Research at the interface of industry, academia and regulatory science

Enlightening kidney pathophysiology

Understanding the mechanics of acute kidney injury from toxins, ischemia and sepsis remains challenging. Molecular probes with high renal clearance have now been developed for real-time optical detection of early-stage biomarkers of drug-induced acute kidney injury, and for the understanding of the mechanisms of injury.

Proteomics for Biomarker Identification and Clinical Application in Kidney Disease

Treatment effectiveness for kidney disease is limited by lack of accuracy, sensitivity, specificity of diagnostic, prognostic, and therapeutic biomarkers. The gold standard test renal biopsy along with serum creatinine and proteinuria is often necessary to establish a diagnosis, particularly in glomerular disease. Proteomics has become a powerful tool for novel biomarker discovery in kidney disease. Novel proteomics offer earlier and more accurate diagnosis of renal pathology than possible with traditional biomarkers such as serum creatinine and urine protein. In addition, proteomic biomarkers could also be useful to choose the most suitable therapeutic targets. This review focuses on the current status of proteomic biomarkers from animal models (5/6 nephrectomy, unilateral ureteral obstruction, and diabetic nephropathy) and human studies (chronic kidney disease, glomerular diseases, transplantation, dialysis, acute and drug-induced kidney injury) to assess relevant findings and clinical usefulness. Current issues and problems related to the discovery, validation, and clinical application of proteomic biomarkers are discussed. We also describe several proteomic strategies highlighting technologic advancements, specimen selection, data processing and analysis. This review might provide help in future proteomic studies to improve the diagnosis and management of kidney disease.

Current practices and future outlook on the integration of biomarkers in the drug development process

Over the last decade, there has been broad incorporation of translational biomarkers into the early drug development process to predict safety concerns, measure target engagement and monitor disease progression. One goal of translational biomarkers is to create a cycle whereby preclinical readouts influence candidate selection and subsequent clinical data are fed back into research to facilitate better decision making. Successes have been limited and not as broad in scope as desired. Collaborations between industry and regulators have increased the number of qualified biomarkers; but the process is lengthy and expensive. A high level overview of translational biomarkers as well as a discussion of some of the successes and failures encountered in development is discussed here.

Regulatory landscapes for biomarkers and diagnostic tests: Qualification, approval, and role in clinical practice

While the term 'biomarker' is relatively new, the concept is millennia old. However, with the introduction of new technologies to discover potential biomarkers comes the need to assess their utility and veracity for any given use. This is particularly true for the use of biomarkers to support regulatory decisions in medical product development. Hence the US Food and Drug Administration has developed processes for the qualification of biomarkers and other medical product development tools, processes that are underscored by recent legislation (i.e. the 21st Century Cures Act). In addition to these qualification processes, diagnostic tests that measure a biomarker may follow a process for regulatory decision through the processes that evaluate companion diagnostics. This mini-review provides an overview of these processes and their role in pharmaceutical development and clinical use. Impact statement This work summarizes very recent developments in the US FDA's biomarker qualification program. Furthermore, it contrasts biomarker qualification with companion diagnostic evaluation. As such, it will be highly informative for researches considering taking a biomarker discovery farther along the road to validation.

Promoting Adoption of the 3Rs through Regulatory Qualification

One mechanism to advance the application of novel safety assessment methodologies in drug development, including in silico or in vitro approaches that reduce the use of animals in toxicology studies, is regulatory qualification. Regulatory qualification, a formal process defined at the the U. S. Food and Drug Administration and the European Medicines Agency, hinges on a central concept of stating an appropriate "context of use" for a novel drug development tool (DDT) that precisely defines how that DDT can be used to support decision making in a regulated drug development setting. When accumulating the data to support a particular "context-of-use," the concept of "fit-for-purpose" often guides assay validation, as well as the type and amount of data or evidence required to evaluate the tool. This paper will review pathways for regulatory acceptance of novel DDTs and discuss examples of safety projects considered for regulatory qualification. Key concepts to be considered when defining the evidence required to formally adopt and potentially replace animal-intensive traditional safety assessment methods using qualified DDTs are proposed. Presently, the use of qualified translational kidney safety biomarkers can refine and reduce the total numbers of animals used in drug development. We propose that the same conceptual regulatory framework will be appropriate to assess readiness of new technologies that may eventually replace whole animal models.

Innovation of Medical Products: The Evolution of Regulatory Science, Research, and Education

We present a commentary on the international aspects of the evolution of regulatory science as a multidisciplinary, multistakeholder academic discipline of education and applied research emphasizing the need for seamless interaction between stakeholders such as regulatory authorities, the pharmaceutical industry, universities, payers, and patient organizations. Regulatory science is the science of developing new tools, standards, and approaches to evaluate the efficacy, safety, quality, and performance of medical products in order to assess benefit/risk and facilitate a sound and transparent regulatory decision making throughout development and life cycle management.

