Integrated modeling of labile and glycated hemoglobin with glucose for enhanced diabetes detection and short-term monitoring.

Metabolic biomarkers, particularly glycated hemoglobin and fasting plasma glucose, are pivotal in the diagnosis and control of diabetes mellitus. Despite their importance, they exhibit limitations in assessing short-term glucose variations. In this study, we propose labile hemoglobin as an additional biomarker, providing insightful perspectives into these fluctuations. By utilizing datasets from 40,652 retrospective general participants and conducting glucose tolerance tests on 60 prospective pediatric subjects, we explored the relationship between plasma glucose and labile hemoglobin. A mathematical model was developed to encapsulate short-term glucose kinetics in the pediatric group. Applying dimensionality reduction techniques, we successfully identified participant subclusters, facilitating the differentiation between diabetic and non-diabetic individuals. Intriguingly, by integrating labile hemoglobin measurements with plasma glucose values, we were able to predict the likelihood of diabetes in pediatric subjects, underscoring the potential of labile hemoglobin as a significant glycemic biomarker for diabetes research.

Deterministic reprogramming of neutrophils within tumors.

Neutrophils are increasingly recognized as key players in the tumor immune response and are associated with poor clinical outcomes. Despite recent advances characterizing the diversity of neutrophil states in cancer, common trajectories and mechanisms governing the ontogeny and relationship between these neutrophil states remain undefined. Here, we demonstrate that immature and mature neutrophils that enter tumors undergo irreversible epigenetic, transcriptional, and proteomic modifications to converge into a distinct, terminally differentiated dcTRAIL-R1+ state. Reprogrammed dcTRAIL-R1+ neutrophils predominantly localize to a glycolytic and hypoxic niche at the tumor core and exert pro-angiogenic function that favors tumor growth. We found similar trajectories in neutrophils across multiple tumor types and in humans, suggesting that targeting this program may provide a means of enhancing certain cancer immunotherapies.

Chromosomal instability in aneuploid acute lymphoblastic leukemia associates with disease progression.

Chromosomal instability (CIN) lies at the core of cancer development leading to aneuploidy, chromosomal copy-number heterogeneity (chr-CNH) and ultimately, unfavorable clinical outcomes. Despite its ubiquity in cancer, the presence of CIN in childhood B-cell acute lymphoblastic leukemia (cB-ALL), the most frequent pediatric cancer showing high frequencies of aneuploidy, remains unknown. Here, we elucidate the presence of CIN in aneuploid cB-ALL subtypes using single-cell whole-genome sequencing of primary cB-ALL samples and by generating and functionally characterizing patient-derived xenograft models (cB-ALL-PDX). We report higher rates of CIN across aneuploid than in euploid cB-ALL that strongly correlate with intraclonal chr-CNH and overall survival in mice. This association was further supported by in silico mathematical modeling. Moreover, mass-spectrometry analyses of cB-ALL-PDX revealed a "CIN signature" enriched in mitotic-spindle regulatory pathways, which was confirmed by RNA-sequencing of a large cohort of cB-ALL samples. The link between the presence of CIN in aneuploid cB-ALL and disease progression opens new possibilities for patient stratification and offers a promising new avenue as a therapeutic target in cB-ALL treatment.

Variable selection for nonlinear dimensionality reduction of biological datasets through bootstrapping of correlation networks.

Identifying the most relevant variables or features in massive datasets for dimensionality reduction can lead to improved and more informative display, faster computation times, and more explainable models of complex systems. Despite significant advances and available algorithms, this task generally remains challenging, especially in unsupervised settings. In this work, we propose a method that constructs correlation networks using all intervening variables and then selects the most informative ones based on network bootstrapping. The method can be applied in both supervised and unsupervised scenarios. We demonstrate its functionality by applying Uniform Manifold Approximation and Projection for dimensionality reduction to several high-dimensional biological datasets, derived from 4D live imaging recordings of hundreds of morpho-kinetic variables, describing the dynamics of thousands of individual leukocytes at sites of prominent inflammation. We compare our method with other standard ones in the field, such as Principal Component Analysis and Elastic Net, showing that it outperforms them. The proposed method can be employed in a wide range of applications, encompassing data analysis and machine learning.

The local microenvironment drives activation of neutrophils in human brain tumors.

