Biomarker candidates for cardiovascular disease and bone metabolism disorders in chronic kidney disease: a systems biology perspective

Inflammation and Adverse Outcomes in Patients With Acute Ischemic Stroke With and Without Chronic Kidney Disease

BACKGROUND

Elevated white blood cell count, fibrinogen levels, and lower levels of albumin signify higher systemic inflammatory response, hypercoagulable state, and poorer nutritional status, respectively. However, a consistent conclusion could not be drawn on whether the association between inflammatory markers and cardiovascular disease was affected by the presence of chronic kidney disease (CKD). We aimed to explore the association between inflammation and adverse outcomes in patients with acute ischemic stroke (AIS), as well as whether this association differs due to the presence of CKD.

METHODS AND RESULTS

This research was based on the Third China National Stroke Registry. The main adverse outcomes were poor functional outcome, stroke recurrence, and combined vascular event after 1 year. Inflammation was defined as the worst quartile of at least 2 of the aforementioned 3 markers. Finally, 8493 patients with AIS were enrolled in this study. The adjusted odds ratios/hazard ratios and 95% CIs of inflammation were 1.58 (1.34-1.86) for poor functional outcomes, 1.25 (1.06-1.47) for stroke recurrence, and 1.25 (1.06-1.46) for combined vascular event. The association between inflammation and adverse outcomes existed only in patients with AIS without CKD, although the interaction between CKD and inflammation was not statistically significant. (P for interaction >0.05).

CONCLUSIONS

Inflammation, which was defined as a combination of fibrinogen, white blood cell count, and albumin, was associated with all 1-year adverse outcomes among patients with AIS. Routine assessment of these biomarkers could become a potential part of the clinical evaluation for patients with AIS, especially those without CKD, aiding clinicians in risk stratification and treatment decision-making.

Comprehensive analysis of fifteen hub genes to identify a promising diagnostic model, regulated networks, and immune cell infiltration in acute kidney injury

BACKGROUND

Acute kidney injury is a common clinical problem with no sensitive and specific diagnostic biomarkers and definitive treatments. The underlying molecular mechanisms of acute kidney injury are unclear. Therefore, it is pivotal to explore the underlying mechanisms and screen for novel diagnostic biomarkers, and therapeutic targets.

METHODS

The present study identified 15 hub genes by WGCNA analysis. LASSO-based logistic regression analysis was used to select key features and construct a diagnostic model of AKI. In addition, GO and KEGG analyses were performed and TF-mRNA and miRNA-mRNA network analysis and immune infiltration analysis of hub genes were performed to reveal the underlying mechanisms of AKI.

RESULTS

A diagnostic model was constructed by LASSO-based logistic regression analysis and was validated by RT-qPCR based on 15 hub genes. GO and KEGG analyses revealed DEGs were enriched in oxidation-reduction process, cell adhesion, proliferation, migration, and metabolic process. The enriched TFs were BRD2, EP300, ETS1, MYC, SPI1, and ZNF263. The enriched miRNAs were miR-181c-5p, miR-218-5p, miR-485-5p, miR-532-5p and miR-6884-5p. The immune infiltration analysis showed that Macrophages M2 was decreasing significantly revealing a protective factor for further AKI treatment.

CONCLUSIONS

The present study identified 15 hub genes based on WGCNA. Development and validation of a potentially diagnostic model based on 15 hub genes. In addition, exploring the interaction between transcriptional factors and 15 hub genes, and miRNA-mRNA relationship pairs. Furthermore, immune infiltration analysis was performed by analyzing gene expression profiles of AKI. Our study provides some basis for further experimental studies.

