Identification of Idiopathic Pulmonary Fibrosis and Prediction of Disease Severity via Machine Learning Analysis of Comprehensive Metabolic Panel and Complete Blood Count Data.

BACKGROUND: Diagnosis of idiopathic pulmonary fibrosis (IPF) typically relies on high-resolution computed tomography imaging (HRCT) or histopathology, while monitoring disease severity is done via frequent pulmonary function testing (PFT). More reliable and convenient methods of diagnosing fibrotic interstitial lung disease (ILD) type and monitoring severity would allow for early identification and enhance current therapeutic interventions. This study tested the hypothesis that a machine learning (ML) ensemble analysis of comprehensive metabolic panel (CMP) and complete blood count (CBC) data can accurately distinguish IPF from connective tissue disease ILD (CTD-ILD) and predict disease severity as seen with PFT. METHODS: Outpatient data with diagnosis of IPF or CTD-ILD (n = 103 visits by 53 patients) were analyzed via ML methodology to evaluate (1) IPF vs CTD-ILD diagnosis; (2) %predicted Diffusing Capacity of Lung for Carbon Monoxide (DLCO) moderate or mild vs severe; (3) %predicted Forced Vital Capacity (FVC) moderate or mild vs severe; and (4) %predicted FVC mild vs moderate or severe. RESULTS: ML methodology identified IPF from CTD-ILD with AUCTEST = 0.893, while PFT was classified as DLCO moderate or mild vs severe with AUCTEST = 0.749, FVC moderate or mild vs severe with AUCTEST = 0.741, and FVC mild vs moderate or severe with AUCTEST = 0.739. Key features included albumin, alanine transaminase, %lymphocytes, hemoglobin, %eosinophils, white blood cell count, %monocytes, and %neutrophils. CONCLUSION: Analysis of CMP and CBC data via proposed ML methodology offers the potential to distinguish IPF from CTD-ILD and predict severity on associated PFT with accuracy that meets or exceeds current clinical practice.

Disease diagnosis and severity classification in pulmonary fibrosis using carbonyl volatile organic compounds in exhaled breath.

BACKGROUND: Pathophysiological conditions underlying pulmonary fibrosis remain poorly understood. Exhaled breath volatile organic compounds (VOCs) have shown promise for lung disease diagnosis and classification. In particular, carbonyls are a byproduct of oxidative stress, associated with fibrosis in the lungs. To explore the potential of exhaled carbonyl VOCs to reflect underlying pathophysiological conditions in pulmonary fibrosis, this proof-of-concept study tested the hypothesis that volatile and low abundance carbonyl compounds could be linked to diagnosis and associated disease severity. METHODS: Exhaled breath samples were collected from outpatients with a diagnosis of Idiopathic Pulmonary Fibrosis (IPF) or Connective Tissue related Interstitial Lung Disease (CTD-ILD) with stable lung function for 3 months before enrollment, as measured by pulmonary function testing (PFT) DLCO (%), FVC (%) and FEV1 (%). A novel microreactor was used to capture carbonyl compounds in the breath as direct output products. A machine learning workflow was implemented with the captured carbonyl compounds as input features for classification of diagnosis and disease severity based on PFT (DLCO and FVC normal/mild vs. moderate/severe; FEV1 normal/mild/moderate vs. moderately severe/severe). RESULTS: The proposed approach classified diagnosis with AUROC=0.877 ± 0.047 in the validation subsets. The AUROC was 0.820 ± 0.064, 0.898 ± 0.040, and 0.873 ± 0.051 for disease severity based on DLCO, FEV1, and FVC measurements, respectively. Eleven key carbonyl VOCs were identified with the potential to differentiate diagnosis and to classify severity. CONCLUSIONS: Exhaled breath carbonyl compounds can be linked to pulmonary function and fibrotic ILD diagnosis, moving towards improved pathophysiological understanding of pulmonary fibrosis.

Anti-tumor effect of pH-sensitive drug-loaded nanoparticles optimized via an integrated computational/experimental approach.