Neutrophils are abundant immune cells in the circulation and frequently infiltrate tumors in substantial numbers. However, their precise functions in different cancer types remain incompletely understood, including in the brain microenvironment. We therefore investigated neutrophils in tumor tissue of glioma and brain metastasis patients, with matched peripheral blood, and herein describe the first in-depth analysis of neutrophil phenotypes and functions in these tissues. Orthogonal profiling strategies in humans and mice revealed that brain tumor-associated neutrophils (TANs) differ significantly from blood neutrophils and have a prolonged lifespan and immune-suppressive and pro-angiogenic capacity. TANs exhibit a distinct inflammatory signature, driven by a combination of soluble inflammatory mediators including tumor necrosis factor alpha (TNF-ɑ) and Ceruloplasmin, which is more pronounced in TANs from brain metastasis versus glioma. Myeloid cells, including tumor-associated macrophages, emerge at the core of this network of pro-inflammatory mediators, supporting the concept of a critical myeloid niche regulating overall immune suppression in human brain tumors.

Metabolic activity grows in human cancers pushed by phenotypic variability.

Different evolutionary processes push cancers to increasingly aggressive behaviors, energetically sustained by metabolic reprogramming. The collective signature emerging from this transition is macroscopically displayed by positron emission tomography (PET). In fact, the most readily PET measure, the maximum standardized uptake value (SUVmax), has been found to have prognostic value in different cancers. However, few works have linked the properties of this metabolic hotspot to cancer evolutionary dynamics. Here, by analyzing diagnostic PET images from 512 patients with cancer, we found that SUVmax scales superlinearly with the mean metabolic activity (SUVmean), reflecting a dynamic preferential accumulation of activity on the hotspot. Additionally, SUVmax increased with metabolic tumor volume (MTV) following a power law. The behavior from the patients data was accurately captured by a mechanistic evolutionary dynamics model of tumor growth accounting for phenotypic transitions. This suggests that non-genetic changes may suffice to fuel the observed sustained increases in tumor metabolic activity.

A Simple 3D Cell Culture Method for Studying the Interactions between Human Mesenchymal Stromal/Stem Cells and Patients Derived Glioblastoma.

We have developed a 3D biosphere model using patient-derived cells (PDCs) from glioblastoma (GBM), the major form of primary brain tumors in adult, plus cancer-activated fibroblasts (CAFs), obtained by culturing mesenchymal stem cells with GBM conditioned media. The effect of MSC/CAFs on the proliferation, cell-cell interactions, and response to treatment of PDCs was evaluated. Proliferation in the presence of CAFs was statistically lower but the spheroids formed within the 3D-biosphere were larger. A treatment for 5 days with Temozolomide (TMZ) and irradiation, the standard therapy for GBM, had a marked effect on cell number in monocultures compared to co-cultures and influenced cancer stem cells composition, similar to that observed in GBM patients. Mathematical analyses of spheroids growth and morphology confirm the similarity with GBM patients. We, thus, provide a simple and reproducible method to obtain 3D cultures from patient-derived biopsies and co-cultures with MSC with a near 100% success. This method provides the basis for relevant in vitro functional models for a better comprehension of the role of tumor microenvironment and, for precision and/or personalized medicine, potentially to predict the response to treatments for each GBM patient.

Behavioural immune landscapes of inflammation.

Transcriptional and proteomic profiling of individual cells have revolutionized interpretation of biological phenomena by providing cellular landscapes of healthy and diseased tissues1,2. These approaches, however, do not describe dynamic scenarios in which cells continuously change their biochemical properties and downstream 'behavioural' outputs3-5. Here we used 4D live imaging to record tens to hundreds of morpho-kinetic parameters describing the dynamics of individual leukocytes at sites of active inflammation. By analysing more than 100,000 reconstructions of cell shapes and tracks over time, we obtained behavioural descriptors of individual cells and used these high-dimensional datasets to build behavioural landscapes. These landscapes recognized leukocyte identities in the inflamed skin and trachea, and uncovered a continuum of neutrophil states inside blood vessels, including a large, sessile state that was embraced by the underlying endothelium and associated with pathogenic inflammation. Behavioural screening in 24 mouse mutants identified the kinase Fgr as a driver of this pathogenic state, and interference with Fgr protected mice from inflammatory injury. Thus, behavioural landscapes report distinct properties of dynamic environments at high cellular resolution.

Influence of Coating and Size of Magnetic Nanoparticles on Cellular Uptake for In Vitro MRI.

