Biomarker qualification at the European Medicines Agency: a review of biomarker qualification procedures from 2008 to 2020

Neuroimaging Biomarkers in Addiction

As a neurobiological process, addiction involves pathological patterns of engagement with substances and a range of behaviors with a chronic and relapsing course. Neuroimaging technologies assess brain activity, structure, physiology, and metabolism at scales ranging from neurotransmitter receptors to large-scale brain networks, providing unique windows into the core neural processes implicated in substance use disorders. Identified aberrations in the neural substrates of reward and salience processing, response inhibition, interoception, and executive functions with neuroimaging can inform the development of pharmacological, neuromodulatory, and psychotherapeutic interventions to modulate the disordered neurobiology. Based on our systematic search, 409 protocols registered on ClinicalTrials.gov include the use of one or more neuroimaging paradigms as an outcome measure in addiction, with the majority (N=268) employing functional magnetic resonance imaging (fMRI), followed by positron emission tomography (PET) (N=71), electroencephalography (EEG) (N=50), structural magnetic resonance imaging (MRI) (N=35) and magnetic resonance spectroscopy (MRS) (N=35). Furthermore, in a PubMed systematic review, we identified 61 meta-analyses including 30 fMRI, 22 structural MRI, 8 EEG, 7 PET, and 3 MRS meta-analyses suggesting potential biomarkers in addictions. These studies can facilitate the development of a range of biomarkers that may prove useful in the arsenal of addiction treatments in the coming years. There is evidence that these markers of large-scale brain structure and activity may indicate vulnerability or separate disease subtypes, predict response to treatment, or provide objective measures of treatment response or recovery. Neuroimaging biomarkers can also suggest novel targets for interventions. Closed or open loop interventions can integrate these biomarkers with neuromodulation in real-time or offline to personalize stimulation parameters and deliver the precise intervention. This review provides an overview of neuroimaging modalities in addiction, potential neuroimaging biomarkers, and their physiologic and clinical relevance. Future directions and challenges in bringing these putative biomarkers from the bench to the bedside are also discussed.

Unlocking the full potential of digital endpoints for decision making: a novel modular evidence concept enabling re-use and advancing collaboration

INTRODUCTION

Over the last decade increasing examples indicate opportunities to measure patient functioning and its relevance for clinical and regulatory decision making via endpoints collected through digital health technologies. More recently, we have seen such measures support primary study endpoints and enable smaller trials. The field is advancing fast: validation requirements have been proposed in the literature and regulators are releasing new guidances to review these endpoints. Pharmaceutical companies are embracing collaborations to develop them and working with academia and patient organizations in their development. However, the road to validation and regulatory acceptance is lengthy. The full value of digital endpoints cannot be unlocked until better collaboration and modular evidence frameworks are developed enabling re-use of evidence and repurposing of digital endpoints.

AREAS COVERED

This paper proposes a solution by presenting a novel modular evidence framework -the Digital Evidence Ecosystem and Protocols (DEEP)- enabling repurposing of measurement solutions, re-use of evidence, application of standards and also facilitates collaboration with health technology assessment bodies.

EXPERT OPINION

The integration of digital endpoints in healthcare, essential for personalized and remote care, requires harmonization and transparency. The proposed novel stack model offers a modular approach, fostering collaboration and expediting the adoption in patient care.

The Evolution of Drug Regulatory Sciences in the Netherlands: More than a Country Report

In the Netherlands, drug regulatory science is a vibrant national and internationally oriented community. In this review, we present the factors that have contributed to this successful collaboration between relevant stakeholders and that led to a surge of activities around how regulatory science became embedded in the ecosystem of medicines research, clinical pharmacology, policymaking and regulation. We distinguished three pivotal episodes: (i) TI Pharma Escher-project, (ii) Dutch Medicines Evaluation Board as catalyst of the big jump, and (iii) Regulatory Science Network Netherlands and multistakeholder engagement. The research agenda has been influenced by the dynamic evolution of legal frameworks in Europe, such as the EU orphan medicines legislation of 2001 and the EU pharmacovigilance legislation of 2012. All these developments have inspired and have raised pertinent regulatory sciences questions. Furthermore, clinical pharmacology as a discipline has been very influential in shaping regulatory science, contributing to discussions on the level of clinical evidence that is necessary to justify marketing approval of a new medicine. With a growing interest of multiple parties such as academics, European Medicines Agency, national agencies, patient organizations and EFPIA, connecting regulatory science activities is key.

Innovative research methodologies in the EU regulatory framework: an analysis of EMA qualification procedures from a pediatric perspective

Introduction

The European Medicines Agency (EMA) offers scientific advice to support the qualification procedure of novel methodologies, such as preclinical and in vitro models, biomarkers, and pharmacometric methods, thereby endorsing their acceptability in medicine research and development (R&D). This aspect is particularly relevant to overcome the scarcity of data and the lack of validated endpoints and biomarkers in research fields characterized by small samples, such as pediatrics.