The acidic pH of tumor tissue has been used to trigger drug release from nanoparticles. However, dynamic interactions between tumor pH and vascularity present challenges to optimize therapy to particular microenvironment conditions. Despite recent development of pH-sensitive nanomaterials that can accurately quantify drug release from nanoparticles, tailoring release to maximize tumor response remains elusive. This study hypothesizes that a computational modeling-based platform that simulates the heterogeneously vascularized tumor microenvironment can enable evaluation of the complex intra-tumoral dynamics involving nanoparticle transport and pH-dependent drug release, and predict optimal nanoparticle parameters to maximize the response. To this end, SPNCD nanoparticles comprising superparamagnetic cores of iron oxide (Fe3O4) and a poly(lactide-co-glycolide acid) shell loaded with doxorubicin (DOX) were fabricated. Drug release was measured in vitro as a function of pH. A 2D model of vascularized tumor growth was calibrated to experimental data and used to evaluate SPNCD effect as a function of drug release rate and tissue vascular heterogeneity. Simulations show that pH-dependent drug release from SPNCD delays tumor regrowth more than DOX alone across all levels of vascular heterogeneity, and that SPNCD significantly inhibit tumor radius over time compared to systemic DOX. The minimum tumor radius forecast by the model was comparable to previous in vivo SPNCD inhibition data. Sensitivity analyses of the SPNCD pH-dependent drug release rate indicate that slower rates are more inhibitory than faster rates. We conclude that an integrated computational and experimental approach enables tailoring drug release by pH-responsive nanomaterials to maximize the tumor response.

A clinical marker-based modeling framework to preoperatively predict lymph node and vascular space involvement in endometrial cancer patients.

INTRODUCTION: Endometrial cancer (EC) has high mortality at advanced stages. Poor prognostic factors include grade 3 tumors, deep myometrial invasion, lymph node metastasis (LNM), and lymphovascular space invasion (LVSI). Preoperative knowledge of patients at higher risk of lymph node involvement, when such involvement is not suspected, would benefit surgery planning and patient prognosis. This study implements an ensemble machine learning approach that evaluates Cancer Antigen 125 (CA125) along with histologic type, preoperative grade, and age to predict LVSI, LNM and stage in EC patients. METHODS: A retrospective chart review spanning January 2000 to January 2015 at a regional hospital was performed. Women 18 years or older with a diagnosis of EC and preoperative or within one-week CA125 measurement were included (n = 842). An ensemble machine learning approach was implemented based on a stacked generalization technique to evaluate CA125 in combination with histologic type, preoperative grade, and age as predictors, and LVSI, LNM and disease stage as outcomes. RESULTS: The ensemble approach predicted LNM and LVSI in EC patients with AUROCTEST of 0.857 and 0.750, respectively, and predicted disease stage with AUROCTEST of 0.665. The approach achieved AUROCTEST for LVSI and LNM of 0.750 and 0.643 for grade 1 patients, and of 0.689 and 0.952 for grade 2 patients, respectively. CONCLUSION: An ensemble machine learning approach offers the potential to preoperatively predict LVSI, LNM and stage in EC patients with adequate accuracy based on CA125, histologic type, preoperative grade, and age.

Metabolomic differentiation of tumor core versus edge in glioma.

OBJECTIVE: Gliomas exhibit high intratumor and interpatient heterogeneity. Recently, it has been shown that the microenvironment and phenotype differ significantly between the glioma core (inner) and edge (infiltrating) regions. This proof-of-concept study differentiates metabolic signatures associated with these regions, with the potential for prognosis and targeted therapy that could improve surgical outcomes. METHODS: Paired glioma core and infiltrating edge samples were obtained from 27 patients after craniotomy. Liquid-liquid metabolite extraction was performed on the samples and metabolomic data were obtained via 2D liquid chromatography-mass spectrometry/mass spectrometry. To gauge the potential of metabolomics to identify clinically relevant predictors of survival from tumor core versus edge tissues, a boosted generalized linear machine learning model was used to predict metabolomic profiles associated with O6-methylguanine DNA methyltransferase (MGMT) promoter methylation. RESULTS: A panel of 66 (of 168) metabolites was found to significantly differ between glioma core and edge regions (p ≤ 0.05). Top metabolites with significantly different relative abundances included DL-alanine, creatine, cystathionine, nicotinamide, and D-pantothenic acid. Significant metabolic pathways identified by quantitative enrichment analysis included glycerophospholipid metabolism; butanoate metabolism; cysteine and methionine metabolism; glycine, serine, alanine, and threonine metabolism; purine metabolism; nicotinate and nicotinamide metabolism; and pantothenate and coenzyme A biosynthesis. The machine learning model using 4 key metabolites each within core and edge tissue specimens predicted MGMT promoter methylation status, with AUROCEdge = 0.960 and AUROCCore = 0.941. Top metabolites associated with MGMT status in the core samples included hydroxyhexanoycarnitine, spermine, succinic anhydride, and pantothenic acid, and in the edge samples metabolites included 5-cytidine monophosphate, pantothenic acid, itaconic acid, and uridine. CONCLUSIONS: Key metabolic differences are identified between core and edge tissue in glioma and, furthermore, demonstrate the potential for machine learning to provide insight into potential prognostic and therapeutic targets.

