Pharmacogenomics-Driven Prediction of Antidepressant Treatment Outcomes: A Machine-Learning Approach With Multi-trial Replication

Kynurenic acid is a potential overlapped biomarker between diagnosis and treatment response for depression from metabolome analysis

Since optimal treatment at an early stage leads to remission of symptoms and recovery of function, putative biomarkers leading to early diagnosis and prediction of therapeutic responses are desired. The current study aimed to use a metabolomic approach to extract metabolites involved in both the diagnosis of major depressive disorder (MDD) and the prediction of therapeutic response for escitalopram. We compared plasma metabolites of MDD patients (n = 88) with those in healthy participants (n = 88) and found significant differences in the concentrations of 20 metabolites. We measured the Hamilton Rating Scale for Depression (HRSD) on 62 patients who completed approximately six-week treatment with escitalopram before and after treatment and found that kynurenic acid and kynurenine were significantly and negatively associated with HRSD reduction. Only one metabolite, kynurenic acid, was detected among 73 metabolites for overlapped biomarkers. Kynurenic acid was lower in MDD, and lower levels showed a better therapeutic response to escitalopram. Kynurenic acid is a metabolite in the kynurenine pathway that has been widely accepted as being a major mechanism in MDD. Overlapping biomarkers that facilitate diagnosis and prediction of the treatment response may help to improve disease classification and reduce the exposure of patients to less effective treatments in MDD.

The State of Our Understanding of the Pathophysiology and Optimal Treatment of Depression: Glass Half Full or Half Empty?

Major depressive disorder is a remarkably common and often severe psychiatric disorder associated with high levels of morbidity and mortality. Patients with major depression are prone to several comorbid psychiatric conditions, including posttraumatic stress disorder, anxiety disorders, obsessive-compulsive disorder, and substance use disorders, and medical conditions, including cardiovascular disease, diabetes, stroke, cancer, which, coupled with the risk of suicide, result in a shortened life expectancy. The goal of this review is to provide an overview of our current understanding of major depression, from pathophysiology to treatment. In spite of decades of research, relatively little is known about its pathogenesis, other than that risk is largely defined by a combination of ill-defined genetic and environmental factors. Although we know that female sex, a history of childhood maltreatment, and family history as well as more recent stressors are risk factors, precisely how these environmental influences interact with genetic vulnerability remains obscure. In recent years, considerable advances have been made in beginning to understand the genetic substrates that underlie disease vulnerability, and the interaction of genes, early-life adversity, and the epigenome in influencing gene expression is now being intensively studied. The role of inflammation and other immune system dysfunction in the pathogenesis of major depression is also being intensively investigated. Brain imaging studies have provided a firmer understanding of the circuitry involved in major depression, providing potential new therapeutic targets. Despite a broad armamentarium for major depression, including antidepressants, evidence-based psychotherapies, nonpharmacological somatic treatments, and a host of augmentation strategies, a sizable percentage of patients remain nonresponsive or poorly responsive to available treatments. Investigational agents with novel mechanisms of action are under active study. Personalized medicine in psychiatry provides the hope of escape from the current standard trial-and-error approach to treatment, moving to a more refined method that augurs a new era for patients and clinicians alike.

Predicting second-generation antidepressant effectiveness in treating sadness using demographic and clinical information: A machine learning approach

INTRODUCTION

Current guidelines for choosing antidepressant medications involve a trial-and-error process. Most patients try multiple antidepressants before finding an effective antidepressant. This study uses demographic and clinical information to create models predicting effectiveness of different antidepressants in treating sadness in a nationally representative sample of US adults.

METHODS

A secondary analysis of the Collaborative Psychiatric Epidemiology Survey (CPES) was performed. Participants with or without a mental health diagnosis who reported sadness as a symptom, and were taking fluoxetine (n=156), sertraline (n=224), citalopram (n=91), paroxetine (n=156), venlafaxine (n=69), bupropion (n=92), or trazadone (n=26) within the past year were included. Two sets of principal component analyses (PCAs) and logistic regressions were performed: one determined associations between symptom clusters and antidepressant effectiveness for sadness, and the other created models to predict effectiveness. Both PCAs controlled for psychiatric and medical diagnoses, substance use, psychiatric medications, alternative treatments, and demographics.

RESULTS

Anxiety was associated with ineffectiveness of fluoxetine in treating sadness. Low mood scores were associated with ineffectiveness of paroxetine and venlafaxine, and fatigue was associated with ineffectiveness of sertraline. The models for predicting drug effectiveness had a mean accuracy of 83% and internal validity of 72%.

LIMITATIONS

CPES data were collected from 2001-2003, so newer drugs were not included. Effectiveness was for sadness, so results are not directly comparable to studies using overall depressive symptom reductions as outcomes.

