Proteomics and personalized medicine: a focus on kidney disease

ABSTRACT

Introduction: Inter-individual variability in response to drug treatment has induced an increased demand for decisions via personalize medicine. Also, the contribution of proteomics to the era of personalized medicine would seem to be vital in improving therapeutic outcomes.

Areas covered: We review validated biomarkers discovered by proteomics techniques and their use in personalized medicine with the focus on kidney diseases. We discuss this topic with a special emphasis on recent publications and relevant initiatives and depict some limitations that remain for personalized medicine.

Expert opinion: The development of highly accurate biomarkers is essential for optimizing the management of kidney diseases. Various biomarkers of kidney diseases have been identified using proteomic techniques. However, only a few of these biomarkers showed the potential to be used in clinical practice concerning personalized medicine. Therefore, it becomes evident that the combination of multiple biomarkers confers higher accuracy and the ability to depict complex pathophysiological conditions, a prerequisite for personalized treatment. CKD273, a multimarker panel for early CKD detection may serve as a first example for personalized medicine in nephrology. Based on this successful example, proteomics is expected to develop into the key technology to guide personalized intervention.     

Cancer genomics: from discovery science to personalized medicine

Recent advances in genome technologies and the ensuing outpouring of genomic information related to cancer have accelerated the convergence of discovery science and clinical medicine. Successful examples of translating cancer genomics into therapeutics and diagnostics reinforce its potential to make possible personalized cancer medicine. However, the bottlenecks along the path of converting a genome discovery into a tangible clinical endpoint are numerous and formidable. In this Perspective, we emphasize the importance of establishing the biological relevance of a cancer genomic discovery in realizing its clinical potential and discuss some of the major obstacles to moving from the bench to the bedside.     

Erratum to: Herbal decoctosome is a novel form of medicine

Science China Life Sciences - Following the published article, we noticed an error duplication in Figure 5G “control” and “PGY-6” that was introduced during the revised...     

PREDICT: a method for inferring novel drug indications with application to personalized medicine

Inferring potential drug indications, for either novel or approved drugs, is a key step in drug development. Previous computational methods in this domain have focused on either drug repositioning or matching drug and disease gene expression profiles. Here, we present a novel method for the large‐scale prediction of drug indications (PREDICT) that can handle both approved drugs and novel molecules. Our method is based on the observation that similar drugs are indicated for similar diseases, and utilizes multiple drug–drug and disease–disease similarity measures for the prediction task. On cross‐validation, it obtains high specificity and sensitivity (AUC=0.9) in predicting drug indications, surpassing existing methods. We validate our predictions by their overlap with drug indications that are currently under clinical trials, and by their agreement with tissue‐specific expression information on the drug targets. We further show that disease‐specific genetic signatures can be used to accurately predict drug indications for new diseases (AUC=0.92). This lays the computational foundation for future personalized drug treatments, where gene expression signatures from individual patients would replace the disease‐specific signatures.     

The pharmocogenomics of warfarin: closing in on personalized medicine

Warfarin, a coumarin anticoagulant, is used worldwide for the treatment and prevention of thromboembolic disease. Warfarin therapy, however, can be difficult to manage because of the drug's narrow therapeutic index and the wide interindividual variability in patient response. It is now clear that genetic polymorphisms in genes influencing metabolism (CYP2C9) and pharmacodynamic response (VKORC1) are strongly associated with warfarin responsiveness. Optimal warfarin dosing in turn drives other positive anticoagulation-related outcomes. Therefore, a strong basic science argument is emerging for prospective genotyping of warfarin patients. Effective clinical translation would establish warfarin pharmacogenomics as a heuristic model for personalized medicine.     

The economics of personalized medicine: commercialization as a driver of return on investment

Optimizing commercialization of drugs is the sine qua non of the pharmaceutical industry and intensive work has been done to characterize fully the drivers of drug adoption and understand the resources required to optimize those drivers for full adoption of drugs. Conversely, while the pharmaceutical industry is actively embracing the new personalized medicine (PM) paradigm, much work remains to be done to understand fully what drives adoption of targeted therapies and how to resource those drivers appropriately. While the industry is slowly learning from its early missteps, progress is still inhibited by a lack of understanding of the specific hurdles that individual development teams face in developing and commercializing targeted therapies and the requirement for budgets specifically aimed at driving test adoption. This article considers the benefits of optimizing commercial planning in the PM space and the potential negative impact in potentially failing to optimize that planning. Real world insights are used to illustrate that a far broader commercial lens is required in the PM space and will touch on functional areas not usually included in the context of 'commercial' decisions.     

