Gaussian and Mixed Graphical Models as (multi-)omics data analysis tools

Depressive symptoms among rural left-behind children and adolescents in China: a large-scale cross-sectional study

BACKGROUND

Left-behind children(LBC) in rural China are at increased risk for mental health problems, including depression. This study aimed to estimate the prevalence of depression and identify key associate factors among Chinese rural LBC.

METHODS

A cross-sectional study was conducted using data from 36,612 LBC aged 6 to 18 years old across 596 data collection sites in Nanchong, Sichuan Province, China. Participants completed questionnaires assessing individual factors, family parenting situation, living events, and health-related data. Depression was measured using the Center for Epidemiological Studies-Depression Scale (CES-D). T-tests, chi-square, and logistic regression were performed to identify factors associated with depression.

RESULTS

The overall prevalence of depression among LBC was 6.75%. Logistic regression analysis revealed that family parenting situations, such as being from blended families (OR = 1.45) or being cared for by other family members (OR = 1.64), and dissatisfaction with the parenting situation (OR = 1.57) were significantly associated with higher odds of depression. Living events, including being misunderstood (OR = 1.82) and having disputes (OR = 1.48), and health-related factors, such as chronic diseases and regular medication use (OR = 2.38), also increased the risk of depression.

CONCLUSIONS

This study highlights the high prevalence of depression among Chinese rural LBC and identifies key associate factors, including family parenting situation, negative living events and health-related factors. Targeted interventions and policies addressing these factors are needed to promote the mental health of this vulnerable population.

Spatial Cellular Networks from omics data with SpaCeNet

Advances in omics technologies have allowed spatially resolved molecular profiling of single cells, providing a window not only into the diversity and distribution of cell types within a tissue, but also into the effects of interactions between cells in shaping the transcriptional landscape. Cells send chemical and mechanical signals which are received by other cells, where they can subsequently initiate context-specific gene regulatory responses. These interactions and their responses shape the individual molecular phenotype of a cell in a given microenvironment. RNAs or proteins measured in individual cells, together with the cells' spatial distribution, provide invaluable information about these mechanisms and the regulation of genes beyond processes occurring independently in each individual cell. "SpaCeNet" is a method designed to elucidate both the intracellular molecular networks (how molecular variables affect each other within the cell) and the intercellular molecular networks (how cells affect molecular variables in their neighbors). This is achieved by estimating conditional independence (CI) relations between captured variables within individual cells and by disentangling these from CI relations between variables of different cells.

A broken network of susceptibility genes in the monocytes of Crohn's disease patients

Genome-wide association studies have identified over 200 genetic loci associated with inflammatory bowel disease; however, the mechanism of such a large amount of susceptibility genes remains uncertain. In this study, we integrated bioinformatics analysis and two independent single-cell transcriptome datasets to investigate the expression network of 232 susceptibility genes in Crohn's disease (CD) patients and healthy controls. The study revealed that most of the susceptibility genes are specifically and strictly expressed in the monocytes of the human intestinal tract. The susceptibility genes established a network within the monocytes of health control. The robustness of a gene network may prevent disease onset that is influenced by the genetic and environmental alteration in the expression of susceptibility genes. In contrast, we showed a sparse network in pediatric/adult CD patients, suggesting the broken network contributed to the CD etiology. The network status of susceptibility genes at the single-cell level of monocytes provided novel insight into the etiology.

Advances in methods for characterizing dietary patterns: A scoping review

There is a growing focus on better understanding the complexity of dietary patterns and how they relate to health and other factors. Approaches that have not traditionally been applied to characterize dietary patterns, such as machine learning algorithms and latent class analysis methods, may offer opportunities to measure and characterize dietary patterns in greater depth than previously considered. However, there has not been a formal examination of how this wide range of approaches has been applied to characterize dietary patterns. This scoping review synthesized literature from 2005-2022 applying methods not traditionally used to characterize dietary patterns, referred to as novel methods. MEDLINE, CINAHL, and Scopus were searched using keywords including machine learning, latent class analysis, and least absolute shrinkage and selection operator (LASSO). Of 5274 records identified, 24 met the inclusion criteria. Twelve of 24 articles were published since 2020. Studies were conducted across 17 countries. Nine studies used approaches that have applications in machine learning to identify dietary patterns. Fourteen studies assessed associations between dietary patterns that were characterized using novel methods and health outcomes, including cancer, cardiovascular disease, and asthma. There was wide variation in the methods applied to characterize dietary patterns and in how these methods were described. The extension of reporting guidelines and quality appraisal tools relevant to nutrition research to consider specific features of novel methods may facilitate complete and consistent reporting and enable evidence synthesis to inform policies and programs aimed at supporting healthy dietary patterns.