Multi-omics approaches for revealing the complexity of cardiovascular disease

The development and progression of cardiovascular disease (CVD) can mainly be attributed to the narrowing of blood vessels caused by atherosclerosis and thrombosis, which induces organ damage that will result in end-organ dysfunction characterized by events such as myocardial infarction or stroke. It is also essential to consider other contributory factors to CVD, including cardiac remodelling caused by cardiomyopathies and co-morbidities with other diseases such as chronic kidney disease. Besides, there is a growing amount of evidence linking the gut microbiota to CVD through several metabolic pathways. Hence, it is of utmost importance to decipher the underlying molecular mechanisms associated with these disease states to elucidate the development and progression of CVD. A wide array of systems biology approaches incorporating multi-omics data have emerged as an invaluable tool in establishing alterations in specific cell types and identifying modifications in signalling events that promote disease development. Here, we review recent studies that apply multi-omics approaches to further understand the underlying causes of CVD and provide possible treatment strategies by identifying novel drug targets and biomarkers. We also discuss very recent advances in gut microbiota research with an emphasis on how diet and microbial composition can impact the development of CVD. Finally, we present various biological network analyses and other independent studies that have been employed for providing mechanistic explanation and developing treatment strategies for end-stage CVD, namely myocardial infarction and stroke.

Deciphering key genes in cardio-renal syndrome using network analysis

Cardio-renal syndrome (CRS) is a rapidly recognized clinical entity which refers to the inextricably connection between heart and renal impairment, whereby abnormality to one organ directly promotes deterioration of the other one. Biological markers help to gain insight into the pathological processes for early diagnosis with higher accuracy of CRS using known clinical findings. Therefore, it is of interest to identify target genes in associated pathways implicated linked to CRS. Hence, 119 CRS genes were extracted from the literature to construct the PPIN network. We used the MCODE tool to generate modules from network so as to select the top 10 modules from 23 available modules. The modules were further analyzed to identify 12 essential genes in the network. These biomarkers are potential emerging tools for understanding the pathophysiologic mechanisms for the early diagnosis of CRS. Ontological analysis shows that they are rich in MF protease binding and endo-peptidase inhibitor activity. Thus, this data help increase our knowledge on CRS to improve clinical management of the disease.

Association of Serum Thyroid Hormones with the Risk and Severity of Chronic Kidney Disease Among 3563 Chinese Adults

Background

Chronic kidney disease (CKD) is a global health problem with an increasing prevalence. We explored the association of serum thyroid hormones with the risk and severity of CKD among Chinese adults.

Material/Methods

This retrospective study involved 3563 participants. CKD was diagnosed according to the clinical practice guidelines of the 2012 Kidney Disease Improving Global Outcomes guidelines. Effect-size estimates are expressed as odds ratio (OR) and 95% confidence interval (CI).

Results

Given the strong magnitude of correlation, only 3 thyroid hormones were analyzed: free triiodothyronine (FT3), free thyroxin (FT4), and thyroid-stimulating hormone (TSH). After propensity score matching on age, sex, diabetes, and hypertension, per 0.2 pg/mL increase in FT3 was significantly associated with 35–38% reduced risk of CKD at stage 1–4, and per 0.3 ng/dL increase in FT4 was only significantly associated with 21% reduced risk of CKD at stage 5 (OR, 95% CI: 0.79, 0.69–0.89), and per 0.5 μIU/mL increment in TSH increased the risk of CKD stage 5 by 8% (1.08, 1.02–1.14). Importantly, 3 thyroid hormones acted interactively, particularly for the interaction between FT3 and FT4 in predicting CKD at stage 5 (OR, 95% CI: 1.81, 1.30–2.55 for high FT3-low FT4, 17.72, 7.18–43.74 for low FT3-high FT4, and 22.28, 9.68–51.30 for low FT3-low FT4).

Conclusions

Our findings indicate that serum FT3 can be used as an early-stage biomarker for CKD, and FT4 and TSH can be used as advanced-stage biomarkers among Chinese adults.

Epigenetics and DOHaD: from basics to birth and beyond

Developmental origins of health and disease (DOHaD) is the study of how the early life environment can impact the risk of chronic diseases from childhood to adulthood and the mechanisms involved. Epigenetic modifications such as DNA methylation, histone modifications and non-coding RNAs are involved in mediating how early life environment impacts later health. This review is a summary of the Epigenetics and DOHaD workshop held at the 2016 DOHaD Society of Australia and New Zealand Conference. Our extensive knowledge of how the early life environment impacts later risk for chronic disease would not have been possible without animal models. In this review we highlight some animal model examples that demonstrate how an adverse early life exposure results in epigenetic and gene expression changes that may contribute to increased risk of chronic disease later in life. Type 2 diabetes and cardiovascular disease are chronic diseases with an increasing incidence due to the increased number of children and adults that are obese. Epigenetic changes such as DNA methylation have been shown to be associated with metabolic health measures and potentially predict future metabolic health status. Although more difficult to elucidate in humans, recent studies suggest that DNA methylation may be one of the epigenetic mechanisms that mediates the effects of early life exposures on later life risk of obesity and obesity related diseases. Finally, we discuss the role of the microbiome and how it is a new player in developmental programming and mediating early life exposures on later risk of chronic disease.

