The dawn of a new era in chronic kidney disease
Chronic kidney disease (CKD) is a common and debilitating condition that affects around 1 in 10 people worldwide,1 and the prevalence is increasing. People living with CKD progressively lose kidney function, but may not know they even have the disease until the later stages.
At AstraZeneca, we are dedicated to changing the future for CKD patients. While there are currently available treatments that benefit patients with CKD, there are no treatments that specifically target the cause of CKD. We are investigating the drivers of disease and progression of CKD using a rigorous, science-led approach and adopting techniques that aim to break new ground in research. Our ambitions are high: we want to stop disease progression, manage morbidity and mortality, and ultimately modify and even reverse the disease itself.
By focusing on early disease detection underpinned by precision medicine, we hope that in the future patients will be matched with treatments most likely to work for them.
Sometimes I look around the room when we have big meetings and consider that every tenth person in the room will have kidney disease. It is concerning that we have this on an epidemic scale. I find it troubling that there are currently limited treatment options for patients who are facing this condition.
Scientific advances have increased our understanding of the links between cardiovascular, renal and metabolic diseases. Many individuals with these diseases have either symptoms or underlying pathologies associated with more than one of these diseases, so treating them collaboratively is essential. At AstraZeneca, our CaReMe approach is to see and embrace the full cardio-renal and metabolic picture and use this knowledge to redefine the way these diseases are understood and treated.
There is an unmet need in CKD. In addition to the increasing prevalence and limited treatment options, CKD is known as a ‘disease multiplier’. As such, CKD is not a disease to be studied in isolation. Around 40% of patients with heart failure also have CKD,2 and patients with both diabetes and early kidney disease may have a reduced life expectancy compared to a healthy person.3
The kidney has critical roles in the human physiology, removing waste products and balancing the body’s fluids. It is also involved in metabolism and vitamin D production, and produces hormones that regulate red blood cell production and blood pressure.4 This all happens as a result of complex interplay with other organs, so CKD has knock-on effects throughout the entire body.5
For these reasons, we take a holistic view of the patient – the CaReMe approach – and are guided by the commonalities between these diseases in our research.
This is an exciting time – recent advances in three important areas lay the foundations for a new era in CKD research:
- Bioinformatics and ‘omics analysis to classify patients and uncover new genetic disease drivers
- The development of advanced models for target validation and understanding disease development
- New modalities for previously undruggable targets
CKD encompasses various primary disorders and stages of progression, and the patient population is highly heterogenous – CKD is really an umbrella term for many diseases. The current symptom-based approach ignores the different underlying molecular causes of disease and leaves potential for misdiagnosis. We aim to close this gap: enrolling the right people for the right trial is critical for research success and patient health.
In the age of ‘omics and data processing, we believe we have reached a turning point. We are working collaboratively to build – and make sense of – huge genetic datasets from real patient samples.
This approach means we are uncovering different underlying molecular disease profiles. We hope then to be able to classify patients more accurately, and identify new biomarkers and disease targets.
Inspiration can sometimes come from unexpected places. Anna Reznichenko, Associate Principal Scientist in Translational Science, Bioinformatics, Research & Development BioPharmaceuticals, has devised a novel method based on market segmentation analysis for handling massive datasets drawn from the financial industry. This approach has revealed distinct new patient categories, and could be used as the base for precision medicine in the future.
Using data from the Renal Pre-competitive Consortium (RPC2) – a unique partnership of industrial and academic collaborators – gives Anna access to the largest-ever patient sample bank for renal transcriptomics (analysis of gene expression in kidney biopsies), containing over 250 genome-wide expression profiled samples, with data from patients at all stages of disease. Distinct, homogeneous patient categories can be most effectively revealed using a dataset of this size. However, access to the data itself is only part of the picture: the next step is analysing the patterns within the data points.
Using the unique datasets, the team applied the above described machine learning and artificial intelligence algorithm to classify patients into homogenous subclasses. For the first time, distinct disease categories based on molecular data which are different from previous clinical classifications for CKD could be seen. We are now looking to identify urinary biomarkers which could be used to reveal patients’ molecular disease classes non-invasively, allowing us greater precision when allocating the right patients to the right trials and in the future, potentially provide tailored treatments based on scientifically-determined individual disease categories.