Consortium sandbox: building and sharing resources

Some common challenges of biomedical product translation-scientific, regulatory, adoption, and reimbursement-can best be addressed by the broad sharing of resources or tools. But, such aids remain undeveloped because the undertaking requires expertise from multiple research sectors as well as validation across organizations. Biomedical resource development can benefit from directed consortia-a partnership framework that provides neutral and temporary collaborative environments for several, oftentimes competing, organizations and leverages the aggregated intellect and resources of stakeholders so as to create versatile solutions. By analyzing 369 biomedical research consortia, we tracked consortia growth around the world and gained insight into how this partnership model advances biomedical research. Our analyses suggest that research-by-consortium provides benefit to biomedical science, but the model needs further optimization before it can be fully integrated into the biomedical research pipeline.

Quantitative mass spectrometry of urinary biomarkers

The effectiveness of treatment of renal diseases is limited because the lack of diagnostic, prognostic and therapeutic markers. Despite the more than a decade of intensive investigation of urinary biomarkers, no new clinical biomarkers were approved. This is in part because the early expectations toward proteomics in biomarkers discovery were significantly higher than the capability of technology at the time. However, during the last decade, proteomic technology has made dramatic progress in both the hardware and software methods. In this review we are discussing modern quantitative methods of mass-spectrometry and providing several examples of their applications for discovery and validation of renal disease biomarkers. We are optimistic about future prospects for the development of novel of specific clinical urinary biomarkers.

Biomarkers of tobacco smoke exposure

Diseases and death caused by exposure to tobacco smoke have become the single most serious preventable public health concern. Thus, biomarkers that can monitor tobacco exposure and health effects can play a critical role in tobacco product regulation and public health policy. Biomarkers of exposure to tobacco toxicants are well established and have been used in population studies to establish public policy regarding exposure to second-hand smoke, an example being the nicotine metabolite cotinine, which can be measured in urine. Biomarkers of biological response to tobacco smoking range from those indicative of inflammation to mRNA and microRNA patterns related to tobacco use and/or disease state. Biomarkers identifying individuals with an increased risk for a pathological response to tobacco have also been described. The challenge for any novel technology or biomarker is its translation to clinical and/or regulatory application, a process that requires first technical validation of the assay and then careful consideration of the context the biomarker assay may be used in the regulatory setting. Nonetheless, the current efforts to investigate new biomarker of tobacco smoke exposure promise to offer powerful new tools in addressing the health hazards of tobacco product use. This review will examine such biomarkers, albeit with a focus on those related to cigarette smoking.

Breaking a vicious cycle

Despite prodigious advances in tumor biology research, few tumor-biomarker tests have been adopted as standard clinical practice. This lack of reliable tests stems from a vicious cycle of undervaluation, resulting from inconsistent regulatory standards and reimbursement, as well as insufficient investment in research and development, scrutiny of biomarker publications by journals, and evidence of analytical validity and clinical utility. We offer recommendations designed to serve as a roadmap to break this vicious cycle and call for a national dialogue, as changes in regulation, reimbursement, investment, peer review, and guidelines development require the participation of all stakeholders.

Kidney injury molecule-1

PURPOSE OF REVIEW

To review the new findings about the physiological roles of kidney injury molecule-1 (KIM-1) and the rapidly expanding evidence for this molecule as a promising biomarker in preclinical kidney toxicity evaluation and various human kidney diseases.

RECENT FINDINGS

KIM-1 has attracted increasing interest because of its possible pathophysiological role in modulating tubular damage and repair. There is rapidly accumulating evidence from both animal models and clinical studies that urinary KIM-1 is a sensitive and specific urinary biomarker for various forms of nephrotoxic injury, cardiac surgery-induced kidney injury, transplant rejection, and chronic kidney diseases.

SUMMARY

KIM-1 mediates epithelial phagocytosis in the injured kidney converting the proximal epithelial cell into a phagocyte, with potentially important pathophysiological implications for modulation of the immune response and repair process after injury. KIM-1 serves as a highly sensitive and specific urinary biomarker for kidney injury and may also be a therapeutic target for various kidney diseases.

An omics strategy for discovering pulmonary biomarkers potentially relevant to the evaluation of tobacco products

Smoking is known to cause serious lung diseases including chronic bronchitis, chronic obstructive lung disease, obstruction of small airways, emphysema and cancer. Tobacco smoke is a complex chemical aerosol containing at least 8000 chemical constituents, either tobacco derived or added by tobacco product manufacturers. Identification of all of the toxic agents in tobacco smoke is challenging, and efforts to understand the mechanisms by which tobacco use causes disease will be informed by new biomarkers of exposure and harm. In 2009, President Obama signed into law the Family Smoking Prevention and Tobacco Control Act granting the US FDA the authority to regulate tobacco products to protect public health. This perspective article presents the background, rationale and strategy for using omics technologies to develop new biomarkers, which may be of interest to the FDA when implementing the Family Smoking Prevention and Tobacco Control Act.

