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Abstract Glioblastoma is the most common and deadliest brain tumour in adults, with a median survival of 15 months under the current standard of care. Immunotherapies like immune checkpoint inhibitors and oncolytic viruses have been extensively studied to improve this endpoint. However, most thus far have failed. To improve the efficacy of immunotherapies to treat glioblastoma, new single-cell imaging modalities like imaging mass cytometry can be leveraged and integrated with computational models. This enables a better understanding of the tumour microenvironment and its role in treatment success or failure in this hard-to-treat tumour. Here, we implemented an agent-based model that allows for spatial predictions of combination chemotherapy, oncolytic virus, and immune checkpoint inhibitors against glioblastoma. We initialised our model with patient imaging mass cytometry data to predict patient-specific responses and found that oncolytic viruses drive combination treatment responses determined by intratumoral cell density. We found that tumours with higher tumour cell density responded better to treatment. When fixing the number of cancer cells, treatment efficacy was shown to be a function of CD4 + T cell and, to a lesser extent, of macrophage counts. Critically, our simulations show that care must be put into the integration of spatial data and agent-based models to effectively capture intratumoral dynamics. Together, this study emphasizes the use of predictive spatial modelling to better understand cancer immunotherapy treatment dynamics, while highlighting key factors to consider during model design and implementation.

Abstract The lipid nanoparticle (LNP)-formulated mRNA vaccines BNT162b2 and mRNA-1273 are a widely adopted multi vaccination public health strategy to manage the COVID-19 pandemic. Clinical trial data has described the immunogenicity of the vaccine, albeit within a limited study time frame. Here, we use a within-host mathematical model for LNP-formulated mRNA vaccines, informed by available clinical trial data from 2020 to September 2021, to project a longer term understanding of immunity as a function of vaccine type, dosage amount, age, and sex. We estimate that two standard doses of either mRNA-1273 or BNT162b2, with dosage times separated by the company-mandated intervals, results in individuals losing more than 99% humoral immunity relative to peak immunity by 8 months following the second dose. We predict that within an 8 month period following dose two (corresponding to the original CDC time-frame for administration of a third dose), there exists a period of time longer than 1 month where an individual has lost more than 99% humoral immunity relative to peak immunity, regardless of which vaccine was administered. We further find that age has a strong influence in maintaining humoral immunity; by 8 months following dose two we predict that individuals aged 18–55 have a four-fold humoral advantage compared to aged 56–70 and 70+ individuals. We find that sex has little effect on the immune response and long-term IgG counts. Finally, we find that humoral immunity generated from two low doses of mRNA-1273 decays at a substantially slower rate relative to peak immunity gained compared to two standard doses of either mRNA-1273 or BNT162b2. Our predictions highlight the importance of the recommended third booster dose in order to maintain elevated levels of antibodies.

Throughout the SARS-CoV-2 pandemic, several variants of concern (VOCs) have been identified, many of which share recurrent mutations in the spike glycoprotein’s receptor-binding domain (RBD). This region coincides with known epitopes and can therefore have an impact on immune escape. Protracted infections in immunosuppressed patients have been hypothesized to lead to an enrichment of such mutations and therefore drive evolution towards VOCs. Here, we present the case of an immunosuppressed patient that developed distinct populations with immune escape mutations throughout the course of their infection. Notably, by investigating the co-occurrence of substitutions on individual sequencing reads in the RBD, we found quasispecies harboring mutations that confer resistance to known monoclonal antibodies (mAbs) such as S:E484K and S:E484A. These mutations were acquired without the patient being treated with mAbs nor convalescent sera and without them developing a detectable immune response to the virus. We also provide additional evidence for a viral reservoir based on intra-host phylogenetics, which led to a viral substrain that evolved elsewhere in the patient’s body, colonizing their upper respiratory tract (URT). The presence of SARS-CoV-2 viral reservoirs can shed light on protracted infections interspersed with periods where the virus is undetectable, and potential explanations for long-COVID cases.