Exploring the Early Molecular Pathogenesis of Osteoarthritis Using Differential Network Analysis of Human Synovial Fluid

The molecular mechanisms that drive the onset and development of osteoarthritis (OA) remain largely unknown. In this exploratory study, we used a proteomic platform (SOMAscan assay) to measure the relative abundance of more than 6000 proteins in synovial fluid (SF) from knees of human donors with healthy or mildly degenerated tissues, and knees with late-stage OA from patients undergoing knee replacement surgery. Using a linear mixed effects model, we estimated the differential abundance of 6251 proteins between the three groups. We found 583 proteins upregulated in the late-stage OA, including MMP1, collagenase 3 and interleukin-6. Further, we selected 760 proteins (800 aptamers) based on absolute fold changes between the healthy and mild degeneration groups. To those, we applied Gaussian Graphical Models (GGMs) to analyze the conditional dependence of proteins and to identify key proteins and subnetworks involved in early OA pathogenesis. After regularization and stability selection, we identified 102 proteins involved in GGM networks. Notably, network complexity was lost in the protein graph for mild degeneration when compared to controls, suggesting a disruption in the regular protein interplay. Furthermore, among our main findings were several downregulated (in mild degeneration versus healthy) proteins with unique interactions in the healthy group, one of which, SLCO5A1, has not previously been associated with OA. Our results suggest that this protein is important for healthy joint function. Further, our data suggests that SF proteomics, combined with GGMs, can reveal novel insights into the molecular pathogenesis and identification of biomarker candidates for early-stage OA.

Plasmacytoid Dendritic Cells Are Not Major Producers of Type 1 IFN in Cutaneous Lupus: An In-Depth Immunoprofile of Subacute and Discoid Lupus

The immunologic drivers of cutaneous lupus erythematosus (CLE) and its clinical subtypes remain poorly understood. We sought to characterize the immune landscape of discoid lupus erythematosus and subacute CLE using multiplexed immunophenotyping. We found no significant differences in immune cell percentages between discoid lupus erythematosus and subacute CLE (P > .05) with the exception of an increase in TBK1 in discoid lupus erythematosus (P < .05). Unbiased clustering grouped subjects into 2 major clusters without respect to clinical subtype. Subjects with a history of smoking had increased percentages of neutrophils, disease activity, and endothelial granzyme B compared with nonsmokers. Despite previous assumptions, plasmacytoid dendritic cells (pDCs) did not stain for IFN-1. Skin-eluted and circulating pDCs from subjects with CLE expressed significantly less IFNα than healthy control pDCs upon toll-like receptor 7 stimulation ex vivo (P < .0001). These data suggest that discoid lupus erythematosus and subacute CLE have similar immune microenvironments in a multiplexed investigation. Our aggregated analysis of CLE revealed that smoking may modulate disease activity in CLE through neutrophils and endothelial granzyme B. Notably, our data suggest that pDCs are not the major producers of IFN-1 in CLE. Future in vitro studies to investigate the role of pDCs in CLE are needed.

Unveiling Fall Triggers in Older Adults: A Machine Learning Graphical Model Analysis

While existing research has identified diverse fall risk factors in adults aged 60 and older across various areas, comprehensively examining the interrelationships between all factors can enhance our knowledge of complex mechanisms and ultimately prevent falls. This study employs a novel approach-a mixed undirected graphical model (MUGM)-to unravel the interplay between sociodemographics, mental well-being, body composition, self-assessed and performance-based fall risk assessments, and physical activity patterns. Using a parameterized joint probability density, MUGMs specify the higher-order dependence structure and reveals the underlying graphical structure of heterogeneous variables. The MUGM consisting of mixed types of variables (continuous and categorical) has versatile applications that provide innovative and practical insights, as it is equipped to transcend the limitations of traditional correlation analysis and uncover sophisticated interactions within a high-dimensional data set. Our study included 120 elders from central Florida whose 37 fall risk factors were analyzed using an MUGM. Among the identified features, 34 exhibited pairwise relationships, while COVID-19-related factors and housing composition remained conditionally independent from all others. The results from our study serve as a foundational exploration, and future research investigating the longitudinal aspects of these features plays a pivotal role in enhancing our knowledge of the dynamics contributing to fall prevention in this population.

Recent advances in application of computer-aided drug design in anti-COVID-19 Virials Drug Discovery

Corona Virus Disease 2019 (COVID-19) is a global pandemic epidemic caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), which poses a serious threat to human health worldwide and results in significant economic losses. With the continuous emergence of new virus strains, small molecule drugs remain the most effective treatment for COVID-19. The traditional drug development process usually requires several years; however, the development of computer-aided drug design (CADD) offers the opportunity to develop innovative drugs quickly and efficiently. The literature review describes the general process of CADD, the viral proteins that play essential roles in the life cycle of SARS-CoV-2 and can serve as therapeutic targets, and examples of drug screening of viral target proteins by applying CADD methods. Finally, the potential of CADD in COVID-19 therapy, the deficiency, and the possible future development direction are discussed.

Network analysis of the proteome and peptidome sheds light on human milk as a biological system

Proteins and peptides found in human milk have bioactive potential to benefit the newborn and support healthy development. Research has been carried out on the health benefits of proteins and peptides, but many questions still need to be answered about the nature of these components, how they are formed, and how they end up in the milk. This study explored and elucidated the complexity of the human milk proteome and peptidome. Proteins and peptides were analyzed with non-targeted nanoLC-Orbitrap-MS/MS in a selection of 297 milk samples from the CHILD Cohort Study. Protein and peptide abundances were determined, and a network was inferred using Gaussian graphical modeling (GGM), allowing an investigation of direct associations. This study showed that signatures of (1) specific mechanisms of transport of different groups of proteins, (2) proteolytic degradation by proteases and aminopeptidases, and (3) coagulation and complement activation are present in human milk. These results show the value of an integrated approach in evaluating large-scale omics data sets and provide valuable information for studies that aim to associate protein or peptide profiles from biofluids such as milk with specific physiological characteristics.