Iron oxide nanoparticles (IONPs) are suitable materials for contrast enhancement in magnetic resonance imaging (MRI). Their potential clinical applications range from diagnosis to therapy and follow-up treatments. However, a deeper understanding of the interaction between IONPs, culture media and cells is necessary for expanding the application of this technology to different types of cancer therapies. To achieve new insights of these interactions, a set of IONPs were prepared with the same inorganic core and five distinct coatings, to study their aggregation and interactions in different physiological media, as well as their cell labelling efficiency. Then, a second set of IONPs, with six different core sizes and the same coating, were used to study how the core size affects cell labelling and MRI in vitro. Here, IONPs suspended in biological media experience a partial removal of the coating and adhesion of molecules. The FBS concentration alters the labelling of all types of IONPs and hydrodynamic sizes ≥ 300 nm provide the greatest labelling using the centrifugation-mediated internalization (CMI). The best contrast for MRI results requires a core size range between 12-14 nm coated with dimercaptosuccinic acid (DMSA) producing R2* values of 393.7 s-1 and 428.3 s-1, respectively. These findings will help to bring IONPs as negative contrast agents into clinical settings.

The interplay of blood flow and temperature in regional hyperthermia: a mathematical approach.

In recent decades, hyperthermia has been used to raise oxygenation levels in tumours undergoing other therapeutic modalities, of which radiotherapy is the most prominent one. It has been hypothesized that oxygenation increases would come from improved blood flow associated with vasodilation. However, no test has determined whether this is a relevant assumption or other mechanisms might be acting. Additionally, since hyperthermia and radiotherapy are not usually co-administered, the crucial question arises as to how temperature and perfusion in tumours will change during and after hyperthermia. Overall, it would seem necessary to find a research framework that clarifies the current knowledge, delimits the scope of the different effects and guides future research. Here, we propose a simple mathematical model to account for temperature and perfusion dynamics in brain tumours subjected to regional hyperthermia. Our results indicate that tumours in well-perfused organs like the brain might only reach therapeutic temperatures if their vasculature is highly disrupted. Furthermore, the characteristic times of return to normal temperature levels are markedly shorter than those required to deliver adjuvant radiotherapy. According to this, a mechanistic coupling of perfusion and temperature would not explain any major oxygenation boost in brain tumours immediately after hyperthermia.

A mesoscopic simulator to uncover heterogeneity and evolutionary dynamics in tumors.

Increasingly complex in silico modeling approaches offer a way to simultaneously access cancerous processes at different spatio-temporal scales. High-level models, such as those based on partial differential equations, are computationally affordable and allow large tumor sizes and long temporal windows to be studied, but miss the discrete nature of many key underlying cellular processes. Individual-based approaches provide a much more detailed description of tumors, but have difficulties when trying to handle full-sized real cancers. Thus, there exists a trade-off between the integration of macroscopic and microscopic information, now widely available, and the ability to attain clinical tumor sizes. In this paper we put forward a stochastic mesoscopic simulation framework that incorporates key cellular processes during tumor progression while keeping computational costs to a minimum. Our framework captures a physical scale that allows both the incorporation of microscopic information, tracking the spatio-temporal emergence of tumor heterogeneity and the underlying evolutionary dynamics, and the reconstruction of clinically sized tumors from high-resolution medical imaging data, with the additional benefit of low computational cost. We illustrate the functionality of our modeling approach for the case of glioblastoma, a paradigm of tumor heterogeneity that remains extremely challenging in the clinical setting.

Evolutionary dynamics at the tumor edge reveal metabolic imaging biomarkers.

Human cancers are biologically and morphologically heterogeneous. A variety of clonal populations emerge within these neoplasms and their interaction leads to complex spatiotemporal dynamics during tumor growth. We studied the reshaping of metabolic activity in human cancers by means of continuous and discrete mathematical models and matched the results to positron emission tomography (PET) imaging data. Our models revealed that the location of increasingly active proliferative cellular spots progressively drifted from the center of the tumor to the periphery, as a result of the competition between gradually more aggressive phenotypes. This computational finding led to the development of a metric, normalized distance from 18F-fluorodeoxyglucose (18F-FDG) hotspot to centroid (NHOC), based on the separation from the location of the activity (proliferation) hotspot to the tumor centroid. The NHOC metric can be computed for patients using 18F-FDG PET-computed tomography (PET/CT) images where the voxel of maximum uptake (standardized uptake value [SUV]max) is taken as the activity hotspot. Two datasets of 18F-FDG PET/CT images were collected, one from 61 breast cancer patients and another from 161 non-small-cell lung cancer patients. In both cohorts, survival analyses were carried out for the NHOC and for other classical PET/CT-based biomarkers, finding that the former had a high prognostic value, outperforming the latter. In summary, our work offers additional insights into the evolutionary mechanisms behind tumor progression, provides a different PET/CT-based biomarker, and reveals that an activity hotspot closer to the tumor periphery is associated to a worst patient outcome.