Mathematical modeling has made significant contributions to drug design, development, and optimization. Virtual clinical trials that integrate mathematical models to explore patient heterogeneity and its impact on a variety of therapeutic questions have recently risen in popularity. Here, we outline best practices for creating virtual patients from mathematical models to ultimately implement and execute a virtual clinical trial. In this practical guide, we discuss and provide examples of model design, parameter estimation, parameter sensitivity, model identifiability, and virtual patient cohort creation. Our goal is to help researchers adopt these approaches to further the use of virtual population-based analysis and virtual clinical trials.

BackgroundCognitive impairment is a clinically important feature of schizophrenia. Polygenic risk score (PRS) methods have demonstrated genetic overlap between schizophrenia, bipolar disorder (BD), major depressive disorder (MDD), educational attainment (EA), and IQ, but very few studies have examined associations between these PRS and cognitive phenotypes within schizophrenia cases.MethodsWe combined genetic and cognitive data in 3034 schizophrenia cases from 11 samples using the general intelligence factor g as the primary measure of cognition. We used linear regression to examine the association between cognition and PRS for EA, IQ, schizophrenia, BD, and MDD. The results were then meta-analyzed across all samples. A genome-wide association studies (GWAS) of cognition was conducted in schizophrenia cases.ResultsPRS for both population IQ (P = 4.39 × 10-28) and EA (P = 1.27 × 10-26) were positively correlated with cognition in those with schizophrenia. In contrast, there was no association between cognition in schizophrenia cases and PRS for schizophrenia (P = .39), BD (P = .51), or MDD (P = .49). No individual variant approached genome-wide significance in the GWAS.ConclusionsCognition in schizophrenia cases is more strongly associated with PRS that index cognitive traits in the general population than PRS for neuropsychiatric disorders. This suggests the mechanisms of cognitive variation within schizophrenia are at least partly independent from those that predispose to schizophrenia diagnosis itself. Our findings indicate that this cognitive variation arises at least in part due to genetic factors shared with cognitive performance in populations and is not solely due to illness or treatment-related factors, although our findings are consistent with important contributions from these factors.

Data analysis is widely used to generate new insights into human disease mechanisms and provide better treatment methods. In this work, we used the mechanistic models of viral infection to generate synthetic data of influenza and COVID-19 patients. We then developed and validated a supervised machine learning model that can distinguish between the two infections. Influenza and COVID-19 are contagious respiratory illnesses that are caused by different pathogenic viruses but appeared with similar initial presentations. While having the same primary signs COVID-19 can produce more severe symptoms, illnesses, and higher mortality. The predictive model performance was externally evaluated by the ROC AUC metric (area under the receiver operating characteristic curve) on 100 virtual patients from each cohort and was able to achieve at least AUC = 91% using our multiclass classifier. The current investigation highlighted the ability of machine learning models to accurately identify two different diseases based on major components of viral infection and immune response. The model predicted a dominant role for viral load and productively infected cells through the feature selection process.

Abstract Objectives Identifying biomarkers causing differential SARS‐CoV‐2 infection kinetics associated with severe COVID‐19 is fundamental for effective diagnostics and therapeutic planning. Methods In this work, we applied mathematical modelling to investigate the relationships between patient characteristics, plasma SARS‐CoV‐2 RNA dynamics and COVID‐19 severity. Using a straightforward mathematical model of within‐host viral kinetics, we estimated key model parameters from serial plasma viral RNA (vRNA) samples from 256 hospitalised COVID‐19+ patients. Results Our model predicted that clearance rates distinguish key differences in plasma vRNA kinetics and severe COVID‐19. Moreover, our analyses revealed a strong correlation between plasma vRNA kinetics and plasma receptor for advanced glycation end products (RAGE) concentrations (a plasma biomarker of lung damage), collected in parallel to plasma vRNA from patients in our cohort, suggesting that RAGE can substitute for viral plasma shedding dynamics to prospectively classify seriously ill patients. Conclusion Overall, our study identifies factors of COVID‐19 severity, supports interventions to accelerate viral clearance and underlines the importance of mathematical modelling to better understand COVID‐19.