Aim

This study aimed to analyze the potential pediatric interest in methodologies qualified as "novel methodologies for medicine development" by the EMA.

Methods

The positive qualification opinions of novel methodologies for medicine development published on the EMA website between 2008 and 2023 were identified. Multi-level analyses were conducted to investigate data with a hierarchical structure and the effects of cluster-level variables and cluster-level variances and to evaluate their potential pediatric interest, defined as the possibility of using the novel methodology in pediatric R&D and the availability of pediatric data. The duration of the procedure, the type of methodology, the specific disease or disease area addressed, the type of applicant, and the availability of pediatric data at the time of the opinion release were also investigated.

Results

Most of the 27 qualifications for novel methodologies issued by the EMA (70%) were potentially of interest to pediatric patients, but only six of them reported pediatric data. The overall duration of qualification procedures with pediatric interest was longer than that of procedures without any pediatric interest (median time: 7 months vs. 3.5 months, respectively; p = 0.082). In parallel, qualification procedures that included pediatric data lasted for a longer period (median time: 8 months vs. 6 months, respectively; p = 0.150). Nephrology and neurology represented the main disease areas (21% and 16%, respectively), while endpoints, biomarkers, and registries represented the main types of innovative methodologies (32%, 26%, and 16%, respectively).

Discussion

Our results underscore the importance of implementing innovative methodologies in regulatory-compliant pediatric research activities. Pediatric-dedicated research infrastructures providing regulatory support and strategic advice during research activities could be crucial to the design of ad hoc pediatric methodologies or to extend and validate them for pediatrics.

Developing medicines for the pre-symptomatic stage of degenerative neurological conditions: Challenges and opportunities

Neurodegenerative disorders have a devastating disease course and an increasing prevalence due to prolonged life expectancy. In the last decades, it has become increasingly clear that these diseases often start much earlier, before the onset of symptoms, creating a potential window for pre-symptomatic treatment, a strategy that is desirable from both the biologic and the ethical point of view. However, studying treatments for a pre-symptomatic population presents objective difficulties. This article intends to give a perspective about opportunities and challenges of pre-symptomatic prevention of neurodegenerative diseases. Besides the requirement for biomarkers that would facilitate both the selection of study population and demonstrating a treatment effect, further considerations about balancing benefits, risks and uncertainties pertaining a pre-symptomatic population will be examined.

The role of early-phase trials and real-world evidence in drug development

Phase 3 randomized controlled trials (RCTs), while the gold standard for treatment efficacy and safety, are not always feasible, are expensive, can be prolonged and can be limited in generalizability. Other under-recognized sources of evidence can also help advance drug development. Basic science, proof-of-concept studies and early-phase RCTs can provide evidence regarding the potential for clinical benefit. Real-world evidence generated from registries or observational datasets can provide insights into the treatment of rare diseases that often pose a challenge for trial recruitment. Pragmatic trials embedded in healthcare systems can assess the treatment effects in clinical settings among patient populations sometimes excluded from trials. This Perspective discusses potential sources of evidence that may be used to complement explanatory phase 3 RCTs and to speed the development of new cardiovascular medications. Content is derived from the 19th Global Cardiovascular Clinical Trialists meeting (December 2022), involving clinical trialists, patients, clinicians, regulators, funders and industry representatives.

Glycoproteomics-based liquid biopsy: translational outlook for colorectal cancer clinical management in Southeast Asia

Colorectal cancer (CRC) signifies a significant healthcare challenge in Southeast Asia. Despite advancements in screening approaches and treatment modalities, significant medical gaps remain, ranging from prevention and early diagnosis to determining targeted therapy and establishing personalized approaches to managing CRC. There is a need to expand more validated biomarkers in clinical practice. An advanced technique incorporating high-throughput mass spectrometry as a liquid biopsy to unravel a repertoire of glycoproteins and glycans would potentially drive the development of clinical tools for CRC screening, diagnosis and monitoring, and it can be further adapted to the existing standard-of-care procedure. Therefore this review offers a perspective on glycoproteomics-driven liquid biopsy and its potential integration into the clinical care of CRC in the southeast Asia region.