Evaluation of Lung Cancer Patient Response to First-Line Chemotherapy by Integration of Tumor Core Biopsy Metabolomics with Multiscale Modeling.

The standard of care for intermediate (Stage II) and advanced (Stages III and IV) non-small cell lung cancer (NSCLC) involves chemotherapy with taxane/platinum derivatives, with or without radiation. Ideally, patients would be screened a priori to allow non-responders to be initially treated with second-line therapies. This evaluation is non-trivial, however, since tumors behave as complex multiscale systems. To address this need, this study employs a multiscale modeling approach to evaluate first-line chemotherapy response of individual patient tumors based on metabolomic analysis of tumor core biopsies obtained during routine clinical evaluation. Model parameters were calculated for a patient cohort as a function of these metabolomic profiles, previously obtained from high-resolution 2DLC-MS/MS analysis. Evaluation metrics were defined to classify patients as Disease-Control (DC) [encompassing complete-response (CR), partial-response (PR), and stable-disease (SD)] and Progressive-Disease (PD) following first-line chemotherapy. Response was simulated for each patient and compared to actual response. The results show that patient classifications were significantly separated from each other, and also when grouped as DC vs. PD and as CR/PR vs. SD/PD, by fraction of initial tumor radius metric at 6 days post simulated bolus drug injection. This study shows that patient first-line chemotherapy response can in principle be evaluated from multiscale modeling integrated with tumor tissue metabolomic data, offering a first step towards individualized lung cancer treatment prognosis.

CA125 as a predictor of endometrial cancer lymphovascular space invasion and lymph node metastasis for risk stratification in the preoperative setting.

Endometrial cancer (EC) is the most common malignancy of the female reproductive system. Cancer antigen 125 (CA125) is a serum tumor marker widely reported in EC patients, particularly those with poor prognostic factors such as grade 3 tumors, deep myometrial invasion, lymph node metastasis (LNM), and extra-uterine disease. This retrospective study stratifies pre-operative CA125 levels to evaluate odds ratios (OR) and relative risk (RR) between CA125 levels and the likelihood of +LNM, lymphovascular space invasion (LVSI), grade, and stage. Patient charts for women 18 years or older with a diagnosis of EC and pre-operative or within one week CA125 measurement from January 2000 to January 2015 at a regional hospital were reviewed. OR and RR were determined by unconditional maximum likelihood estimation for CA125 levels as the predictor with staging, grade, +LVSI and +LNM as outcomes. The largest increase in risk for patients having stage I/II/III disease was 52% greater (1.52-fold risk) while largest increase in risk for patients having stage III/IV disease was 67% greater (1.67-fold risk), both at CA125 ≥ 222U/ml. Patients with CA125 ≥ 122U/ml had significantly increased risk of +LNM, with maximum increase in risk of 98% (1.98-fold risk) at 222U/ml. Patients with CA125 ≥ 175U/ml had significantly increased risk of +LVSI, with maximum increase in risk of 39% (1.39-fold risk) at 222U/ml. This study shows that elevated CA125 levels correspond to increased stage, +LVSI, and +LNM in patients with EC.

Lung cancer survival prediction and biomarker identification with an ensemble machine learning analysis of tumor core biopsy metabolomic data.