Universal scaling laws rule explosive growth in human cancers.

Most physical and other natural systems are complex entities composed of a large number of interacting individual elements. It is a surprising fact that they often obey the so-called scaling laws relating an observable quantity with a measure of the size of the system. Here we describe the discovery of universal superlinear metabolic scaling laws in human cancers. This dependence underpins increasing tumour aggressiveness, due to evolutionary dynamics, which leads to an explosive growth as the disease progresses. We validated this dynamic using longitudinal volumetric data of different histologies from large cohorts of cancer patients. To explain our observations we put forward increasingly-complex biologically-inspired mathematical models that captured the key processes governing tumor growth. Our models predicted that the emergence of superlinear allometric scaling laws is an inherently three-dimensional phenomenon. Moreover, the scaling laws thereby identified allowed us to define a set of metabolic metrics with prognostic value, thus providing added clinical utility to the base findings.

Mitochondria transfer from tumor-activated stromal cells (TASC) to primary Glioblastoma cells.

The tumor microenvironment (TME) controls many aspects of cancer development but little is known about its effect in Glioblastoma (GBM), the main brain tumor in adults. Tumor-activated stromal cell (TASC) population, a component of TME in GBM, was induced in vitro by incubation of MSCs with culture media conditioned by primary cultures of GBM under 3D/organoid conditions. We observed mitochondrial transfer by Tunneling Nanotubes (TNT), extracellular vesicles (EV) and cannibalism from the TASC to GBM and analyzed its effect on both proliferation and survival. We created primary cultures of GBM or TASC in which we have eliminated mitochondrial DNA [Rho 0 (ρ0) cells]. We found that TASC, as described in other cancers, increased GBM proliferation and resistance to standard treatments (radiotherapy and chemotherapy). We analyzed the incorporation of purified mitochondria by ρ0 and ρ+ cells and a derived mathematical model taught us that ρ+ cells incorporate more rapidly pure mitochondria than ρ0 cells.

SURFWET: A biokinetic model for surface flow constructed wetlands.

Constructed wetlands are an alternative biotechnology for wastewater treatment that have several advantages over conventional systems. In this work, a biokinetic model for surface flow constructed wetlands is presented (SURFWET). SURFWET belongs to a class of models that are not only interesting from a theoretical viewpoint, as they allow to improve the understanding of the underlying processes; but also from a practical viewpoint, because they can be useful for optimal designs of constructed wetlands, complementing current empirical methods. The proposed model is centered on the intervening physical and biochemical processes involved in pollutant removal in wastewater (organic matter, nitrogen, phosphorus, suspended solids), capturing the interplay of the main agents on contaminant removal (bacteria, macrophytes and phytoplankton). Furthermore, the hydraulic model considers water volume as a variable depending on the outlet hydraulic capacity, and dissolved oxygen has also been introduced as a key driver of reaction kinetics of wetlands. Beyond putting forward a theoretical framework, SURFWET has been applied to simulate a specific case to demonstrate its robustness, in a 12-year-interval simulation. The results show the typical seasonality of this biotechnology, highlighting the importance of dissolved oxygen, which is a key limiting factor on a large number of biochemical processes.

Identification of a transient state during the acquisition of temozolomide resistance in glioblastoma.

Drug resistance limits the therapeutic efficacy in cancers and leads to tumor recurrence through ill-defined mechanisms. Glioblastoma (GBM) are the deadliest brain tumors in adults. GBM, at diagnosis or after treatment, are resistant to temozolomide (TMZ), the standard chemotherapy. To better understand the acquisition of this resistance, we performed a longitudinal study, using a combination of mathematical models, RNA sequencing, single cell analyses, functional and drug assays in a human glioma cell line (U251). After an initial response characterized by cell death induction, cells entered a transient state defined by slow growth, a distinct morphology and a shift of metabolism. Specific genes expression associated to this population revealed chromatin remodeling. Indeed, the histone deacetylase inhibitor trichostatin (TSA), specifically eliminated this population and thus prevented the appearance of fast growing TMZ-resistant cells. In conclusion, we have identified in glioblastoma a population with tolerant-like features, which could constitute a therapeutic target.