Secreted klotho and chronic kidney disease

Soluble Klotho (sKl) in the circulation can be generated directly by alterative splicing of the Klotho transcript or the extracellular domain of membrane Klotho can be released from membrane-anchored Klotho on the cell surface. Unlike membrane Klotho which functions as a coreceptor for fibroblast growth factor-23 (FGF23), sKl, acts as hormonal factor and plays important roles in anti-aging, anti-oxidation, modulation of ion transport, and Wnt signaling. Emerging evidence reveals that Klotho deficiency is an early biomarker for chronic kidney diseases as well as a pathogenic factor. Klotho deficiency is associated with progression and chronic complications in chronic kidney disease including vascular calcification, cardiac hypertrophy, and secondary hyperparathyroidism. In multiple experimental models, replacement of sKl, or manipulated up-regulation of endogenous Klotho protect the kidney from renal insults, preserve kidney function, and suppress renal fibrosis, in chronic kidney disease. Klotho is a highly promising candidate on the horizon as an early biomarker, and as a novel therapeutic agent for chronic kidney disease.

Soluble guanylate cyclase stimulation prevents fibrotic tissue remodeling and improves survival in salt-sensitive Dahl rats

BACKGROUND

A direct pharmacological stimulation of soluble guanylate cyclase (sGC) is an emerging therapeutic approach to the management of various cardiovascular disorders associated with endothelial dysfunction. Novel sGC stimulators, including riociguat (BAY 63-2521), have a dual mode of action: They sensitize sGC to endogenously produced nitric oxide (NO) and also directly stimulate sGC independently of NO. Little is known about their effects on tissue remodeling and degeneration and survival in experimental malignant hypertension.

METHODS AND RESULTS

Mortality, hemodynamics and biomarkers of tissue remodeling and degeneration were assessed in Dahl salt-sensitive rats maintained on a high salt diet and treated with riociguat (3 or 10 mg/kg/d) for 14 weeks. Riociguat markedly attenuated systemic hypertension, improved systolic heart function and increased survival from 33% to 85%. Histological examination of the heart and kidneys revealed that riociguat significantly ameliorated fibrotic tissue remodeling and degeneration. Correspondingly, mRNA expression of the pro-fibrotic biomarkers osteopontin (OPN), tissue inhibitor of matrix metalloproteinase-1 (TIMP-1) and plasminogen activator inhibitor-1 (PAI-1) in the myocardium and the renal cortex was attenuated by riociguat. In addition, riociguat reduced plasma and urinary levels of OPN, TIMP-1, and PAI-1.

CONCLUSIONS

Stimulation of sGC by riociguat markedly improves survival and attenuates systemic hypertension and systolic dysfunction, as well as fibrotic tissue remodeling in the myocardium and the renal cortex in a rodent model of pressure and volume overload. These findings suggest a therapeutic potential of sGC stimulators in diseases associated with impaired cardiovascular and renal functions.

Mapping of molecular pathways, biomarkers and drug targets for diabetic nephropathy

PURPOSE

For diseases with complex phenotype such as diabetic nephropathy (DN), integration of multiple Omics sources promises an improved description of the disease pathophysiology, being the basis for novel diagnostics and therapy, but equally important personalization aspects.

EXPERIMENTAL DESIGN

Molecular features on DN were retrieved from public domain Omics studies and by mining scientific literature, patent text and clinical trial specifications. Molecular feature sets were consolidated on a human protein interaction network and interpreted on the level of molecular pathways in the light of the pathophysiology of the disease and its clinical context defined as associated biomarkers and drug targets.