INTRODUCTION: While prediction of short versus long term survival from lung cancer is clinically relevant in the context of patient management and therapy selection, it has proven difficult to identify reliable biomarkers of survival. Metabolomic markers from tumor core biopsies have been shown to reflect cancer metabolic dysregulation and hold prognostic value. OBJECTIVES: Implement and validate a novel ensemble machine learning approach to evaluate survival based on metabolomic biomarkers from tumor core biopsies. METHODS: Data were obtained from tumor core biopsies evaluated with high-resolution 2DLC-MS/MS. Unlike biofluid samples, analysis of tumor tissue is expected to accurately reflect the cancer metabolism and its impact on patient survival. A comprehensive suite of machine learning algorithms were trained as base learners and then combined into a stacked-ensemble meta-learner for predicting "short" versus "long" survival on an external validation cohort. An ensemble method of feature selection was employed to find a reliable set of biomarkers with potential clinical utility. RESULTS: Overall survival (OS) is predicted in external validation cohort with AUROCTEST of 0.881 with support vector machine meta learner model, while progression-free survival (PFS) is predicted with AUROCTEST of 0.833 with boosted logistic regression meta learner model, outperforming a nomogram using covariate data (staging, age, sex, treatment vs. non-treatment) as predictors. Increased relative abundance of guanine, choline, and creatine corresponded with shorter OS, while increased leucine and tryptophan corresponded with shorter PFS. In patients that expired, N6,N6,N6-Trimethyl-L-lysine, L-pyrogluatmic acid, and benzoic acid were increased while cystine, methionine sulfoxide and histamine were decreased. In patients with progression, itaconic acid, pyruvate, and malonic acid were increased. CONCLUSION: This study demonstrates the feasibility of an ensemble machine learning approach to accurately predict patient survival from tumor core biopsy metabolomic data.

Prediction of lung cancer immunotherapy response via machine learning analysis of immune cell lineage and surface markers.

BACKGROUND: Although advances have been made in cancer immunotherapy, patient benefits remain elusive. For non-small cell lung cancer (NSCLC), monoclonal antibodies targeting programmed death-1 (PD-1) and programmed death ligand-1 (PD-L1) have shown survival benefit compared to chemotherapy. Personalization of treatment would be facilitated by a priori identification of patients likely to benefit. OBJECTIVE: This pilot study applied a suite of machine learning methods to analyze mass cytometry data of immune cell lineage and surface markers from blood samples of a small cohort (n= 13) treated with Pembrolizumab, Atezolizumab, Durvalumab, or Nivolumab as monotherapy. METHODS: Four different comparisons were evaluated between data collected at an initial visit (baseline), after 12-weeks of immunotherapy, and from healthy (control) samples: healthy vs patients at baseline, Responders vs Non-Responders at baseline, Healthy vs 12-week Responders, and Responders vs Non-Responders at 12-weeks. The algorithms Random Forest, Partial Least Squares Discriminant Analysis, Multi-Layer Perceptron, and Elastic Net were applied to find features differentiating between these groups and provide for the capability to predict outcomes. RESULTS: Particular combinations and proportions of immune cell lineage and surface markers were sufficient to accurately discriminate between the groups without overfitting the data. In particular, markers associated with the B-cell phenotype were identified as key features. CONCLUSIONS: This study illustrates a comprehensive machine learning analysis of circulating immune cell characteristics of NSCLC patients with the potential to predict response to immunotherapy. Upon further evaluation in a larger cohort, the proposed methodology could help guide personalized treatment selection in clinical practice.

Lung cancer metabolomic data from tumor core biopsies enables risk-score calculation for progression-free and overall survival.

INTRODUCTION: Metabolomics has emerged as a powerful method to provide insight into cancer progression, including separating patients into low- and high-risk groups for overall (OS) and progression-free survival (PFS). However, survival prediction based mainly on metabolites obtained from biofluids remains elusive. OBJECTIVES: This proof-of-concept study evaluates metabolites as biomarkers obtained directly from tumor core biopsies along with covariates age, sex, pathological stage at diagnosis (I/II vs. III/VI), histological subtype, and treatment vs. no treatment to risk stratify lung cancer patients in terms of OS and PFS. METHODS: Tumor core biopsy samples obtained during routine lung cancer patient care at the University of Louisville Hospital and Norton Hospital were evaluated with high-resolution 2DLC-MS/MS, and the data were analyzed by Kaplan-Meier survival analysis and Cox proportional hazards regression. A linear equation was developed to stratify patients into low and high risk groups based on log-transformed intensities of key metabolites. Sparse partial least squares discriminant analysis (SPLS-DA) was performed to predict OS and PFS events. RESULTS: Univariable Cox proportional hazards regression model coefficients divided by the standard errors were used as weight coefficients multiplied by log-transformed metabolite intensity, then summed to generate a risk score for each patient. Risk scores based on 10 metabolites for OS and 5 metabolites for PFS were significant predictors of survival. Risk scores were validated with SPLS-DA classification model (AUROC 0.868 for OS and AUROC 0.755 for PFS, when combined with covariates). CONCLUSION: Metabolomic analysis of lung tumor core biopsies has the potential to differentiate patients into low- and high-risk groups based on OS and PFS events and probability.