Metabolome biomarkers linking dietary fibre intake with cardiometabolic effects: results from the Danish Diet, Cancer and Health-Next Generations MAX study

Biomarkers associated with dietary fibre intake, as complements to traditional dietary assessment tools, may improve the understanding of its role in human health. Our aim was to discover metabolite biomarkers related to dietary fibre intake and investigate their association with cardiometabolic risk factors. We used data and samples from the Danish Diet Cancer and Health Next Generation (DCH-NG) MAX-study, a one-year observational study with evaluations at baseline, six and 12 months (n = 624, 55% female, mean age: 43 years, 1353 observations). Direct associations between fibre intake and plasma concentrations of 2,6-dihydroxybenzoic acid (2,6-DHBA) and indolepropionic acid were observed at the three time-points. Both metabolites showed an intraclass-correlation coefficient (ICC) > 0.50 and were associated with the self-reported intake of wholegrain cereals, and of fruits and vegetables, respectively. Other metabolites associated with dietary fibre intake were linolenoyl carnitine, 2-aminophenol, 3,4-DHBA, and proline betaine. Based on the metabolites associated with dietary fibre intake we calculated predicted values of fibre intake using a multivariate, machine-learning algorithm. Metabolomics-based predicted fibre, but not self-reported fibre values, showed negative associations with cardiometabolic risk factors (i.e. high sensitivity C-reactive protein, systolic and diastolic blood pressure, all FDR-adjusted p-values <0.05). Furthermore, different correlations with gut microbiota composition were observed. In conclusion, 2,6-DHBA and indolepropionic acid in plasma may better link dietary fibre intake with its metabolic effects than self-reported values. These metabolites may represent a novel class of biomarkers reflecting both dietary exposure and host and/or gut microbiota characteristics providing a read-out that is differentially related to cardiometabolic risk.

The development of depressive symptoms in older adults from a network perspective in the English Longitudinal Study of Ageing

An increased understanding of the interrelations between depressive symptoms among older populations could help improve interventions. However, studies often use sum scores to understand depression in older populations, neglecting important symptom dynamics that can be elucidated in evolving depressive symptom networks. We computed Cross-Lagged Panel Network Models (CLPN) of depression symptoms in 11,391 adults from the English Longitudinal Study of Ageing. Adults aged 50 and above (mean age 65) were followed over 16 years throughout this nine-wave representative population study. Using the eight-item Center for Epidemiological Studies Depression Scale, we computed eight CLPNs covering each consecutive wave. Across waves, networks were consistent with respect to the strength of lagged associations (edge weights) and the degree of interrelationships among symptoms (centrality indices). Everything was an effort and could not get going displayed the strongest reciprocal cross-lagged associations across waves. These two symptoms and loneliness were core symptoms as reflected in strong incoming and outgoing connections. Feeling depressed was strongly predicted by other symptoms only (incoming but not strong outgoing connections were observed) and thus was not related to new symptom onset. Restless sleep had outgoing connections only and thus was a precursor to other depression symptoms. Being happy and enjoying life were the least central symptoms. This research underscores the relevance of somatic symptoms in evolving depression networks among older populations. Findings suggest the central symptoms from the present study (everything was an effort, could not get going, loneliness) may be potential key intervention targets to mitigate depression in older adults.

Family characteristics in adolescents with overweight or obesity: a network analysis

Background

Rates of overweight and obesity continue to grow in adolescents. Overweight and obesity in adolescence are associated with numerous immediate and long-term adverse health conditions. Throughout adolescence, parents and the family have an important and central influence on adolescents' health and lifestyle. The home environment may be a major factor in shaping children's weight. However, our current understanding of the interplay between family-related variables in adolescents with overweight or obesity is limited and fragmented. This study aimed to assess the relationship between family-related variables in adolescents who are overweight or obese using network analysis and inform future health promotion for family-based intervention.

Methods

Participants (n = 488) were recruited from middle schools in Nanjing from October 2022 to March 2023. Participants, together with their parents, completed a questionnaire at school about the family food environment, family size, family APGAR index, family physical activity facilities, parental mental health, rearing behavior, parental weight status, drinking history, marital satisfaction, and sociodemographic characteristics.

Results

The network split into three distinct communities of items. Network analysis showed that parental mental health and paternal rearing styles-rejection were the most central nodes in the network. In contrast, maternal weight status was the most peripheral and least connected nodes.

Conclusion

Family-related variables constituted a connected network in adolescents with overweight or obesity. The pattern of network node connections supports that interventions could prioritize targeting changing parental mental health and paternal rearing styles in adolescents with overweight or obesity.