Precision medicine in regulatory decision making: Biomarkers used for patient selection in European Public Assessment Reports from 2018 to 2020

Biomarkers can guide precision medicine in clinical trials and practice. They can increase clinical trials' efficiency through selection of study populations more likely to benefit from treatment, thus increasing statistical power and reducing sample size requirements or study duration. We performed a narrative synthesis to explore biomarker utilization for patient selection to guide precision medicine trials in marketing authorization dossiers of centrally approved medicines in Europe between 2018 and 2020 and analyzed in-depth those that eventually included biomarkers in the medicines' indications. From 119 eligible products, 26 included a biomarker in the indication, of which most were oncology products (n = 15). Included biomarkers were often known from literature or from previously approved products in the European Union or the United States. Additionally, 52 dossiers mentioned one or more biomarkers for patient selection in their clinical efficacy and safety information. Although these were not always included in the medicines' indication, they were often implicitly embedded in condition definitions adopted from clinical guidelines or practice. In 15 out of the 26 medicines with a biomarker-guided indication, only biomarker-positive populations were included in the main clinical studies supporting the marketing authorization. These studies were mostly randomized controlled trials or single-arm trials; only two products were studied for multiple indications in an innovative basket trial. Definitions of biomarkers could be subject of debate and needed adaptation after post hoc analyses requested by the assessment committee in four cases, stressing the importance of thorough justification of these definitions to include the right population for an optimal benefit-risk balance, enabling precise medicine.

Currently Used Methods to Evaluate the Efficacy of Therapeutic Drugs and Kidney Safety

Kidney diseases with kidney failure or damage, such as chronic kidney disease (CKD) and acute kidney injury (AKI), are common clinical problems worldwide and have rapidly increased in prevalence, affecting millions of people in recent decades. A series of novel diagnostic or predictive biomarkers have been discovered over the past decade, enhancing the investigation of renal dysfunction in preclinical studies and clinical risk assessment for humans. Since multiple causes lead to renal failure, animal studies have been extensively used to identify specific disease biomarkers for understanding the potential targets and nephropathy events in therapeutic insights into disease progression. Mice are the most commonly used model to investigate the mechanism of human nephropathy, and the current alternative methods, including in vitro and in silico models, can offer quicker, cheaper, and more effective methods to avoid or reduce the unethical procedures of animal usage. This review provides modern approaches, including animal and nonanimal assays, that can be applied to study chronic nonclinical safety. These specific situations could be utilized in nonclinical or clinical drug development to provide information on kidney disease.

Biomarkers to predict disease progression and therapeutic response in isolated methylmalonic acidemia

Methylmalonic Acidemia (MMA) is a heterogenous group of inborn errors of metabolism caused by a defect in the methylmalonyl-CoA mutase (MMUT) enzyme or the synthesis and transport of its cofactor, 5'-deoxy-adenosylcobalamin. It is characterized by life-threatening episodes of ketoacidosis, chronic kidney disease, and other multiorgan complications. Liver transplantation can improve patient stability and survival and thus provides clinical and biochemical benchmarks for the development of hepatocyte-targeted genomic therapies. Data are presented from a US natural history protocol that evaluated subjects with different types of MMA including mut-type (N = 91), cblB-type (15), and cblA-type MMA (17), as well as from an Italian cohort of mut-type (N = 19) and cblB-type MMA (N = 2) subjects, including data before and after organ transplantation in both cohorts. Canonical metabolic markers, such as serum methylmalonic acid and propionylcarnitine, are variable and affected by dietary intake and renal function. We have therefore explored the use of the 1-13 C-propionate oxidation breath test (POBT) to measure metabolic capacity and the changes in circulating proteins to assess mitochondrial dysfunction (fibroblast growth factor 21 [FGF21] and growth differentiation factor 15 [GDF15]) and kidney injury (lipocalin-2 [LCN2]). Biomarker concentrations are higher in patients with the severe mut0 -type and cblB-type MMA, correlate with a decreased POBT, and show a significant response postliver transplant. Additional circulating and imaging markers to assess disease burden are necessary to monitor disease progression. A combination of biomarkers reflecting disease severity and multisystem involvement will be needed to help stratify patients for clinical trials and assess the efficacy of new therapies for MMA.

A unified classification approach rating clinical utility of protein biomarkers across neurologic diseases

A major evolution from purely clinical diagnoses to biomarker supported clinical diagnosing has been occurring over the past years in neurology. High-throughput methods, such as next-generation sequencing and mass spectrometry-based proteomics along with improved neuroimaging methods, are accelerating this development. This calls for a consensus framework that is broadly applicable and provides a spot-on overview of the clinical validity of novel biomarkers. We propose a harmonized terminology and a uniform concept that stratifies biomarkers according to clinical context of use and evidence levels, adapted from existing frameworks in oncology with a strong focus on (epi)genetic markers and treatment context. We demonstrate that this framework allows for a consistent assessment of clinical validity across disease entities and that sufficient evidence for many clinical applications of protein biomarkers is lacking. Our framework may help to identify promising biomarker candidates and classify their applications by clinical context, aiming for routine clinical use of (protein) biomarkers in neurology.