Modeling of Tumor Growth with Input from Patient-Specific Metabolomic Data.

Advances in omic technologies have provided insight into cancer progression and treatment response. However, the nonlinear characteristics of cancer growth present a challenge to bridge from the molecular- to the tissue-scale, as tumor behavior cannot be encapsulated by the sum of the individual molecular details gleaned experimentally. Mathematical modeling and computational simulation have been traditionally employed to facilitate analysis of nonlinear systems. In this study, for the first time tumor metabolomic data are linked via mathematical modeling to the tumor tissue-scale behavior, showing the capability to mechanistically simulate cancer progression personalized to omic information obtainable from patient tumor core biopsy analysis. Generally, a higher degree of metabolic dysregulation has been correlated with more aggressive tumor behavior. Accordingly, key parameters influenced by metabolomic data in this model include tumor proliferation, vascularization, aggressiveness, lactic acid production, monocyte infiltration and macrophage polarization, and drug effect. The model enables evaluating interactions of interest between these parameters which drive tumor growth based on the metabolomic data. The results show that the model can group patients consistently with the clinically observed outcomes of response/non-response to chemotherapy. This modeling approach provides a first step towards evaluation of tumor growth based on tumor-specific metabolomic data.

Multicellular Ovarian Cancer Model for Evaluation of Nanovector Delivery in Ascites and Metastatic Environments.

A novel multicellular model composed of epithelial ovarian cancer and fibroblast cells was developed as an in vitro platform to evaluate nanovector delivery and ultimately aid the development of targeted therapies. We hypothesized that the inclusion of peptide-based scaffold (PuraMatrix) in the spheroid matrix, to represent in vivo tumor microenvironment alterations along with metastatic site conditions, would enhance spheroid cell growth and migration and alter nanovector transport. The model was evaluated by comparing the growth and migration of ovarian cancer cells exposed to stromal cell activation and tissue hypoxia. Fibroblast activation was achieved via the TGF-ß1 mediated pathway and tissue hypoxia via 3D spheroids incubated in hypoxia. Surface-modified nanovector transport was assessed via fluorescence and confocal microscopy. Consistent with previous in vivo observations in ascites and at distal metastases, spheroids exposed to activated stromal microenvironment were denser, more contractile and with more migratory cells than nonactivated counterparts. The hypoxic conditions resulted in negative radial spheroid growth over 5 d compared to a radial increase in normoxia. Nanovector penetration attenuated in PuraMatrix regardless of surface modification due to a denser environment. This platform may serve to evaluate nanovector transport based on ovarian ascites and metastatic environments, and longer term, it provide a means to evaluate nanotherapeutic efficacy.

Evaluation of disease staging and chemotherapeutic response in non-small cell lung cancer from patient tumor-derived metabolomic data.

OBJECTIVES: Despite extensive effort, the search for clinically-relevant metabolite biomarkers for early detection, disease monitoring, and outcome prediction in lung cancer remains unfulfilled. Although biofluid evaluation has been explored, the complexity inherent in metabolite data and the dynamic discrepancy between metabolites in biofluids vs. tumor tissue have prevented conclusive results. This proof-of-concept study explored models predictive of staging and chemotherapy response based on metabolomic analysis of fresh, patient-derived non-small cell lung cancer (NSCLC) core biopsies. MATERIALS AND METHODS: Samples (n = 36) were evaluated with high-resolution 2DLC-MS/MS and 13C-glucose enrichment, and the data were comprehensively analyzed with machine learning techniques. Patients were categorized as Disease-Control (DC) [encompassing complete-response (CR), partial-response (PR), and stable-disease (SD)] and Progressive-Disease (PD) in terms of first-line chemotherapy. Four major types of learning methods (partial least squares discriminant analysis (PLS-DA), support vector machines (SVM), artificial neural networks, and random forests (RF)) were applied to differentiate between positive (DC and CR/PR) and poor (PD and SD/PD) responses, and between stage I/II/III and stage IV disease. Models were trained with forward feature selection based on variable importance and tested on validation subsets. RESULTS: The models predicted patient classifications in the validation subsets with AUC (95 % CI): DC vs. PD (SVM), 0.970(0.961-0.979); CR/PR vs. SD/PD (PLS-DA), 0.880(0.865-0.895); stage I/II/III vs. IV (SVM), 0.902(0.880-0.924). Highest performing model was SVM for DC vs. PD (balanced accuracy = 0.92; kappa = 0.74). CONCLUSION: This study illustrates a comprehensive evaluation of patient tumor-specific metabolic profiles, with the potential to identify disease stage and predict response to first-line chemotherapy.