We are not only using ‘omics in our attempts to classify disease, but to build an understanding of its cause. Many of the underlying mechanisms of CKD have been a mystery until recently. However, exome sequencing – the analysis of the protein coding regions of the genome – could change this. Exome sequencing is emerging as an important analytical and potential diagnostic technique in many fields, and we are now applying it to CKD. For a disease with many different underlying causes that produce the same symptoms, a molecular approach to diagnosis is a logical step and is essential if we are to develop effective, patient-specific treatments.
In collaboration with Columbia University, led by Professor David Goldstein and Professor Ali Gharavi, we have conducted the largest-ever exome sequencing study of CKD patients. The research results have given us valuable clinical insights into the genetic causes and therapeutic opportunities for this condition.
Published in the New England Journal of Medicine, the study is based on the results of exome sequencing more than 3,300 patients. It identified potentially causative genetic variants for a significant number (~9%) of patients. The research also revealed that six genes collectively account for almost two thirds of genetic diagnoses, and genetic diagnoses could be assigned to ~17% of previously uncharacterised CKD cases. This research could represent a significant breakthrough for those patients with a genetic diagnosis, as these data could potentially provide novel clinical insights to help inform treatment and care options.
These data enhance our disease understanding, as well as suggesting that genetic diagnosis can now be used in patients with previously unknown causes of the disease, and highlights the potential of early genetic testing to accurately identify and target patient subpopulations towards relevant clinical trials and targeted therapies.
In collaboration with scientists from Columbia University, we have shown for the first time that adult onset CKD can be stratified into distinct underlying causes through the use of genetics, with direct relevance both to clinical care and clinical trial design.
This work emphasizes the critical role of careful genomic analyses, both in the management of patients living with chronic kidney disease and in the appropriate design of trials dedicated to the evaluation of new and more effective treatments.
We are in a stronger position than ever before to look for targets and treatments now we have a deeper molecular understanding of CKD. To use this new knowledge to our best advantage, we need the right research tools to simulate the disease and test our hypotheses. We are investing in the development of new, sophisticated models that mimic the human kidney more accurately than has ever previously been possible.
The complexity of the kidney means it has been virtually impossible to emulate in classical in vitro systems, while in vivo models are resource intensive to produce, and not always translatable to human systems.
The new model systems we are embedding into our research pipeline to bridge this gap include 3D bioprinting and organs-on-chips. With these groundbreaking techniques, we can test compound behaviour and hope to shed new light on previously elusive disease mechanisms.
A 3D model with the vascular and tubular aspects of the kidney to emulate cell cross-talk in different organ compartments is the goal that until now may have seemed beyond scientists’ reach. However, we have moved a step closer towards modelling the human system by using 3D bioprinting in our collaboration with world-leading experts at Harvard University.
3D bioprinting involves printing-like techniques, where fugitive ‘ink’ is printed onto a gelatin/fibrogen matrix to pattern open vascular and tubular channels. These are then populated with cells to create biological structures. Organ segments can be created that preserve the architecture and heterogeneity of their biological counterparts – major progress from 2D modelling.
We have already bioprinted a 3D model with both kidney tubules and blood vessels, which replicates the behaviour of the two structures and importantly the interactions between the different tissue types. Modelling this interplay, which would take place in a real, living kidney is crucial for the creation of a realistic, relevant model system.
We now have the possibility of using 3D bioprinting to delve deeper into cellular crosstalk. 3D bioprinting also offers us unique flexibility – we print a matrix, to which we can effectively add any cell type we want in an almost modular fashion.
We are excited to partner with AstraZeneca to increase the complexity and utility of our 3D kidney tissue models – bioprinting enables us to rapidly design and fabricate a wide range of vascularised human tissues.