A network analysis investigating the associations between posttraumatic stress symptoms, markers of inflammation and metabolic syndrome

Chronic systemic inflammation has been implicated in trauma exposure, independent of a psychiatric diagnosis, and in posttraumatic stress disorder (PTSD) and its highly comorbid conditions, such as metabolic syndrome (MetS). The present study used network analysis to examine the interacting associations between pro-inflammatory cytokines, posttraumatic stress (PTS) symptoms and symptom clusters, and individual components of MetS, in a cohort of 312 participants (n = 139 PTSD cases, n = 173 trauma-exposed controls). Pro-inflammatory cytokines were measured in serum samples using immunoturbidimetric and multiplex assays. Three network models were assessed, and the decision on which model to use was guided by network stability estimates and denseness. Weak negative associations were observed between interleukin one beta (IL-1β) and detachment (D6) and irritability (E1); tumour necrosis factor alpha (TNFα) and hypervigilance (E3); and C-reactive protein (CRP) and emotional cue reactivity (B4), which could be due to high cortisol levels present in a female-majority cohort. Network models also identified positive associations between CRP and waist circumference, blood pressure, and high-density lipoprotein cholesterol (HDL-C). The strongest association was observed between CRP and waist circumference, providing evidence that central obesity is an important inflammatory component of MetS. Some networks displayed high instability, which could be due to the small pool of participants with viable cytokine data. Overall, this study provides evidence for associations between inflammation, PTS symptoms and components of MetS. Future longitudinal studies measuring pro-inflammatory cytokines in the immediate aftermath of trauma are required to gain better insight into the role of inflammation in trauma-exposure and PTSD.

Anomaly detection in mixed high-dimensional molecular data

MOTIVATION

Mixed molecular data combines continuous and categorical features of the same samples, such as OMICS profiles with genotypes, diagnoses, or patient sex. Like all high-dimensional molecular data, it is prone to incorrect values that can stem from various sources for example the technical limitations of the measurement devices, errors in the sample preparation, or contamination. Most anomaly detection algorithms identify complete samples as outliers or anomalies. However, in most cases, not all measurements of those samples are erroneous but only a few one-dimensional features within the samples are incorrect. These one-dimensional data errors are continuous measurements that are either located outside or inside the normal ranges of their features but in both cases show atypical values given all other continuous and categorical features in the sample. Additionally, categorical anomalies can occur for example when the genotype or diagnosis was submitted wrongly.

RESULTS

We introduce ADMIRE (Anomaly Detection using MIxed gRaphical modEls), a novel approach for the detection and correction of anomalies in mixed high-dimensional data. Hereby, we focus on the detection of single (one-dimensional) data errors in the categorical and continuous features of a sample. For that the joint distribution of continuous and categorical features is learned by mixed graphical models, anomalies are detected by the difference between measured and model-based estimations and are corrected using imputation. We evaluated ADMIRE in simulation and by screening for anomalies in one of our own metabolic datasets. In simulation experiments, ADMIRE outperformed the state-of-the-art methods of Local Outlier Factor, stray, and Isolation Forest.

AVAILABILITY AND IMPLEMENTATION

All data and code is available at https://github.com/spang-lab/adadmire. ADMIRE is implemented in a Python package called adadmire which can be found at https://pypi.org/project/adadmire.

Network Differential in Gaussian Graphical Models from Multimodal Neuroimaging Data. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023;2023:1-6. [PMID: 38083176 DOI: 10.1109/embc40787.2023.10340856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Multimodal brain network analysis has the potential to provide insights into the mechanisms of brain disorders. Most previous studies have analyzed either unimodal brain graphs or focused on local/global graphic metrics with little consideration of details of disrupted paths in the patient group. As we show, the combination of multimodal brain graphs and disrupted path-based analysis can be highly illuminating to recognize path-based disease biomarkers. In this study, we first propose a way to estimate multimodal brain graphs using static functional network connectivity (sFNC) and gray matter features using a Gaussian graphical model of schizophrenia versus controls. Next, applying the graph theory approach we identify disconnectors or connectors in the patient group graph that create additional paths or cause absent paths compared to the control graph. Results showed several edges in the schizophrenia group graph that trigger missing or additional paths. Identified edges associated with these disrupted paths were identified both within and between dFNC and gray matter which highlights the importance of considering multimodal studies and moving beyond pairwise edges to provide a more comprehensive understanding of brain disorders.Clinical Relevance- We identified a path-based biomarker in schizophrenia, by imitating the structure of paths in a multimodal (sMIR+fMRI) brain graph of the control group. Identified cross-modal edges associated with disrupted paths were related to the middle temporal gyrus and cerebellar regions.

The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks

Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.io) is a collection of open-source methods to infer GRNs, conduct differential network analyses, estimate community structure, and explore the transitions between biological states. The netZoo builds on our ongoing development of network methods, harmonizing the implementations in various computing languages and between methods to allow better integration of these tools into analytical pipelines. We demonstrate the utility using multi-omic data from the Cancer Cell Line Encyclopedia. We will continue to expand the netZoo to incorporate additional methods.

Machine learning approaches to predict drug efficacy and toxicity in oncology

In recent years, there has been a surge of interest in using machine learning algorithms (MLAs) in oncology, particularly for biomedical applications such as drug discovery, drug repurposing, diagnostics, clinical trial design, and pharmaceutical production. MLAs have the potential to provide valuable insights and predictions in these areas by representing both the disease state and the therapeutic agents used to treat it. To fully utilize the capabilities of MLAs in oncology, it is important to understand the fundamental concepts underlying these algorithms and how they can be applied to assess the efficacy and toxicity of therapeutics. In this perspective, we lay out approaches to represent both the disease state and the therapeutic agents used by MLAs to derive novel insights and make relevant predictions.

DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks

The increasing quantity of multi-omic data, such as methylomic and transcriptomic profiles collected on the same specimen or even on the same cell, provides a unique opportunity to explore the complex interactions that define cell phenotype and govern cellular responses to perturbations. We propose a network approach based on Gaussian Graphical Models (GGMs) that facilitates the joint analysis of paired omics data. This method, called DRAGON (Determining Regulatory Associations using Graphical models on multi-Omic Networks), calibrates its parameters to achieve an optimal trade-off between the network's complexity and estimation accuracy, while explicitly accounting for the characteristics of each of the assessed omics 'layers.' In simulation studies, we show that DRAGON adapts to edge density and feature size differences between omics layers, improving model inference and edge recovery compared to state-of-the-art methods. We further demonstrate in an analysis of joint transcriptome - methylome data from TCGA breast cancer specimens that DRAGON can identify key molecular mechanisms such as gene regulation via promoter methylation. In particular, we identify Transcription Factor AP-2 Beta (TFAP2B) as a potential multi-omic biomarker for basal-type breast cancer. DRAGON is available as open-source code in Python through the Network Zoo package (netZooPy v0.8; netzoo.github.io).

Hub Genes in Non-Small Cell Lung Cancer Regulatory Networks

There are currently no accurate biomarkers for optimal treatment selection in early-stage non-small cell lung cancer (NSCLC). Novel therapeutic targets are needed to improve NSCLC survival outcomes. This study systematically evaluated the association between genome-scale regulatory network centralities and NSCLC tumorigenesis, proliferation, and survival in early-stage NSCLC patients. Boolean implication networks were used to construct multimodal networks using patient DNA copy number variation, mRNA, and protein expression profiles. T statistics of differential gene/protein expression in tumors versus non-cancerous adjacent tissues, dependency scores in in vitro CRISPR-Cas9/RNA interference (RNAi) screening of human NSCLC cell lines, and hazard ratios in univariate Cox modeling of the Cancer Genome Atlas (TCGA) NSCLC patients were correlated with graph theory centrality metrics. Hub genes in multi-omics networks involving gene/protein expression were associated with oncogenic, proliferative potentials and poor patient survival outcomes (p < 0.05, Pearson's correlation). Immunotherapy targets PD1, PDL1, CTLA4, and CD27 were ranked as top hub genes within the 10th percentile in most constructed multi-omics networks. BUB3, DNM1L, EIF2S1, KPNB1, NMT1, PGAM1, and STRAP were discovered as important hub genes in NSCLC proliferation with oncogenic potential. These results support the importance of hub genes in NSCLC tumorigenesis, proliferation, and prognosis, with implications in prioritizing therapeutic targets to improve patient survival outcomes.

Gaussian graphical models with applications to omics analyses

Gaussian graphical models (GGMs) provide a framework for modeling conditional dependencies in multivariate data. In this tutorial, we provide an overview of GGM theory and a demonstration of various GGM tools in R. The mathematical foundations of GGMs are introduced with the goal of enabling the researcher to draw practical conclusions by interpreting model results. Background literature is presented, emphasizing methods recently developed for high-dimensional applications such as genomics, proteomics, or metabolomics. The application of these methods is illustrated using a publicly available dataset of gene expression profiles from 578 participants with ovarian cancer in The Cancer Genome Atlas. Stand-alone code for the demonstration is available as an RMarkdown file at https://github.com/katehoffshutta/ggmTutorial.

Network-based methods for psychometric data of eating disorders: A systematic review

BACKGROUND

Network science represents a powerful and increasingly promising method for studying complex real-world problems. In the last decade, it has been applied to psychometric data in the attempt to explain psychopathologies as complex systems of causally interconnected symptoms. One category of mental disorders, relevant for their severity, incidence and multifaceted structure, is that of eating disorders (EDs), serious disturbances that negatively affect a person's eating behavior.

AIMS

We aimed to review the corpus of psychometric network analysis methods by scrutinizing a large sample of network-based studies that exploit psychometric data related to EDs. A particular focus is given to the description of the methodologies for network estimation, network description and network stability analysis providing also a review of the statistical software packages currently used to carry out each phase of the network estimation and analysis workflow. Moreover, we try to highlight aspects with potential clinical impact such as core symptoms, influences of external factors, comorbidities, and related changes in network structure and connectivity across both time and subpopulations.

METHODS

A systematic search was conducted (February 2022) on three different literature databases to identify 57 relevant research articles. The exclusion criteria comprehended studies not based on psychometric data, studies not using network analysis, studies with different aims or not focused on ED, and review articles.

RESULTS

Almost all the selected 57 papers employed the same analytical procedures implemented in a collection of R packages specifically designed for psychometric network analysis and are mostly based on cross-sectional data retrieved from structured psychometric questionnaires, with just few exemptions of panel data. Most of them used the same techniques for all phases of their analysis. In particular, a pervasive use of the Gaussian Graphical Model with LASSO regularization was registered for in network estimation step. Among the clinically relevant results, we can include the fact that all papers found strong symptom interconnections between specific and nonspecific ED symptoms, suggesting that both types should therefore be addressed by clinical treatment.

CONCLUSIONS

We here presented the largest and most comprehensive review to date about psychometric network analysis methods. Although these methods still need solid validation in the clinical setting, they have already been able to show many strengths and important results, as well as great potentials and perspectives, which have been analyzed here to provide suggestions on their use and their possible improvement.

