neck curvature is shown to lead to bud scission. The mechanisms presented here offer fundamental insights into cell growth and division, which are important for understanding early protocells and designing synthetic cells that are able to grow and divide.

High-grade serous carcinoma (HGSC) is the most common ovarian cancer subtype, typically diagnosed at late stages with poor prognosis. Understanding early molecular events driving HGSC progression is crucial for timely detection and development of effective treatment strategies. We performed and integrated spatial cell-type resolved proteomics and paired transcriptomics across 25 women with precursor lesions of the fallopian tube and/or HGSC. Epithelial cell signatures revealed early activation of SUMOylation machinery, increased ATR and Wnt signaling, and enhanced MHC-I antigen presentation along the disease trajectory. The stroma exhibited extracellular matrix remodeling and interferon-mediated inflammation. Serous tubal intraepithelial carcinomas (STICs) in cancer patients contained a pro-coagulative signature and reduced APOA1/2 compared to STICs in individuals without cancer. We functionally established important roles of epithelial-derived TRIP13 and SUMOylation, and cancer-associated fibroblast-derived SULF1 and BGN in HGSC progression. These findings provide unique molecular insights into HGSC pathogenesis and identify potential new therapeutic targets for intervention.

Classical r- vs. K-selection theory describes the trade-offs between high reproductive output and competitiveness and guides research in evolutionary ecology1-5. While its impact has waned in the recent past, cancer evolution may rekindle it6-10. Indeed, solid tumors are an ideal theater for r- and K-selection and, hence, a good testing ground for ideas on life-history strategy evolution11,12. In this study, we impose r- or K-selection on HeLa cells to obtain strongly proliferative r cells and highly competitive K cells. RNA-seq analysis indicates that phenotypic trade-offs in r and K cells are associated with distinct patterns of expression of genes involved in the cell cycle, adhesion, apoptosis, and contact inhibition. Both empirical observations and simulations based on an ecological competition model show that the trade-off between cell proliferation and competitiveness can evolve adaptively and rapidly in naive cell lines. It is conceivable that the contrasting selective pressure may operate in a realistic ecological setting of actual tumors. When the r and K cells are mixed in vitro, they exhibit strikingly different spatial and temporal distributions in the resultant cultures. Thanks to this niche separation, the fitness of the entire tumor increases. Our analyses of life-history trade-offs are pertinent to evolutionary ecology as well as cancer biology.

The cognitive mechanisms linking chronic pain to motivational symptoms remain poorly understood. We demonstrate that individuals with chronic temporomandibular disorder (TMD), a common cause of chronic pain, exhibit a specific deficit in adaptive learning in uncertain environments, characterized by failure to reduce uncertainty over time and maintain efficient learning rates. Using a probabilistic reward task, we pioneered the application of a novel volatile Kalman filter to model behavior in 26 TMD participants and 39 matched controls, uniquely tracking trial-wise updates in uncertainty, volatility, and learning rate. Although surface-level performance did not differ across groups, model-based analysis revealed that those with TMD failed to reduce uncertainty and adapt their learning over time. TMD participants also reported significantly greater apathy, depression, and pain catastrophizing, as well as lower health-related quality of life. Mediation analysis confirmed that impaired uncertainty adaptation partially mediated the relationship specifically between TMD and apathy. These findings identify a computational signature of disrupted uncertainty adaptation in people with TMD and provide evidence for a mechanistic link between chronic pain and motivational dysfunction. This work lays a foundation for future studies examining how belief-updating deficits contribute to broader affective and cognitive symptoms in chronic pain.

Endocytosis at synapses is accelerated by the pre-accumulation of Dynamin 1xA at the endocytic zone by Syndapin 1. However, it is unclear how these proteins support the ultrafast kinetics of endocytosis. Here we report that these proteins phase separate at the presynaptic endocytic zone where ultrafast endocytosis takes place. Specifically, the proline-rich motif of Dynamin 1xA interacts with the Src-Homology 3 domain of Syndapin 1 and forms liquid-like condensates. Single-particle tracking of Dynamin 1xA molecules at synapses shows that their diffusion slows down substantially when they are in the condensates, indicating the presence of molecular crowding and intermolecular interaction. When Dynamin 1xA is mutated to disrupt its interaction with Syndapin 1 the condensates do not form. Thus, the liquid-like assembly of these endocytic proteins provides a catalytic platform for ultrafast endocytosis.