Background and Hypotheses Affective recovery, operationalized as the time needed for affect to return to baseline levels after daily stressors, may be a putative momentary representation of resilience. This study aimed to investigate affective recovery in positive and negative affect across subclinical and clinical stages of psychosis and whether this is associated with exposure to childhood trauma (sexual, physical, and emotional abuse). Study Design We used survival analysis to predict the time-to-recovery from a daily event-related stressor in a pooled sample of 3 previously conducted experience sampling studies including 113 individuals with first-episode psychosis, 162 at-risk individuals, and 94 controls. Study Results Negative affective recovery (ie, return to baseline following an increase in negative affect) was longer in individuals with first-episode psychosis compared with controls (hazard ratio [HR] = 1.71, 95% confidence interval [CI; 1.03, 2.61], P  = .04) and in at-risk individuals exposed to high vs low levels of emotional abuse (HR = 1.31, 95% CI [1.06, 1.62], P  = .01). Positive affective recovery (ie, return to baseline following a decrease in positive affect) did not differ between groups and was not associated with childhood trauma. Conclusions Our results give first indications that negative affective recovery may be a putative momentary representation of resilience across stages of psychosis and may be amplified in at-risk individuals with prior experiences of emotional abuse. Understanding how affective recovery contributes to the development of psychosis may help identify new targets for prevention and intervention to buffer risk or foster resilience in daily life. [ABSTRACT FROM AUTHOR]

Background: Psychotic experiences (PEs) and social isolation (SI) seem related during early stages of psychosis, but the temporal dynamics between the two are not clear. Literature so far suggests a self-perpetuating cycle wherein momentary increases in PEs lead to social withdrawal, which, subsequently, triggers PEs at a next point in time, especially when SI is associated with increased distress. The current study investigated the daily-life temporal associations between SI and PEs, as well as the role of SI-related and general affective distress in individuals at clinical high risk (CHR) for psychosis. Methods: We used experience sampling methodology in a sample of 137 CHR participants. We analyzed the association between SI, PEs, and distress using time-lagged linear mixed-effects models. Results: SI did not predict next-moment fluctuations in PEs, or vice versa. Furthermore, although SI-related distress was not predictive of subsequent PEs, general affective distress during SI was a robust predictor of next-moment PEs. Conclusions: Our results suggest that SI and PEs are not directly related on a moment-to-moment level, but a negative emotional state when alone does contribute to the risk of PEs. These findings highlight the role of affective wellbeing during early-stage psychosis development. [ABSTRACT FROM AUTHOR]

Background Growing evidence suggests that population mental health outcomes have worsened since the pandemic started. The extent that these changes have altered common age-related trends in psychological distress, where distress typically rises until midlife and then falls after midlife in both sexes, is unknown. We aimed to analyse whether long-term pre-pandemic psychological distress trajectories were disrupted during the pandemic, and whether these changes have been different across cohorts and by sex. Methods and findings We used data from three nationally representative birth cohorts comprising all people born in Great Britain in a single week of 1946 (National Survey of Health and Development, NSHD), 1958 (National Child Development Study, NCDS), or 1970 (British Cohort Study, BCS70). The follow-up data used spanned 39 years in NSHD (1982 to 2021), 40 years in NCDS (1981 to 2001), and 25 years in BCS70 (1996 to 2021). We used psychological distress factor scores, as measured by validated self-reported questionnaires (NSHD: Present State Examination, Psychiatric Symptoms Frequency, and 28- and 12-item versions of General Health Questionnaire; NCDS and BCS70: Malaise Inventory; all: 2-item versions of Generalized Anxiety Disorder scale and Patient Health Questionnaire). We used a multilevel growth curve modelling approach to model the trajectories of distress across cohorts and sexes and obtained estimates of the differences between the distress levels observed during the pandemic and those observed at the most recent pre-pandemic assessment and at the peak in the cohort-specific pre-pandemic distress trajectory, located at midlife. We further analysed whether pre-existing cohort and sex inequalities had changed with the pandemic onset using a difference-in-differences (DiD) approach. The analytic sample included 16,389 participants. By September/October 2020, distress levels had reached or exceeded the levels of the peak in the pre-pandemic life-course trajectories, with larger increases in younger cohorts (standardised mean differences [SMD] and 95% confidence intervals of SMD.sub.NSHD,pre-peak = -0.02 [-0.07, 0.04], SMD.sub.NCDS,pre-peak = 0.05 [0.02, 0.07], and SMD.sub.BCS70,pre-peak = 0.09 [0.07, 0.12] for the 1946, 1958, and 1970 birth cohorts, respectively). Increases in distress were larger among women than men, widening pre-existing sex inequalities (DiD and 95% confidence intervals of DiD.sub.NSHD,sex,pre-peak = 0.17 [0.06, 0.28], DiD.sub.NCDS,sex,pre-peak = 0.11 [0.07, 0.16], and DiD.sub.BCS70,sex,pre-peak = 0.11 [0.05, 0.16] when comparing sex inequalities in the pre-pandemic peak in midlife to those observed by September/October 2020). As expected in cohort designs, our study suffered from high proportions of attrition with respect to the original samples. Although we used non-response weights to restore sample representativeness to the target populations (those born in the United Kingdom in 1946, 1958, and 1970, alive and residing in the UK), results may not be generalisable to other sections within the UK population (e.g., migrants and ethnic minority groups) and countries different than the UK. Conclusions Pre-existing long-term psychological distress trajectories of adults born between 1946 and 1970 were disrupted during the COVID-19 pandemic, particularly among women, who reached the highest levels ever recorded in up to 40 years of follow-up data. This may impact future trends of morbidity, disability, and mortality due to common mental health problems., Author(s): Darío Moreno-Agostino 1,2,*, Helen L. Fisher 2,3, Alissa Goodman 1, Stephani L. Hatch 2,4, Craig Morgan 2,5, Marcus Richards 6, Jayati Das-Munshi 2,4,7, George B. Ploubidis 1,2 Introduction Mental [...]