Combining Molecular, Imaging, and Clinical Data Analysis for Predicting Cancer Prognosis

Simple Summary

The rise of Big Data, the widespread use of Machine Learning, and the cheapening of omics techniques have allowed for the creation of more sophisticated and accurate models in biomedical research. This article presents the state-of-the-art predictive models of cancer prognosis that use multimodal data, considering clinical, molecular (omics and non-omics), and image data. The subject of study, the data modalities used, the data processing and modelling methods applied, the validation strategies involved, the integration strategies encompassed, and the evolution of prognostic predictive models are discussed. Finally, we discuss challenges and opportunities in this field of cancer research, with great potential impact on the clinical management of patients and, by extension, on the implementation of personalised and precision medicine.

Abstract

Cancer is one of the most detrimental diseases globally. Accordingly, the prognosis prediction of cancer patients has become a field of interest. In this review, we have gathered 43 state-of-the-art scientific papers published in the last 6 years that built cancer prognosis predictive models using multimodal data. We have defined the multimodality of data as four main types: clinical, anatomopathological, molecular, and medical imaging; and we have expanded on the information that each modality provides. The 43 studies were divided into three categories based on the modelling approach taken, and their characteristics were further discussed together with current issues and future trends. Research in this area has evolved from survival analysis through statistical modelling using mainly clinical and anatomopathological data to the prediction of cancer prognosis through a multi-faceted data-driven approach by the integration of complex, multimodal, and high-dimensional data containing multi-omics and medical imaging information and by applying Machine Learning and, more recently, Deep Learning techniques. This review concludes that cancer prognosis predictive multimodal models are capable of better stratifying patients, which can improve clinical management and contribute to the implementation of personalised medicine as well as provide new and valuable knowledge on cancer biology and its progression.

Educational Attainment Is Associated With Kidney and Cardiovascular Outcomes in CKD

Introduction

Prospective data on impact of educational attainment on prognosis in patients with chronic kidney disease (CKD) are scarce. We investigated the association between educational attainment and all-cause mortality, major adverse cardiovascular (CV) events (MACEs), kidney failure requiring dialysis, and CKD etiology.

Methods

Participants (N = 5095, aged 18–74 years) of the ongoing multicenter German Chronic Kidney Disease (GCKD) cohort, enrolled on the basis of an estimated glomerular filtration rate (eGFR) of 30 to 60 ml/min (stages G3, A1–A3) or overt proteinuria (stages G1–G2, A3), were divided into 3 categories according to their educational attainment and were followed for 6.5 years.

Results

Participants with low educational attainment (vs. high) had a higher risk for mortality (hazard ratio [HR] 1.48, 95% CI: 1.16–1.90), MACE (HR 1.37, 95% CI: 1.02–1.83), and kidney failure (HR 1.54, 95% CI: 1.15–2.05). Mediators between low educational attainment and mortality were smoking, CV disease (CVD) at baseline, low income, higher body mass index, and higher serum levels of CRP, high-density lipoprotein cholesterol, uric acid, NGAL, BAP, NT-proBNP, OPN, H-FABP, and urea. Low educational attainment was positively associated with diabetic nephropathy (odds ratio [OR] 1.65, 95% CI: 1.36–2.0) and CKD subsequent to acute kidney injury (OR 1.56, 95% CI: 1.03–2.35), but negatively associated with IgA nephropathy (OR 0.68, 95% CI: 0.52–0.90).

Conclusion

Low educational attainment is associated with adverse outcomes and CKD etiology. Lifestyle habits and biomarkers mediate associations between low educational attainment and mortality. Recognition of the role of educational attainment and the associated health-relevant risk factors is important to optimize the care of patients with CKD and improve prognosis.

Analysis of cancer omics data: a selective review of statistical techniques

Cancer is an omics disease. The development in high-throughput profiling has fundamentally changed cancer research and clinical practice. Compared with clinical, demographic and environmental data, the analysis of omics data-which has higher dimensionality, weaker signals and more complex distributional properties-is much more challenging. Developments in the literature are often 'scattered', with individual studies focused on one or a few closely related methods. The goal of this review is to assist cancer researchers with limited statistical expertise in establishing the 'overall framework' of cancer omics data analysis. To facilitate understanding, we mainly focus on intuition, concepts and key steps, and refer readers to the original publications for mathematical details. This review broadly covers unsupervised and supervised analysis, as well as individual-gene-based, gene-set-based and gene-network-based analysis. We also briefly discuss 'special topics' including interaction analysis, multi-datasets analysis and multi-omics analysis.

Recent Integrations of Latent Variable Network Modeling With Psychometric Models

The combination of network modeling and psychometric models has opened up exciting directions of research. However, there has been confusion surrounding differences among network models, graphic models, latent variable models and their applications in psychology. In this paper, I attempt to remedy this gap by briefly introducing latent variable network models and their recent integrations with psychometric models to psychometricians and applied psychologists. Following this introduction, I summarize developments under network psychometrics and show how graphical models under this framework can be distinguished from other network models. Every model is introduced using unified notations, and all methods are accompanied by available R packages inducive to further independent learning.