CONCLUSION

Since fewer than 50% of patients currently respond to their first antidepressant, this model could provide modest improvement to choosing starting antidepressants in treating sadness.

From Real-World Patient Data to Individualized Treatment Effects Using Machine Learning: Current and Future Methods to Address Underlying Challenges

Clinical decision making needs to be supported by evidence that treatments are beneficial to individual patients. Although randomized control trials (RCTs) are the gold standard for testing and introducing new drugs, due to the focus on specific questions with respect to establishing efficacy and safety vs. standard treatment, they do not provide a full characterization of the heterogeneity in the final intended treatment population. Conversely, real-world observational data, such as electronic health records (EHRs), contain large amounts of clinical information about heterogeneous patients and their response to treatments. In this paper, we introduce the main opportunities and challenges in using observational data for training machine learning methods to estimate individualized treatment effects and make treatment recommendations. We describe the modeling choices of the state-of-the-art machine learning methods for causal inference, developed for estimating treatment effects both in the cross-section and longitudinal settings. Additionally, we highlight future research directions that could lead to achieving the full potential of leveraging EHRs and machine learning for making individualized treatment recommendations. We also discuss how experimental data from RCTs and Pharmacometric and Quantitative Systems Pharmacology approaches can be used to not only improve machine learning methods, but also provide ways for validating them. These future research directions will require us to collaborate across the scientific disciplines to incorporate models based on RCTs and known disease processes, physiology, and pharmacology into these machine learning models based on EHRs to fully optimize the opportunity these data present.

Variant discovery using next-generation sequencing and its future role in pharmacogenetics

Next-generation sequencing (NGS) has enabled the discovery of a multitude of novel and mostly rare variants in pharmacogenes that may alter a patient’s therapeutic response to drugs. In addition to single nucleotide variants, structural variation affecting the number of copies of whole genes or parts of genes can be detected. While current guidelines concerning clinical implementation mostly act upon well-documented, common single nucleotide variants to guide dosing or drug selection, in silico and large-scale functional assessment of rare variant effects on protein function are at the forefront of pharmacogenetic research to facilitate their clinical integration. Here, we discuss the role of NGS in variant discovery, paving the way for more comprehensive genotype-guided pharmacotherapy that can translate to improved clinical care.

Precision Psychiatry Applications with Pharmacogenomics: Artificial Intelligence and Machine Learning Approaches

A growing body of evidence now suggests that precision psychiatry, an interdisciplinary field of psychiatry, precision medicine, and pharmacogenomics, serves as an indispensable foundation of medical practices by offering the accurate medication with the accurate dose at the accurate time to patients with psychiatric disorders. In light of the latest advancements in artificial intelligence and machine learning techniques, numerous biomarkers and genetic loci associated with psychiatric diseases and relevant treatments are being discovered in precision psychiatry research by employing neuroimaging and multi-omics. In this review, we focus on the latest developments for precision psychiatry research using artificial intelligence and machine learning approaches, such as deep learning and neural network algorithms, together with multi-omics and neuroimaging data. Firstly, we review precision psychiatry and pharmacogenomics studies that leverage various artificial intelligence and machine learning techniques to assess treatment prediction, prognosis prediction, diagnosis prediction, and the detection of potential biomarkers. In addition, we describe potential biomarkers and genetic loci that have been discovered to be associated with psychiatric diseases and relevant treatments. Moreover, we outline the limitations in regard to the previous precision psychiatry and pharmacogenomics studies. Finally, we present a discussion of directions and challenges for future research.

Pharmacogenomics at the center of precision medicine: challenges and perspective in an era of Big Data

Pharmacogenomics (PGx) is one of the core elements of personalized medicine. PGx information reduces the likelihood of adverse drug reactions and optimizes therapeutic efficacy. St Catherine Specialty Hospital in Zagreb/Zabok, Croatia has implemented a personalized patient approach using the RightMed^® Comprehensive PGx panel of 25 pharmacogenes plus Facor V Leiden, Factor II and MTHFR genes, which is interpreted by a special counseling team to offer the best quality of care. With the advent of significant technological advances comes another challenge: how can we harness the data to inform clinically actionable measures and how can we use it to develop better predictive risk models? We propose to apply the principles artificial intelligence to develop a medication optimization platform to prevent, manage and treat different diseases.