Discrepancies in metabolomic biomarker identification from patient-derived lung cancer revealed by combined variation in data pre-treatment and imputation methods.

INTRODUCTION: The identification of metabolomic biomarkers predictive of cancer patient response to therapy and of disease stage has been pursued as a "holy grail" of modern oncology, relying on the metabolic dysfunction that characterizes cancer progression. In spite of the evaluation of many candidate biomarkers, however, determination of a consistent set with practical clinical utility has proven elusive. OBJECTIVE: In this study, we systematically examine the combined role of data pre-treatment and imputation methods on the performance of multivariate data analysis methods and their identification of potential biomarkers. METHODS: Uniquely, we are able to systematically evaluate both unsupervised and supervised methods with a metabolomic data set obtained from patient-derived lung cancer core biopsies with true missing values. Eight pre-treatment methods, ten imputation methods, and two data analysis methods were applied in combination. RESULTS: The combined choice of pre-treatment and imputation methods is critical in the definition of candidate biomarkers, with deficient or inappropriate selection of these methods leading to inconsistent results, and with important biomarkers either being overlooked or reported as a false positive. The log transformation appeared to normalize the original tumor data most effectively, but the performance of the imputation applied after the transformation was highly dependent on the characteristics of the data set. CONCLUSION: The combined choice of pre-treatment and imputation methods may need careful evaluation prior to metabolomic data analysis of human tumors, in order to enable consistent identification of potential biomarkers predictive of response to therapy and of disease stage.

Pharmacokinetic/Pharmacodynamics Modeling of Drug-Loaded PLGA Nanoparticles Targeting Heterogeneously Vascularized Tumor Tissue.

PURPOSE: Nanoparticle-mediated drug delivery and efficacy for cancer applications depends on systemic as well as local microenvironment characteristics. Here, a novel coupling of a nanoparticle (NP) kinetic model with a drug pharmacokinetic/pharmacodynamics model evaluates efficacy of cisplatin-loaded poly lactic-co-glycolic acid (PLGA) NPs in heterogeneously vascularized tumor tissue. METHODS: Tumor lesions are modeled with various levels of vascular heterogeneity, as would be encountered with different types of tumors. The magnitude of the extracellular to cytosolic NP transport is varied to assess tumor-dependent cellular uptake. NP aggregation is simulated to evaluate its effects on drug distribution and tumor response. RESULTS: Cisplatin-loaded PLGA NPs are most effective in decreasing tumor size in the case of high vascular-induced heterogeneity, a high NP cytosolic transfer coefficient, and no NP aggregation. Depending on the level of tissue heterogeneity, NP cytosolic transfer and drug half-life, NP aggregation yielding only extracellular drug release could be more effective than unaggregated NPs uptaken by cells and releasing drug both extra- and intra-cellularly. CONCLUSIONS: Model-based customization of PLGA NP and drug design parameters, including cellular uptake and aggregation, tailored to patient tumor tissue characteristics such as proportion of viable tissue and vascular heterogeneity, could help optimize the NP-mediated tumor drug response.

Computational/experimental evaluation of liver metastasis post hepatic injury: interactions with macrophages and transitional ECM.

The complex interactions between subclinical changes to hepatic extracellular matrix (ECM) in response to injury and tumor-associated macrophage microenvironmental cues facilitating metastatic cell seeding remain poorly understood. This study implements a combined computational modeling and experimental approach to evaluate tumor growth following hepatic injury, focusing on ECM remodeling and interactions with local macrophages. Experiments were performed to determine ECM density and macrophage-associated cytokine levels. Effects of ECM remodeling along with macrophage polarization on tumor growth were evaluated via computational modeling. For primary or metastatic cells in co-culture with macrophages, TNF-α levels were 5× higher with M1 vs. M2 macrophages. Metastatic cell co-culture exhibited 10× higher TNF-α induction than with primary tumor cells. Although TGFß1 induction was similar between both co-cultures, levels were slightly higher with primary cells in the presence of M1. Simulated metastatic tumors exhibited decreased growth compared to primary tumors, due to high local M1-induced cytotoxicity, even in a highly vascularized microenvironment. Experimental analysis combined with computational modeling may provide insight into interactions between ECM remodeling, macrophage polarization, and liver tumor growth.