Validity and Prognostic Value of a Polygenic Risk Score for Parkinson's Disease

Idiopathic Parkinson’s disease (PD) is a complex multifactorial disorder caused by the interplay of both genetic and non-genetic risk factors. Polygenic risk scores (PRSs) are one way to aggregate the effects of a large number of genetic variants upon the risk for a disease like PD in a single quantity. However, reassessment of the performance of a given PRS in independent data sets is a precondition for establishing the PRS as a valid tool to this end. We studied a previously proposed PRS for PD in a separate genetic data set, comprising 1914 PD cases and 4464 controls, and were able to replicate its ability to differentiate between cases and controls. We also assessed theoretically the prognostic value of the PD-PRS, i.e., its ability to predict the development of PD in later life for healthy individuals. As it turned out, the PD-PRS alone can be expected to perform poorly in this regard. Therefore, we conclude that the PD-PRS could serve as an important research tool, but that meaningful PRS-based prognosis of PD at an individual level is not feasible.

NMF-Based Approach for Missing Values Imputation of Mass Spectrometry Metabolomics Data

In mass spectrometry (MS)-based metabolomics, missing values (NAs) may be due to different causes, including sample heterogeneity, ion suppression, spectral overlap, inappropriate data processing, and instrumental errors. Although a number of methodologies have been applied to handle NAs, NA imputation remains a challenging problem. Here, we propose a non-negative matrix factorization (NMF)-based method for NA imputation in MS-based metabolomics data, which makes use of both global and local information of the data. The proposed method was compared with three commonly used methods: k-nearest neighbors (kNN), random forest (RF), and outlier-robust (ORI) missing values imputation. These methods were evaluated from the perspectives of accuracy of imputation, retrieval of data structures, and rank of imputation superiority. The experimental results showed that the NMF-based method is well-adapted to various cases of data missingness and the presence of outliers in MS-based metabolic profiles. It outperformed kNN and ORI and showed results comparable with the RF method. Furthermore, the NMF method is more robust and less susceptible to outliers as compared with the RF method. The proposed NMF-based scheme may serve as an alternative NA imputation method which may facilitate biological interpretations of metabolomics data.

Variability of multi-omics profiles in a population-based child cohort

BACKGROUND

Multiple omics technologies are increasingly applied to detect early, subtle molecular responses to environmental stressors for future disease risk prevention. However, there is an urgent need for further evaluation of stability and variability of omics profiles in healthy individuals, especially during childhood.

METHODS

We aimed to estimate intra-, inter-individual and cohort variability of multi-omics profiles (blood DNA methylation, gene expression, miRNA, proteins and serum and urine metabolites) measured 6 months apart in 156 healthy children from five European countries. We further performed a multi-omics network analysis to establish clusters of co-varying omics features and assessed the contribution of key variables (including biological traits and sample collection parameters) to omics variability.

RESULTS

All omics displayed a large range of intra- and inter-individual variability depending on each omics feature, although all presented a highest median intra-individual variability. DNA methylation was the most stable profile (median 37.6% inter-individual variability) while gene expression was the least stable (6.6%). Among the least stable features, we identified 1% cross-omics co-variation between CpGs and metabolites (e.g. glucose and CpGs related to obesity and type 2 diabetes). Explanatory variables, including age and body mass index (BMI), explained up to 9% of serum metabolite variability.

CONCLUSIONS

Methylation and targeted serum metabolomics are the most reliable omics to implement in single time-point measurements in large cross-sectional studies. In the case of metabolomics, sample collection and individual traits (e.g. BMI) are important parameters to control for improved comparability, at the study design or analysis stage. This study will be valuable for the design and interpretation of epidemiological studies that aim to link omics signatures to disease, environmental exposures, or both.

Chronic Kidney Disease Cohort Studies: A Guide to Metabolome Analyses

Kidney diseases still pose one of the biggest challenges for global health, and their heterogeneity and often high comorbidity load seriously hinders the unraveling of their underlying pathomechanisms and the delivery of optimal patient care. Metabolomics, the quantitative study of small organic compounds, called metabolites, in a biological specimen, is gaining more and more importance in nephrology research. Conducting a metabolomics study in human kidney disease cohorts, however, requires thorough knowledge about the key workflow steps: study planning, sample collection, metabolomics data acquisition and preprocessing, statistical/bioinformatics data analysis, and results interpretation within a biomedical context. This review provides a guide for future metabolomics studies in human kidney disease cohorts. We will offer an overview of important a priori considerations for metabolomics cohort studies, available analytical as well as statistical/bioinformatics data analysis techniques, and subsequent interpretation of metabolic findings. We will further point out potential research questions for metabolomics studies in the context of kidney diseases and summarize the main results and data availability of important studies already conducted in this field.

Integration strategies of multi-omics data for machine learning analysis

Increased availability of high-throughput technologies has generated an ever-growing number of omics data that seek to portray many different but complementary biological layers including genomics, epigenomics, transcriptomics, proteomics, and metabolomics. New insight from these data have been obtained by machine learning algorithms that have produced diagnostic and classification biomarkers. Most biomarkers obtained to date however only include one omic measurement at a time and thus do not take full advantage of recent multi-omics experiments that now capture the entire complexity of biological systems.

Multi-omics data integration strategies are needed to combine the complementary knowledge brought by each omics layer. We have summarized the most recent data integration methods/ frameworks into five different integration strategies: early, mixed, intermediate, late and hierarchical. In this mini-review, we focus on challenges and existing multi-omics integration strategies by paying special attention to machine learning applications.