Integrating machine learning and multiscale modeling-perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences

Fueled by breakthrough technology developments, the biological, biomedical, and behavioral sciences are now collecting more data than ever before. There is a critical need for time- and cost-efficient strategies to analyze and interpret these data to advance human health. The recent rise of machine learning as a powerful technique to integrate multimodality, multifidelity data, and reveal correlations between intertwined phenomena presents a special opportunity in this regard. However, machine learning alone ignores the fundamental laws of physics and can result in ill-posed problems or non-physical solutions. Multiscale modeling is a successful strategy to integrate multiscale, multiphysics data and uncover mechanisms that explain the emergence of function. However, multiscale modeling alone often fails to efficiently combine large datasets from different sources and different levels of resolution. Here we demonstrate that machine learning and multiscale modeling can naturally complement each other to create robust predictive models that integrate the underlying physics to manage ill-posed problems and explore massive design spaces. We review the current literature, highlight applications and opportunities, address open questions, and discuss potential challenges and limitations in four overarching topical areas: ordinary differential equations, partial differential equations, data-driven approaches, and theory-driven approaches. Towards these goals, we leverage expertise in applied mathematics, computer science, computational biology, biophysics, biomechanics, engineering mechanics, experimentation, and medicine. Our multidisciplinary perspective suggests that integrating machine learning and multiscale modeling can provide new insights into disease mechanisms, help identify new targets and treatment strategies, and inform decision making for the benefit of human health.

Artificial intelligence for precision medicine in neurodevelopmental disorders

The ambition of precision medicine is to design and optimize the pathway for diagnosis, therapeutic intervention, and prognosis by using large multidimensional biological datasets that capture individual variability in genes, function and environment. This offers clinicians the opportunity to more carefully tailor early interventions- whether treatment or preventative in nature-to each individual patient. Taking advantage of high performance computer capabilities, artificial intelligence (AI) algorithms can now achieve reasonable success in predicting risk in certain cancers and cardiovascular disease from available multidimensional clinical and biological data. In contrast, less progress has been made with the neurodevelopmental disorders, which include intellectual disability (ID), autism spectrum disorder (ASD), epilepsy and broader neurodevelopmental disorders. Much hope is pinned on the opportunity to quantify risk from patterns of genomic variation, including the functional characterization of genes and variants, but this ambition is confounded by phenotypic and etiologic heterogeneity, along with the rare and variable penetrant nature of the underlying risk variants identified so far. Structural and functional brain imaging and neuropsychological and neurophysiological markers may provide further dimensionality, but often require more development to achieve sensitivity for diagnosis. Herein, therefore, lies a precision medicine conundrum: can artificial intelligence offer a breakthrough in predicting risks and prognosis for neurodevelopmental disorders? In this review we will examine these complexities, and consider some of the strategies whereby artificial intelligence may overcome them.

Concepts Driving Pharmacogenomics Implementation Into Everyday Healthcare

Pharmacogenomics (PGx) is often promoted as the domain of precision medicine with the greatest potential to readily impact everyday healthcare. Rapid advances in PGx knowledge derived from extensive basic and clinical research along with decreasing costs of laboratory testing have led to an increased interest in PGx and expectations of imminent clinical translation with substantial clinical impact. However, the implementation of PGx into clinical workflows is neither simple nor straightforward, and comprehensive processes and multidisciplinary collaboration are required. Several national and international institutions have pioneered models for implementing clinical PGx, and these initial models have led to a better understanding of unresolved challenges. In this review, we have categorized and explored the most relevant of these challenges to highlight potential gaps and present possible solutions. We describe the ongoing need for basic and clinical research to drive further developments in evidence-based medicine. Integration into daily clinical workflows introduces new challenges requiring innovative solutions; specifically those related to the electronic health record and embedded clinical decision support. We describe advances in PGx testing and result reporting and describe the critical need for increased standardization in these areas across laboratories. We also explore the complexity of the PGx knowledge required for clinical practice and the need for educational strategies to ensure adequate understanding among members of current and future healthcare teams. Finally, we evaluate knowledge obtained from previous implementation efforts and discuss how to best apply these learnings to future projects. Despite these challenges, the future of precision medicine appears promising due to the rapidity of recent advances in the field and current multidisciplinary efforts to effectively translate PGx to everyday clinical practice.

Pharmacogenomics in chronic pain therapy: from disease to treatment and challenges for clinical practice

Pharmacogenomics (PGx) has emerged as an encouraging tool in chronic pain therapy. Genetic variations associated with drug effectiveness or adverse reactions (amitriptyline/nortriptyline/codeine/oxycodone/tramadol-CYP2D6, amitriptyline-CYP2C19, carbamazepine-HLA-A, carbamazepine/oxcarbazepine-HLA-B) can be used to guide chronic pain management. Despite this evidence, many obstacles still need to be overcome for the effective clinical implementation of PGx. To translate the pharmacogenetic testing into actionable clinical decisions, the Clinical Pharmacogenetics Implementation Consortium has been developing guidelines for several drug–gene pairs. This review will show the applicability of PGx in chronic pain from disease to treatment; report the drug–gene pairs with strongest evidences in the clinic; and the challenges for the clinical implementation of PGx.