Evaluation of Drug-Loaded Gold Nanoparticle Cytotoxicity as a Function of Tumor Vasculature-Induced Tissue Heterogeneity.

The inherent heterogeneity of tumor tissue presents a major challenge to nanoparticle-mediated drug delivery. This heterogeneity spans from the molecular (genomic, proteomic, metabolomic) to the cellular (cell types, adhesion, migration) and to the tissue (vasculature, extra-cellular matrix) scales. In particular, tumor vasculature forms abnormally, inducing proliferative, hypoxic, and necrotic tumor tissue regions. As the vasculature is the main conduit for nanotherapy transport into tumors, vasculature-induced tissue heterogeneity can cause local inadequate delivery and concentration, leading to subpar response. Further, hypoxic tissue, although viable, would be immune to the effects of cell-cycle specific drugs. In order to enable a more systematic evaluation of such effects, here we employ computational modeling to study the therapeutic response as a function of vasculature-induced tumor tissue heterogeneity. Using data with three-layered gold nanoparticles loaded with cisplatin, nanotherapy is simulated interacting with different levels of tissue heterogeneity, and the treatment response is measured in terms of tumor regression. The results quantify the influence that varying levels of tumor vascular density coupled with the drug strength have on nanoparticle uptake and washout, and the associated tissue response. The drug strength affects the proportion of proliferating, hypoxic, and necrotic tissue fractions, which in turn dynamically affect and are affected by the vascular density. Higher drug strengths may be able to achieve stronger tumor regression but only if the intra-tumoral vascular density is above a certain threshold that affords sufficient transport. This study establishes an initial step towards a more systematic methodology to assess the effect of vasculature-induced tumor tissue heterogeneity on the response to nanotherapy.

Modeling of nanoparticle transport through the female reproductive tract for the treatment of infectious diseases.

The secreted mucus layer in the vaginal epithelium presents a formidable barrier to the transport of active agents for the prevention and treatment of female reproductive tract (FRT) infections. Nanoparticle-mediated drug delivery has been proposed to help facilitate the transport and release of active agents through the cervicovaginal mucus (CVM) and underlying mucosa. However, both nanoparticles (NPs) and free active agents face a variety of challenges, often requiring the administration of high localized doses to circumvent leakage and poor penetration to targeted intravaginal tissue compartments. To address these challenges, "stealth" NP modifications have been investigated, due to their favorable mucus-penetrating properties, resulting in improved intravaginal active agent retention and transport. A number of other NP characteristics including size, surface modification type, ligand density, and co-modification, as well as the complexity of the FRT tissue are involved in obtaining adequate tissue penetration and, if needed, cell internalization. Studies that systematically investigate variations of these characteristics have yet to be conducted, with the goal to obtain a better understanding of what properties most impact prophylactic and therapeutic benefit. To complement the progress made with experimental evaluation of active agent transport in in vitro and in vivo, mathematical modeling has recently been applied to analyze the transport performance of agents and delivery vehicles in the FRT. Here, we build upon this work to simulate NP transport through mucus gel, epithelial, and stromal compartments, with the goal to provide a platform that can systematically evaluate transport based on NP and tissue characteristics. Model parameters such as PEG density and NP release (decay) rate from mucus gel into the epithelium, are set from previous in vitro and in vivo experimental work that assessed the transport of poly(lactic-co-glycolic acid (PLGA) NPs. The modeling results show that while unmodified and 2% PEG-modified NPs were retained in mucus for ∼1-4 h, dependent upon decay constant values, and traverse to the epithelium, no NP penetration was observed in the stroma. In contrast, NPs modified with 3% PEG, exhibited prolonged retention in each compartment, remaining for ∼4-6 h. Moreover, a significant concentration of NPs is observed in the stroma, indicating a transition in transport behavior. For NPs modified with 5, 8, or 25% PEG, steady retention profiles were noted, which gradually decline over 24 h. To supplement this modeling study and to develop a more representative experimental system that may be useful in future work, we report on the feasibility of constructing single and multicellular layered (MCL) culture systems to represent the epithelial and stromal tissue of the FRT. We anticipate that a combined mathematical/experimental approach may longer term enable prediction and customization of patient tissue-specific approaches to attain effective NP-mediated drug delivery and release for the treatment of infectious disease.