Interplay of Darwinian Selection, Lamarckian Induction and Microvesicle Transfer on Drug Resistance in Cancer.

Development of drug resistance in cancer has major implications for patients' outcome. It is related to processes involved in the decrease of drug efficacy, which are strongly influenced by intratumor heterogeneity and changes in the microenvironment. Heterogeneity arises, to a large extent, from genetic mutations analogously to Darwinian evolution, when selection of tumor cells results from the adaptation to the microenvironment, but could also emerge as a consequence of epigenetic mutations driven by stochastic events. An important exogenous source of alterations is the action of chemotherapeutic agents, which not only affects the signalling pathways but also the interactions among cells. In this work we provide experimental evidence from in vitro assays and put forward a mathematical kinetic transport model to describe the dynamics displayed by a system of non-small-cell lung carcinoma cells (NCI-H460) which, depending on the effect of a chemotherapeutic agent (doxorubicin), exhibits a complex interplay between Darwinian selection, Lamarckian induction and the nonlocal transfer of extracellular microvesicles. The role played by all of these processes to multidrug resistance in cancer is elucidated and quantified.

Changes in the retreatment radiation tolerance of the spinal cord with time after the initial treatment.

PURPOSE: To estimate, from experimental data, the retreatment radiation 'tolerances' of the spinal cord at different times after initial treatment. MATERIALS AND METHODS: A model was developed to show the relationship between the biological effective doses (BEDs) for two separate courses of treatment with the BED of each course being expressed as a percentage of the designated 'retreatment tolerance' BED value, denoted [Formula: see text] and [Formula: see text]. The primate data of Ang et al. ( 2001 ) were used to determine the fitted parameters. However, based on rodent data, recovery was assumed to commence 70 days after the first course was complete, and with a non-linear relationship to the magnitude of the initial BED (BEDinit). RESULTS: The model, taking into account the above processes, provides estimates of the retreatment tolerance dose after different times. Extrapolations from the experimental data can provide conservative estimates for the clinic, with a lower acceptable myelopathy incidence. Care must be taken to convert the predicted [Formula: see text] value into a formal BED value and then a practical dose fractionation schedule. CONCLUSIONS: Used with caution, the proposed model allows estimations of retreatment doses with elapsed times ranging from 70 days up to three years after the initial course of treatment.

Hypoxia in Gliomas: Opening Therapeutical Opportunities Using a Mathematical-Based Approach.

This chapter explores the use of mathematical models as promising and powerful tools to understand the complexity of tumors and their, frequently, hypoxic environment. We focus on gliomas, which are primary brain tumors derived from glial cells, mainly astrocytes and/or oligodendrocytes. A variety of mathematical models, based on ordinary and/or partial differential equations, have been developed both at the micro and macroscopic levels. The aim here is to describe in a quantitative way key physiopathological mechanisms relevant in these types of malignancies and to suggest optimal therapeutical strategies. More specifically, we consider novel therapies targeting thromboembolic phenomena to decrease cell invasion in high grade glioma or to delay the malignant transformation in low grade gliomas. This study has been the basis of a multidisciplinary collaboration involving, among others, neuro-oncologists, radiation oncologists, pathologists, cancer biologists, surgeons and mathematicians.

Combined therapies of antithrombotics and antioxidants delay in silico brain tumour progression.

Glioblastoma multiforme (GBM), the most frequent type of primary brain tumour, is a rapidly evolving and spatially heterogeneous high-grade astrocytoma that presents areas of necrosis, hypercellularity and microvascular hyperplasia. The aberrant vasculature leads to hypoxic areas and results in an increase in oxidative stress, selecting for more invasive tumour cell phenotypes. In our study, we assay in silico different therapeutic approaches which combine antithrombotics (ATs), antioxidants and standard radiotherapy (RT). To do so, we have developed a biocomputational model of GBM that incorporates the spatio-temporal interplay among two glioma cell phenotypes corresponding to oxygenated and hypoxic cells, a necrotic core and the local vasculature whose response evolves with tumour progression. Our numerical simulations predict that suitable combinations of ATs and antioxidants may diminish, in a synergistic way, oxidative stress and the subsequent hypoxic response. This novel therapeutical strategy, with potentially low or no toxicity, might reduce tumour invasion and further sensitize GBM to conventional RT or other cytotoxic agents, hopefully increasing median patient overall survival time.