RESULTS

About 1000 gene symbols each could be assigned to the pathophysiological description of DN and to the clinical context. Direct feature comparison showed minor overlap, whereas on the level of molecular pathways, the complement and coagulation cascade, PPAR signaling, and the renin-angiotensin system linked the disease descriptor space with biomarkers and targets.

CONCLUSION AND CLINICAL RELEVANCE

Only the combined molecular feature landscapes closely reflect the clinical implications of DN in the context of hypertension and diabetes. Omics data integration on the level of interaction networks furthermore provides a platform for identification of pathway-specific biomarkers and therapy options.

Integrative analysis of -omics data and histologic scoring in renal disease and transplantation: renal histogenomics

The histologic scoring of renal biopsies is still the gold standard for renal disease classification. The Banff classification scheme and the chronic allograft damage index are histopathologic scoring schemes widely used in renal transplantation. The determination of genome-wide gene expression profiles in human renal biopsies has the potential to serve as independent validation data sets and also provide a more precise evaluation of the functional status behind the visible morphologic alterations. It is expected that results from high-throughput-omics experiments will lead to improved classification schemes in the near future as also discussed at recent Banff meetings. In this review we give an overview on-omics studies, focusing on the association of molecular changes on the transcript as well as on the protein level and morphologic scoring schemes in renal disease and transplantation.

The new kidney disease: improving global outcomes (KDIGO) guidelines - expert clinical focus on bone and vascular calcification

Chronic kidney disease-mineral and bone disorder (CKD-MBD) defines a triad of interrelated abnormalities of serum biochemistry, bone and the vasculature associated with chronic kidney disease (CKD). The new kidney disease: improving global outcomes (KDIGO) guidelines define the quality and depth of evidence supporting therapeutic intervention in CKD-MBD. They also highlight where patient management decisions lack a strong evidence base. Expert interpretation of the guidelines, along with informed opinion, where evidence is weak, may help develop effective clinical practice. The body of evidence linking poor bone health and reservoir function (the ability of bone to buffer calcium and phosphorus) with vascular calcification and cardiovascular outcomes is growing. Treating renal bone disease should be one of the primary aims of therapy for CKD. Evaluation of the biochemical parameters of CKD-MBD (primarily phosphorus, calcium, parathyroid hormone and vitamin D levels) as early as CKD Stage 3, and an assessment of bone status (by the best means available), should be used to guide treatment decisions. The adverse effects of high phosphorus intake relative to renal clearance (including stimulation of hyperparathyroidism) precede hyperphosphatemia, which presents late in CKD. Early reduction of phosphorus load may ameliorate these adverse effects. Evidence that calcium load may influence progression of vascular calcification with effects on mortality should also be considered when choosing the type and dose of phosphate binder to be used. The risks, benefits, and strength of evidence for various treatment options for the abnormalities of CKD-MBD are considered.

Integrative bioinformatics analysis of proteins associated with the cardiorenal syndrome

The cardiorenal syndrome refers to the coexistence of kidney and cardiovascular disease, where cardiovascular events are the most common cause of death in patients with chronic kidney disease. Both, cardiovascular as well as kidney diseases have been extensively analyzed on a molecular level, resulting in molecular features and associated processes indicating a cross-talk of the two disease etiologies on a pathophysiological level. In order to gain a comprehensive picture of molecular factors contributing to the bidirectional interplay between kidney and cardiovascular system, we mined the scientific literature for molecular features reported as associated with the cardiorenal syndrome, resulting in 280 unique genes/proteins. These features were then analyzed on the level of molecular processes and pathways utilizing various types of protein interaction networks. Next to well established molecular features associated with the renin-angiotensin system numerous proteins involved in signal transduction and cell communication were found, involving specific molecular functions covering receptor binding with natriuretic peptide receptor and ligands as well known example. An integrated analysis of identified features pinpointed a protein interaction network involving mediators of hemodynamic change and an accumulation of features associated with the endothelin and VEGF signaling pathway. Some of these features may function as novel therapeutic targets.