Stem cell differentiation cascades are critical components of healthy tissue maintenance. Dysregulation in these systems can lead to serious diseases, including cancer. Myoepithelial mammary cells are produced from differentiated mammary stem cells in processes regulated, in part, by estrogen signalling and concentrations. To quantify and predict the production of mammary myoepithelial cell production by estrogen, we developed a mechanistic, quantitative systems pharmacology (QSP) model that includes the explicit characterization of free and unbound estrogen concentrations in circulation. Linking this model to a previously developed population pharmacokinetics model for ethinyl estradiol, a synthetic form of estrogen included in oral contraceptives, we predicted the effects of estrogen on myoepithelial cell development. Interestingly, pharmacokinetic intraindividual variability alone did not significantly impact on our modelos predictions, suggesting that combinations of physiological and pharmacokinetic variability drive heterogeneity in mechanistic QSP models. Our model is one component of an improved understanding of mammary myoepithelial cell production and development, and our results support the call for mechanistically constructed systems models for disease and pharmaceutical modelling.

Abstract Ovarian cancer is commonly diagnosed in its late stages, and new treatment modalities are needed to improve patient outcomes and survival. We have recently established the synergistic effects of combination tumor necrosis factor‐related apoptosis‐inducing ligand (TRAIL) and procaspase activating compound (PAC‐1) therapies in granulosa cell tumors (GCT) of the ovary, a rare form of ovarian cancer, using a mathematical model of the effects of both drugs in a GCT cell line. Here, to understand the mechanisms of combined TRAIL and PAC‐1 therapy, study the viability of this treatment strategy, and accelerate preclinical translation, we leveraged our mathematical model in combination with population pharmacokinetics (PKs) models of both TRAIL and PAC‐1 to expand a realistic heterogeneous cohort of virtual patients and optimize treatment schedules. Using this approach, we investigated treatment responses in this virtual cohort and determined optimal therapeutic schedules based on patient‐specific PK characteristics. Our results showed that schedules with high initial doses of PAC‐1 were required for therapeutic efficacy. Further analysis of individualized regimens revealed two distinct groups of virtual patients within our cohort: one with high PAC‐1 elimination and one with normal PAC‐1 elimination. In the high elimination group, high weekly doses of both PAC‐1 and TRAIL were necessary for therapeutic efficacy; however, virtual patients in this group were predicted to have a worse prognosis when compared to those in the normal elimination group. Thus, PAC‐1 PK characteristics, particularly clearance, can be used to identify patients most likely to respond to combined PAC‐1 and TRAIL therapy. This work underlines the importance of quantitative approaches in preclinical oncology.