Metal implants are commonly used in orthopaedic surgery. The mechanical stability and longevity of implants depend on adequate bone deposition along the implant surface. The cellular and molecular mechanisms underlying peri-implant bone formation (i.e. osseointegration) are incompletely understood. Herein, our goal was to determine the specific bone marrow stromal cell populations that contribute to bone formation around metal implants. To do this, we utilized a mouse tibial implant model that is clinically representative of human joint replacement procedures. Using a lineage-tracing approach with the Acta2.creERT2 and Tmem100.creERT2 transgenic alleles, we found that Pdgfra- and Ly6a/Sca1-expressing stromal cells (PS cells) multiply and differentiate in the peri-implant environment to give rise to osteocytes in newly formed bone tissue. Single cell RNA-seq analysis indicated that PS cells are quiescent in uninjured bone tissue; however, they express markers of proliferation and osteogenic differentiation shortly after implantation surgery. Our findings indicate that PS cells are mobilized to repair bone tissue and facilitate implant osseointegration following surgery. Biologic therapies targeting PS cells might improve osseointegration in patients undergoing orthopaedic procedures.

Nitazenes are driving a wave of overdose deaths in the United States and Europe and often require additional doses of naloxone to reverse. To understand the molecular basis, we conducted a joint experimental and simulation study of three common nitazenes, eto-, etodes-, and protonitazene. Radioligand experiments demonstrated that all three nitazenes display higher receptor affinity and longer dissociation half-lives than fentanyl. Notably, protonitazene dissociates slower than carfentanil and its displacement requires fourfold higher antagonist concentrations. The observed trend in nitazene half-lives is recapitulated by molecular dynamics simulations, which suggest that kinetics is controlled by specific interactions with two receptor subpockets. A newly published cryo-EM structure of fluetonitazene-OR complex confirms the predicted interactions, including a{pi} -hole bond between the nitro group and Tyr1.39, a residue recently shown to modulate OR signaling bias. Our findings suggest slow receptor dissociation as a key factor challenging overdose reversal. The mechanistic insights have implications for understanding opioid toxicity and designing more effective countermeasures.

Non-pharmaceutical interventions (NPIs) have been a cornerstone in managing emergent diseases such as COVID-191-4. However, despite their potential to contain or attenuate the epidemic, the effects of NPIs on disease dynamics are not well understood1,5-7. We show that saturation of NPIs with the increase in infected individuals, an expected consequence of limited contact tracing and healthcare capacities, produces a positive feedback in the disease growth rate and a threshold between two alternative states--containment and outbreak8. These alternative states were previously related with the strength of NPIs but not with the infection number2,9-11. Furthermore, the transition between these states involves an abrupt acceleration in disease dynamics, which we report here for several COVID-19 outbreaks around the world. The consequences of a positive feedback in population dynamics at low numbers is a phenomenon widely studied in ecology--the Allee effect. This effect is a determinant of extinction-outbreak states, geographic synchronization, spatial spread, and the effect of exogenous variables, as vaccination12-15. As countries are relaxing containing measures, recognizing an NPI-induced Allee effect may be essential for deploying containment strategies within and among countries16 and acknowledges the need for early warning indicators of approaching epidemic tipping points17.

Placebo analgesia is a well-established medical phenomenon with overlapping neural representations between humans and rodents, but the genetic contribution to this conserved neural circuitry remains unknown. Using functional brain imaging in 305 monozygotic and dizygotic twins, we quantified the heritability of neural activation in placebo analgesia brain circuity during evoked pain, including the rostral anterior cingulate cortex, brainstem and cerebellum, using the ACE model. Neural responses showed significant heritability, with additive genetics accounting for 21 to 49% of the variance (A = 0.21-0.49), indicating that genetics have a moderate effect on pain-evoked brain activity within the placebo analgesia circuitry. For the first time, our findings reveal a heritable component of the neural network supporting placebo analgesia. By linking genetic variations to neural responses in placebo analgesia circuitry, this study bridges human and preclinical research and opens new ways for improving clinical trial methodology and tailoring pain therapies to individual genetic profiles.