Biomarkers in renal transplantation ischemia reperfusion injury

Ischemia reperfusion injury (IRI) is a choreographed process leading to delayed graft function (DGF) and reduced long-term patency of the transplanted organ. Early identification of recipients of grafts at risk would allow modification of the posttransplant management, and thereby potentially improve short- and long-term outcomes. The recently emerged "omics" technologies together with bioinformatics workup have allowed the integration and analysis of IRI-associated molecular profiles in the context of DGF. Such a systems biological approach promises qualitative information about interdependencies of complex processes such as IRI regulation, rather than offering descriptive tables of differentially regulated features on a transcriptome, proteome, or metabolome level leaking the functional, biological framework. In deceased-donor kidney transplantation as the primary causative factor resulting in IRI and DGF, a distinct signature and choreography of molecular events in the graft before harvesting seems to be associated with subsequent DGF. A systems biological assessment of these molecular changes suggests that processes along inflammation are of pivotal importance for the early stage of IRI. The causal proof of this association has been tested by a double-blinded, randomized, controlled trial of steroid or placebo infusion into deceased donors before the organs were harvested. Thorough systems biological analysis revealed a panel of biomarkers with excellent discrimination. In summary, integrated analysis of omics data has brought forward biomarker candidates and candidate panels that promise early assessment of IRI. However, the clinical utility of these markers still needs to be established in prospective trials in independent patient populations.

Biomarkers-a potential route for improved diagnosis and management of ongoing renal damage

Currently, the identification and validation of biomarkers of kidney injury is among the top priorities of many diagnostic biotechnology companies as well as academic research institutes. Specifically, in renal transplantation, validated biomarkers of tissue injury with good discriminatory power between the various renal compartments and the underlying pathophysiology are desired, because sequential allograft biopsies are limited in number and cannot be used as a screening tool. Given the high demands on these markers, it is not surprising that none of those currently under evaluation has been thoroughly validated for a specific entity. Published biomarker candidates for early tubular damage include neutrophil gelatinase-associated lipocalin (NGAL), interleukin (IL)-18, soluble CD30, perforin, and granzyme B. Recently, C4d flow panel reactive antibodies were evaluated as biomarkers for humoral alloimmune responses. Additional biomarkers such as FOXP3 and kidney injury molecule 1 have been studied in the maintenance phase of renal transplantation. Given the complex prerequisites, it is not surprising that no biomarker panel has been sufficiently validated for clinical use. However, in the near future a biomarker for use as an indicator of renal tubule cell injury will be available. Troponin T or transaminase of the kidney may then at least be used to differentiate between functional renal failure (equivalent to a rise in creatinine) and intrinsic kidney injury.

Access to immunology through the Gene Ontology

The Gene Ontology (GO) is widely recognized as the premier tool for the organization and functional annotation of molecular aspects of cellular systems. However, for many immunologists the use of GO is a very foreign concept. Indeed, as a controlled vocabulary, GO can almost be considered a new language, and it can be difficult to appreciate the use and value of this approach for understanding the immune system. This review reflects on the application of GO to the field of immunology and explains the process of GO annotation. Finally, this review hopes to inspire immunologists to invest time and energy in improving both the content of the GO and the quality of GO annotations associated with genes of immunological interest.

Improvements to cardiovascular gene ontology

Gene Ontology (GO) provides a controlled vocabulary to describe the attributes of genes and gene products in any organism. Although one might initially wonder what relevance a ‘controlled vocabulary’ might have for cardiovascular science, such a resource is proving highly useful for researchers investigating complex cardiovascular disease phenotypes as well as those interpreting results from high-throughput methodologies. GO enables the current functional knowledge of individual genes to be used to annotate genomic or proteomic datasets. In this way, the GO data provides a very effective way of linking biological knowledge with the analysis of the large datasets of post-genomics research. Consequently, users of high-throughput methodologies such as expression arrays or proteomics will be the main beneficiaries of such annotation sets. However, as GO annotations increase in quality and quantity, groups using small-scale approaches will gradually begin to benefit too. For example, genome wide association scans for coronary heart disease are identifying novel genes, with previously unknown connections to cardiovascular processes, and the comprehensive annotation of these novel genes might provide clues to their cardiovascular link. At least 4000 genes, to date, have been implicated in cardiovascular processes and an initiative is underway to focus on annotating these genes for the benefit of the cardiovascular community. In this article we review the current uses of Gene Ontology annotation to highlight why Gene Ontology should be of interest to all those involved in cardiovascular research.