Individual Characteristics as Prognostic Factors of the Evolution of Hospitalized COVID-19 Romanian Patients: A Comparative Observational Study between the First and Second Waves Based on Gaussian Graphical Models and Structural Equation Modeling

This study examines the role played by individual characteristics and specific treatment methods in the evolution of hospitalized patients with coronavirus disease 2019 (COVID-19), through the lens of an observational study performed in a comparative approach between the first and second waves of coronavirus pandemic in Romania. The research endeavor is configured on a two-fold approach, including a detailed observation of the evolution of 274 hospitalized patients with COVID-19 (145 in the first wave and 129 in the second wave of infection) according to specific treatment methods applied and patients' individual features, as well as an econometric (quantitative) analysis through structural equation modeling and Gaussian graphical models designed to acknowledge the correlations and causal relationship between all considered coordinates. The main results highlight that the specific treatment methods applied had a positive influence on the evolution of COVID-19 patients, particularly in the second wave of coronavirus pandemic. In case of the first wave of COVID-19 infection, GGM results entail that there is a strong positive correlation between the evolution of the patients and the COVID-19 disease form, which is further positively correlated with the treatment scheme. The evolution of the patients is strongly and inversely correlated with the symptomatology and the ICU hospitalization. Moreover, the disease form is strongly and inversely correlated with oxygen saturation and the residence of patients (urban/rural). The symptomatology at first appearance also strongly depends on the age of the patients (positive correlation) and of the fact that the patient is a smoker or non-smoker and has other comorbidities. Age and gender are also important credentials that shape the disease degree and patient evolution in responding to treatment as well, our study attesting strong interconnections between these coordinates, the form of disease, symptomatology and overall evolution of the patients.

Multi-omics integration in biomedical research - A metabolomics-centric review

Recent advances in high-throughput technologies have enabled the profiling of multiple layers of a biological system, including DNA sequence data (genomics), RNA expression levels (transcriptomics), and metabolite levels (metabolomics). This has led to the generation of vast amounts of biological data that can be integrated in so-called multi-omics studies to examine the complex molecular underpinnings of health and disease. Integrative analysis of such datasets is not straightforward and is particularly complicated by the high dimensionality and heterogeneity of the data and by the lack of universal analysis protocols. Previous reviews have discussed various strategies to address the challenges of data integration, elaborating on specific aspects, such as network inference or feature selection techniques. Thereby, the main focus has been on the integration of two omics layers in their relation to a phenotype of interest. In this review we provide an overview over a typical multi-omics workflow, focusing on integration methods that have the potential to combine metabolomics data with two or more omics. We discuss multiple integration concepts including data-driven, knowledge-based, simultaneous and step-wise approaches. We highlight the application of these methods in recent multi-omics studies, including large-scale integration efforts aiming at a global depiction of the complex relationships within and between different biological layers without focusing on a particular phenotype.

Differences in Dietary Patterns Identified by the Gaussian Graphical Model in Korean Adults With and Without a Self-Reported Cancer Diagnosis

BACKGROUND

The synergistic effect of food groups on health outcomes is better captured by examining dietary patterns (DPs) than single food groups. Regarding this issue, a Gaussian graphical model (GGM) can identify pairwise correlations between food groups and adjust for the remaining items. However, the application of GGMs in the nutritional field has not been widely investigated, especially in Korean adults.

OBJECTIVE

The aim of this study was to identify the major DPs of Korean adults by using a GGM and to examine the associations between the DP scores and prevalence of self-reported cancer.

DESIGN

This cross-sectional study used baseline data from the 2007-2019 Cancer Screenee Cohort of the National Cancer Center, Korea.

PARTICIPANTS/SETTING

In total, 10,777 Korean adults who completed a questionnaire regarding their general medical history, including clinical test results, and a validated food frequency questionnaire were included.

MAIN OUTCOME MEASURES

The main outcome measure was the prevalence of self-reported cancer at baseline.

STATISTICAL ANALYSIS

DP networks were identified using a GGM. The GGM-identified networks were scored and categorized into tertiles, and their association with the prevalence of self-reported cancer was investigated using a multivariable logistic regression model.

RESULTS

The GGM identified the following 4 DP networks: principal, oil-sweet, meat, and fruit. After adjusting for covariates, the odds of moderate and high consumption of foods in the oil-sweet DP for participants who self-reported cancer were 25% and 34% lower than those for participants who did not report a cancer diagnosis (odds ratio [OR] = 0.75, 95% confidence interval [CI] = 0.62-0.90 and OR = 0.66, 95% CI = 0.53-0.81, respectively). Additionally, the odds of meat DP consumption in the self-reported cancer group was 29% lower than in participants who did not report a cancer diagnosis (OR = 0.71 and 95% CI = 0.57-0.88). In contrast, an increase in the odds of fruit DP consumption was observed for self-reported cancer participants (OR = 1.34 and 95% CI = 1.09-1.65). Similar results were observed among the female but not the male subjects.

CONCLUSIONS

GGM is a novel method that can distinguish the direct pairwise correlation of food groups and control for the indirect effect of other foods. Future large-scale longitudinal population-based studies are needed to build on these findings in general populations.