Summary: Oncolytic viruses (OVs) are emerging cancer immunotherapy. Despite notable successes in the treatment of some tumors, OV therapy for central nervous system cancers has failed to show efficacy. We used an ex vivo tumor model developed from human glioblastoma tissue to evaluate the infiltration of herpes simplex OV rQNestin (oHSV-1) into glioblastoma tumors. We next leveraged our data to develop a computational, model of glioblastoma dynamics that accounts for cellular interactions within the tumor. Using our computational model, we found that low stromal density was highly predictive of oHSV-1 therapeutic success, suggesting that the efficacy of oHSV-1 in glioblastoma may be determined by stromal-to-tumor cell regional density. We validated these findings in heterogenous patient samples from brain metastatic adenocarcinoma. Our integrated modeling strategy can be applied to suggest mechanisms of therapeutic responses for central nervous system cancers and to facilitate the successful translation of OVs into the clinic.

Heart failure (HF), which is a major clinical and public health challenge, commonly develops when the myocardial muscle is unable to pump an adequate amount of blood at typical cardiac pressures to fulfill the body’s metabolic needs, and compensatory mechanisms are compromised or fail to adjust. Treatments consist of targeting the maladaptive response of the neurohormonal system, thereby decreasing symptoms by relieving congestion. Sodium–glucose co-transporter 2 (SGLT2) inhibitors, which are a recent antihyperglycemic drug, have been found to significantly improve HF complications and mortality. They act through many pleiotropic effects, and show better improvements compared to others existing pharmacological therapies. Mathematical modeling is a tool used to describe the pathophysiological processes of the disease, quantify clinically relevant outcomes in response to therapies, and provide a predictive framework to improve therapeutic scheduling and strategies. In this review, we describe the pathophysiology of HF, its treatment, and how an integrated mathematical model of the cardiorenal system was built to capture body fluid and solute homeostasis. We also provide insights into sex-specific differences between males and females, thereby encouraging the development of more effective sex-based therapies in the case of heart failure.

Summary: Glioblastoma is a complex disease that is difficult to treat. Network and data science offer alternative approaches to classical bioinformatics pipelines to study gene expression patterns from single-cell datasets, helping to distinguish genes associated with the control of differentiation and aggression. To identify the key molecular regulators of the networks driving glioblastoma/GSC and predict their cell fate dynamics, we applied a host of data theoretic techniques to gene expression patterns from pediatric and adult glioblastoma, and adult glioma-derived stem cells (GSCs). We identified eight transcription factors (OLIG1/2, TAZ, GATA2, FOXG1, SOX6, SATB2, and YY1) and four signaling genes (ATL3, MTSS1, EMP1, and TPT1) as coordinators of cell state transitions and, thus, clinically targetable putative factors differentiating pediatric and adult glioblastomas from adult GSCs. Our study provides strong evidence of complex systems approaches for inferring complex dynamics from reverse-engineering gene networks, bolstering the search for new clinically relevant targets in glioblastoma.

The genome of the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the pathogen that causes coronavirus disease 2019 (COVID-19), has been sequenced at an unprecedented scale leading to a tremendous amount of viral genome sequencing data. To assist in tracing infection pathways and design preventive strategies, a deep understanding of the viral genetic diversity landscape is needed. We present here a set of genomic surveillance tools from population genetics which can be used to better understand the evolution of this virus in humans. To illustrate the utility of this toolbox, we detail an in depth analysis of the genetic diversity of SARS-CoV-2 in first year of the COVID-19 pandemic. We analyzed 329,854 high-quality consensus sequences published in the GISAID database during the pre-vaccination phase. We demonstrate that, compared to standard phylogenetic approaches, haplotype networks can be computed efficiently on much larger datasets. This approach enables real-time lineage identification, a clear description of the relationship between variants of concern, and efficient detection of recurrent mutations. Furthermore, time series change of Tajima's D by haplotype provides a powerful metric of lineage expansion. Finally, principal component analysis (PCA) highlights key steps in variant emergence and facilitates the visualization of genomic variation in the context of SARS-CoV-2 diversity. The computational framework presented here is simple to implement and insightful for real-time genomic surveillance of SARS-CoV-2 and could be applied to any pathogen that threatens the health of populations of humans and other organisms.