Translating Academic Drug Discovery Into Clinical Development: A Survey of the Awareness of Regulatory Support and Requirements Among Stakeholders in Europe

Important discoveries by academic drug developers hold the promise of bringing innovative treatments that address unmet medical needs to the market. However, the drug development process has proved to be challenging and demanding for academic researchers, and regulatory challenges are an important barrier to implementing academic findings in clinical practice. European regulators offer varying degrees of support services to help drug developers meet regulatory standards and requirements. "Strengthening Training of Academia in Regulatory Sciences and Supporting Regulatory Scientific Advice" (STARS) is a European Commission-funded consortium aiming to strengthen the training of academics in regulatory science and requirements. Here, we report the results of four surveys that investigated the awareness and utilization of support tools offered by European regulators and identified the regulatory challenges and support needs of researchers. The surveys targeted four main European stakeholders in academic medicines research: academic research groups (706 respondents), academic research centers (99), funding organizations (49), and regulators (22). The results show that while European regulators provide various regulatory support tools, less than half of the responding academic researchers were aware of these tools and many experienced challenges in reaching a sufficient level of regulatory knowledge. There was a general lack of understanding of the regulatory environment that was aggravated by poor communication between stakeholders. The results of this study form a foundation for an improved European medicines regulatory network, in which regulatory challenges faced by academia are tackled.

Biomarkers in Medicines Development-From Discovery to Regulatory Qualification and Beyond

Biomarkers are important tools in medicines development and clinical practice. Besides their use in clinical trials, such as for enrichment of patients, monitoring safety or response to treatment, biomarkers are a cornerstone of precision medicine. The European Medicines Agency (EMA) emphasised the importance of the discovery, qualification, and use of biomarkers in their Regulatory Science Strategy to 2025, which included the recommendation to enhance early engagement with biomarker developers to facilitate regulatory qualification. This study explores the journey of biomarkers through the EU regulatory system and beyond, based on a review of interactions between developers and the EMA from 2008 to 2020, as well as the use of qualified biomarkers in clinical trials. Of applicants that used early interaction platforms such as the Innovation Task Force, less than half engaged in fee-related follow-up procedures. Results showed that, as compared to companies, consortia were more likely to opt for the Qualification of Novel Methodologies procedure and engage in follow-up procedures. Our results highlight the importance of early engagement with regulators for achieving biomarker qualification, including pre-submission discussions in the context of the qualification procedure. A review of clinical trials showed that all qualified biomarkers are used in practice, although not always according to the endorsed context of use. Overall, this study highlights important aspects of biomarker qualification, including opportunities to improve the seamless support for developers by EMA. The use of qualified biomarkers in clinical trials underlines the importance of regulatory qualification, which will further enable precision medicine for the benefit of patients.

Evaluation of Companion Diagnostics in Scientific Advice and Drug Marketing Authorization Applications by the European Medicines Agency

With the implementation of the new EU regulation on in vitro diagnostics (IVDR) in May 2022, notified bodies will be required to assess Companion Diagnostics (CDx). The EMA and national medicines agencies will be consulted on the performance and safety of CDx. In this paper, we report on our systematic review on how the EMA has dealt with CDx in dossiers for marketing authorization procedures, in 2017–2019, and in scientific advice procedures in 2016–2020, prior to the implementation of the new IVDR. Out of 167 medicines approved or refused by the EMA, CDx played a role for 20 medicines during assessment. Both European public assessment reports (EPARs) and the internal day 80 and day 120 assessment reports (ARs) of the EMA centralized marketing authorization procedures for these 20 medicines were analyzed in detail to determine how CDx were assessed. Likewise, in 46 of 159 cases in which scientific advice was provided, CDx were mentioned in the question-and-answer section of the scientific advice, and these were analyzed in an analogous manner. Our analysis indicates that clinical performance and analytical performance of the CDx were the most-discussed topics, being discussed 11 and seven times in the 20 EPARs and 59 and 29 times in the ARs, respectively. For scientific advice, clinical and analytical performance was discussed 65 and 22 times in the 46 retrieved mentions of scientific advice. Other aspects in relation to CDx were discussed as well, although at a lower frequency, in assessment reports and scientific advice. Overall, our analysis demonstrates that, despite the absence of an obligation from a legal point of view, EMA has gained experience on the assessment of CDx, most notably regarding its analytical and clinical performance. This experience may be useful in situations in which the EMA and national agencies of EU member states will formally be consulted by notified bodies regarding the performance and safety of CDx. In addition, the issues raised in the EPARs, ARs and scientific advice reports provide insight for applicants on aspects of CDx that need careful consideration.