Creating realistic, living components of a healthy kidney will be a vital tool for understanding kidney function. As our aim is also to understand kidney dysfunction, we also are embarking on an ambitious project to create kidney components with diseased cells, using human induced pluripotent stem (iPS) cells from real patients. Ultimately, the logical conclusion of this work would be to print all the components needed to create an entire synthetic kidney. Although we are not at this stage yet, it is not outside the realm of future possibility.
Organs-on-Chips technology is a game changer for scientists in IMED: these micro-engineered systems model the in vivo micro-environment, and represent a new paradigm for cell-based models. We are using them to model the glomerulus – the kidney’s filtration barrier – which breaks down in CKD. Why this happens is still a mystery; we hope this technology might help bring some answers.
Observing a complete system enables a better understanding of kidney function – and dysfunction. Kidneys are made up of over 20 different cell types, arranged within an intricate architecture. Crosstalk between these cells and their interaction with their micro-environment drastically influences their behaviours in normal function, disease processes, and how they respond to potential drugs.
Until now, cell-based models that have been used for compound testing have not been able to reflect the complexity of the kidney environment and results would not always be a faithful representation of what happens in the body. Animal models go some way towards addressing this; although even mammalian systems can lack translatability to human systems, especially with compounds that show species differences in metabolism and toxicity.
Organs-on-Chip technology provides an environment that emulates key aspects of the physiology of a real kidney; including fluidic channels that are lined with living cells in the correct architecture. The flow represents the flow of blood carrying nutrients, takes away waste products, and also creates mechanical forces, all critical factors for the functioning of the kidney.
We have, for years, been investigating cells in isolation in a dish. When we put two cell types together, we suddenly see that they behave differently – one cell influences the results from the other. With organ on a chip technology we can go even further than this and add conditions such as flow and shear stress, mimicking the conditions in the kidney even further. Imagine how much more information we will get from this system. The ultimate aim will be to try to induce disease conditions and then treat them.
With our partner, Emulate, Inc., we are developing Organ-Chip models to demonstrate the utility of this technology as a more predictive alternative for efficacy and safety testing of new chemical entities. We have two postdoctorate fellows focused on this project – the first aims to create a completely new type of chip with a three-cell-type culture, and the second will use an established chip to try to reconstitute the subtleties of chronic human disease in a way that could never have been done in vitro, by fine tuning factors like flow rates and shear stresses.
Julie Williams believes that one reason for the limited number of treatment options for kidney patients is strongly linked to the lack of translatable systems as there is a high attrition rate with kidney candidate drugs in clinical trials. Organs-on-Chip technology could help solve this challenge.
The next step on from our breakthrough genetic research and increased understanding of disease mechanisms is using precision medicine approaches with the aim of targeting the underlying causes of CKD. We are looking to a future where we can identify drugs that target the root cause of disease and recruit patients with specific genotypes to the right trials.
In partnership with Ionis Pharmaceuticals, we are researching APOL-1 – a gene with variants that is related to an increased risk of early onset kidney disease and rapid progression. People of West-African ancestry are at increased risk of developing end stage renal disease, and common APOL-1 polymorphisms may account for this risk.6
Understanding that APOL-1 is a genetic driver of disease leads us a step closer to addressing a high unmet need in a defined population. If we can target the high-risk APOL-1 variants, this could lead to potential treatments for people who have limited options.
One emerging treatment strategy is to target protein expression using antisense oligonucleotides (ASOs). These are short chains of nucleotides that bind to mRNA, thereby modulating protein expression. ASOs can be designed to bind to almost any defined genetic sequences, meaning they have potential for use in diseases with genetic origin.
Our antisense-based drug discovery platform is a rapid and efficient route to use genomic information to make novel drug candidates. This platform allows us to explore drug candidates that specifically address disease targets, many of which cannot be treated by traditional drug types. We’re excited to work with AstraZeneca on this and other targets with the hope to provide benefits to patients with unmet medical needs.
We have shown some encouraging preclinical results in our work with Ionis: ASOs directed against APOL-1 mRNA can reduce proteinuria in a transgenic mouse model of APOL-1 nephropathy. Although it is early days, APOL-1 knockdown could hopefully deliver the first precision medicine approach in CKD, and this would be the first step towards a treatment breakthrough for APOL-1 nephropathy.