Contribution of macrophages to immediate hypersensitivity reaction

The interaction of mast cells with other leukocytes during immediate hypersensitivity reactions was tested by in vivo and in vitro experiments. Intraperitoneal challenge of passively sensitized rats with antigen caused the production of peptidoleukotrienes, leukotriene (LT)B4, thromboxane (TX)B2, and 6-keto-prostaglandin (PG) F1 alpha in the peritoneal cavity. Pretreatment of the rats with thioglycollate i.p. markedly changed the amount of eicosanoids formed. When polymorphonuclear leukocytes were the predominant cell type in the peritoneal exudate, both LTC4 and 6-keto-PGF1 alpha were decreased by 75% each and TXB2 by 50%. When elicited macrophages were predominant, there was an additional reduction in LTC4 by 68% as compared with 18 hr after thioglycollate treatment, but no additional change in the other arachidonic acid metabolites. In vitro antigen challenge of passively sensitized mouse bone marrow-derived mast cells caused the release of LTC4, LTB4, 6-trans-LTB4, 5-hydroxyeicosatetraenoic (5-HETE), and TXB2. Exposure to antigen of these mast cells in the presence of resident peritoneal macrophages markedly altered eicosanoid formation. Early in the time course (2 to 15 min), macrophages markedly enhanced all 5-lipoxygenase products. However, later in the time course (30 to 120 min), these products were decreased. This decrease was reversed by catalase and superoxide dismutase, which suggests the involvement of oxygen radicals. These active oxygen species also seemed to be generated by mast cells, because these enzymes caused an increase in 5-lipoxygenase products when mast cells were challenged alone. RIA of cyclooxygenase products showed that mast cells released only TXB2 when stimulated with antigen. When they were stimulated in the presence of macrophages, TXB2 and also PGE2 and 6-keto-PGF1 alpha were synthesized. Therefore, macrophages probably contribute the PGE2 and 6-keto-PGF1 alpha. Because the same amount of TXB2 was generated whether macrophages were present or not, the mast cells seem to be the major source of this compound. These data indicate that macrophages and possibly polymorphonuclear leukocytes participate in immediate hypersensitivity reactions.     

Screens, maps & networks: from genome sequences to personalized medicine

Genome sequencing of tumors provides a wealth of information on mutations and structural variations, instilling hope that this data can be used to predict individual tumor progression and response to treatment. Yet currently, our ability to predict the functional consequences of these aberrations remains poor. How do cancer-associated mutations give rise to the hallmark phenotypes of cancer? Recently, information about the genetic makeup of cancer cells has been combined with novel functional genomics approaches to identify novel targets, exploit synthetic lethality and explore the rewiring of cellular pathways. Here, we highlight recent developments revealing the hidden landscape of genetic interactions in model organisms and cancer cells, a key step toward personalized cancer diagnostics and therapy.     

From modules to medicine: How modular domains and their associated networks can enable personalized medicine

Unveiling of cancer genomes is unleashing new therapeutic strategies for cancer. With cancer parts lists in hand, new approaches to personalized medicine can be developed by understanding the assembly of cancer machines using modular domains in proteins and their associated networks. Using the Src-homology-2 (SH2) domain as an example, new profiling approaches can discern global patterns of tyrosine phosphorylation in cancer cells that can enable molecular cancer medicine. Identifying and quantifying protein-protein interactions also has the potential to subtype tumors and guide clinical decision making. These approaches should extend the impact of genomics through viewing the architecture of cancer systems and improve predictions of patient outcome and therapeutic response, as well as guide combination therapy approaches that attack cancer systems.     

Redefining clinical trials: the age of personalized medicine

The triumph of personalized cancer therapeutics in recent years is prompting some oncologists to rethink clinical trial design; other researchers have different priorities for trial reform.     

Worldwide variations in EGFR somatic mutations: a challenge for personalized medicine

Two studies recently reported around 10% of EGFR activating mutations in triple negative breast cancers from Asian patients. However, we did not find any EGFR activating mutation in a series of 229 breast tumor samples from European patients. Like in lung cancer, the EGFR mutation profiles seem to be related to the ethnical origin of patients. This is an important point that should be considered when developing anti-EGFR therapies.