Promise of new translational safety biomarkers in drug development and challenges to regulatory qualification

One promise of new translational safety biomarkers (TSBs) is their ability to demonstrate that toxicities in animal studies are monitorable at an early stage, such that human relevance of potential adverse effects of drugs can be safely and definitively evaluated in clinical trials. Another is that they would provide an earlier, more definitive and deeper insight to patient prognosis compared with conventional biomarkers. Recent experience with regulatory authorities indicates that resource demands for new TSB qualifications under the current framework are daunting and the rate of their expansion will be slow, particularly in light of mounting financial pressures on the pharmaceutical industry. Sponsors face a dilemma over engaging in safety biomarker qualification consortia. While it is clear new TSBs could be considered catalysts to drug development and that patient health, business and scientific benefits, described here using examples, should outweigh qualification costs, concerns exist that early ambiguities in biomarker interpretations at the introduction of such new TSBs might hinder drug development.

Qualified kidney biomarkers and their potential significance in drug safety evaluation and prediction

The kidney is one of the major organs drug toxicity may target. Some renal safety biomarkers have been proposed to measure kidney injury and function accordingly. Despite the widespread use for diagnosis and monitoring of renal injury and function for decades, serum creatinine and blood urea nitrogen are nonspecific biomarkers with insensitive and delayed response in the clinical setting. There is an urgent need to identify and qualify novel kidney safety biomarkers that would be used to detect and predict drug-induced nephrotoxicity in preclinical toxicological studies, clinical trials and patient care in sequence. To do that, eight novel renal safety biomarkers have been well characterized and qualified for preclinical drug safety screening, and their clinical bridging validation is underway as well. Of them, some are used to detect or predict proximal tubular injury, and others are used to diagnose and monitor glomerular damage. Thus, measurement of a panel of kidney safety biomarkers in parallel would help maximally capture all potential safety signals for a more informative decision to be made in drug research and development as well as for optimal selection of the drug and its dose in clinical practice.

A performance evaluation of three drug-induced liver injury biomarkers in the rat: alpha-glutathione S-transferase, arginase 1, and 4-hydroxyphenyl-pyruvate dioxygenase

Alanine aminotransferase (ALT) activity is the most frequently relied upon reference standard for monitoring liver injury in humans and nonclinical species. However, limitations of ALT include a lack of specificity for diagnosing liver injury (e.g., present in muscle and the gastrointestinal tract), its inability to monitor certain types of hepatic injury (e.g., biliary injury), and ambiguity with respect to interpretation of modest or transient elevations (< 3× upper limit of normal). As an initial step to both understand and qualify additional biomarkers of hepatotoxicity that may add value to ALT, three novel candidates have been evaluated in 34 acute toxicity rat studies: (1) alpha-glutathione S-transferase (GSTA), (2) arginase 1 (ARG1), and (3) 4-hydroxyphenylpyruvate dioxygenase (HPD). The performance of each biomarker was assessed for its diagnostic ability to accurately detect hepatocellular injury (i.e., microscopic histopathology), singularly or in combination with ALT. All three biomarkers, either alone or in combination with ALT, improved specificity when compared with ALT alone. Hepatocellular necrosis and/or degeneration were detected by all three biomarkers in the majority of animals. ARG1 and HPD were also sensitive in detecting single-cell necrosis in the absence of more extensive hepatocellular necrosis/degeneration. ARG1 showed the best sensitivity for detecting biliary injury with or without ALT. All the biomarkers were able to detect biliary injury with single-cell necrosis. Taken together, these novel liver toxicity biomarkers, GSTA, ARG1, and HPD, add value (both enhanced specificity and sensitivity) to the measurement of ALT alone for monitoring drug-induced liver injury in rat.

Searching for new biomarkers of renal diseases through proteomics

BACKGROUND

Technological advances have resulted in a renaissance of proteomic studies directed at finding markers of disease progression, diagnosis, or responsiveness to therapy. Renal diseases are ideally suited for such research, given that urine is an easily accessible biofluid and its protein content is derived mainly from the kidney. Current renal prognostic markers have limited value, and renal biopsy remains the sole method for establishing a diagnosis. Mass spectrometry instruments, which can detect thousands of proteins at nanomolar (or even femtomolar) concentrations, may be expected to allow the discovery of improved markers of progression, diagnosis, or treatment responsiveness.

CONTENT

In this review we describe the strengths and limitations of proteomic methods and the drawbacks of existing biomarkers, and provide an overview of opportunities in the field. We also highlight several proteomic studies of biomarkers of renal diseases selected from the plethora of studies performed.

SUMMARY

It is clear that the field of proteomics has not yet fulfilled its promise. However, ongoing efforts to standardize sample collection and preparation, improve study designs, perform multicenter validations, and create joint industry-regulatory bodies offer promise for the recognition of novel molecules that could change clinical nephrology forever.