Development and validation of a multiplexed LC-MS/MS ketone body assay for clinical diagnostics

Objectives

Ketone bodies (KBs) serve as important energy sources that spare glucose, providing the primary energy for cardiac muscle, skeletal muscle during aerobic exercise, and the brain during periods of catabolism. The levels and relationships between the KBs are critical indicators of metabolic health and disease. However, challenges in separating isomeric KBs and concerns about sample stability have previously limited their clinical measurement.

Methods

A novel 6.5-minute liquid chromatography-mass spectrometry-based assay was developed, enabling the precise measurement of alpha-, beta- and gamma-hydroxybutyrate, beta-hydroxyisobutyrate, and acetoacetate. This method was fully validated for human serum and plasma samples by investigating extraction efficiency, matrix effects, accuracy, recovery, intra- and inter-precision, linearity, lower limit of quantitation (LLOQ), carryover, specificity, stability, and more. From 107 normal samples, reference ranges were established for all analytes and the beta-hydroxybutyrate/acetoacetate ratio.

Results

All five analytes were adequately separated chromatographically. An extraction efficiency between 80 and 120 % was observed for all KBs. Accuracy was evaluated through spike and recovery using 10 random patient samples, with an average recovery of 85-115 % for all KBs and a coefficient of variation of ≤ 3 %. Coefficients of variation for intra- and inter-day imprecision were < 5 %, and the total imprecision was < 10 %. No significant interferences were observed. Specimens remained stable for up to 6 h on ice or 2 h at room temperature.

Conclusions

The developed method is highly sensitive and robust. It has been validated for use with human serum and plasma, overcoming stability concerns and providing a reliable and efficient quantitative estimation of ketone bodies.

Enterobacteriaceae Growth Promotion by Intestinal Acylcarnitines, a Biomarker of Dysbiosis in Inflammatory Bowel Disease

BACKGROUND & AIMS

Altered plasma acylcarnitine levels are well-known biomarkers for a variety of mitochondrial fatty acid oxidation disorders and can be used as an alternative energy source for the intestinal epithelium when short-chain fatty acids are low. These membrane-permeable fatty acid intermediates are excreted into the gut lumen via bile and are increased in the feces of patients with inflammatory bowel disease (IBD).

METHODS

Herein, based on studies in human subjects, animal models, and bacterial cultures, we show a strong positive correlation between fecal carnitine and acylcarnitines and the abundance of Enterobacteriaceae in IBD where they can be consumed by bacteria both in vitro and in vivo.

RESULTS

Carnitine metabolism promotes the growth of Escherichia coli via anaerobic respiration dependent on the cai operon, and acetylcarnitine dietary supplementation increases fecal carnitine levels with enhanced intestinal colonization of the enteric pathogen Citrobacter rodentium.

CONCLUSIONS

In total, these results indicate that the increased luminal concentrations of carnitine and acylcarnitines in patients with IBD may promote the expansion of pathobionts belonging to the Enterobacteriaceae family, thereby contributing to disease pathogenesis.

Biochemical characterization of patients with dihydrolipoamide dehydrogenase deficiency

Dihydrolipoamide dehydrogenase (DLD; E3) oxidizes lipoic acid. Restoring the oxidized state allows lipoic acid to act as a necessary electron sink for the four mitochondrial keto-acid dehydrogenases: pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase, branched-chain α-keto-acid dehydrogenase, and 2-oxoadipate dehydrogenase. DLD deficiency (DLDD) is caused by biallelic pathogenic variants in DLD. Three major forms have been described: encephalopathic, hepatic, and myopathic, although DLDD patients exhibit overlapping phenotypes. Hyperlactatemia, hyperexcretion of tricarboxylic acid cycle (TCA) metabolites and branched-chain keto acids, increased plasma branched-chain amino acids and allo-isoleucine are intermittent metabolic abnormalities reported in patients with DLDD. However, the diagnostic performance of these metabolites has never been studied. Therefore, we sought to systematically evaluate the diagnostic utility of these biomarkers for DLDD. We retrospectively analyzed the results of biochemical testing of six unrelated DLDD patients, including values obtained during both well visits and acute decompensation episodes. Elevation of branched-chain amino acid concentrations was not consistently observed. We found that five of six patients in our cohort had a maximum lifetime value of allo-isoleucine of 6 μmol/L, showing that alloisoleucine elevations even during illness may be subtle. Urine organic acid analysis (UOA) during acute decompensation episodes was abnormal in all cases; however, the pattern of abnormalities had high intersubject variability. No single biomarker was universally present, even in patients experiencing metabolic decompensation. We also observed novel biochemical associations: three patients had hyperexcretion of TCA cycle metabolites during crisis; in two patients, 2-ketoadipic and 2-hydroxyadipic acids, by products of lysine degradation, were detected. We propose that these result from 2-oxoadipate dehydrogenase deficiency, an underappreciated biochemical abnormality in DLD. Given the diversity of biochemical profiles among the patients with DLDD, we conclude that accurate biochemical diagnosis relies on a high index of suspicion and multipronged biochemical analysis, including both plasma amino acid and urine organic acid quantitation during decompensation. Biochemical diagnosis during the well state is challenging. We emphasize the critical importance of multiple simultaneous biochemical tests for diagnosis and monitoring of DLDD. We also highlight the under-recognized role of DLD in the lysine degradation pathway. Larger cohorts of patients are needed to establish a correlation between the biochemical pattern and clinical outcomes, as well as a genotype-phenotype correlation.

Machine Learning in Laboratory Medicine: Recommendations of the IFCC Working Group

BACKGROUND

Machine learning (ML) has been applied to an increasing number of predictive problems in laboratory medicine, and published work to date suggests that it has tremendous potential for clinical applications. However, a number of groups have noted the potential pitfalls associated with this work, particularly if certain details of the development and validation pipelines are not carefully controlled.

METHODS

To address these pitfalls and other specific challenges when applying machine learning in a laboratory medicine setting, a working group of the International Federation for Clinical Chemistry and Laboratory Medicine was convened to provide a guidance document for this domain.

RESULTS

This manuscript represents consensus recommendations for best practices from that committee, with the goal of improving the quality of developed and published ML models designed for use in clinical laboratories.

CONCLUSIONS

The committee believes that implementation of these best practices will improve the quality and reproducibility of machine learning utilized in laboratory medicine.

SUMMARY

We have provided our consensus assessment of a number of important practices that are required to ensure that valid, reproducible machine learning (ML) models can be applied to address operational and diagnostic questions in the clinical laboratory. These practices span all phases of model development, from problem formulation through predictive implementation. Although it is not possible to exhaustively discuss every potential pitfall in ML workflows, we believe that our current guidelines capture best practices for avoiding the most common and potentially dangerous errors in this important emerging field.

Methodologies in Mitochondrial Testing: Diagnosing a Primary Mitochondrial Respiratory Chain Disorder

BACKGROUND

Mitochondria are cytosolic organelles within most eukaryotic cells. Mitochondria generate the majority of cellular energy in the form of adenosine triphosphate (ATP) through oxidative phosphorylation (OxPhos). Pathogenic variants in mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) lead to defects in OxPhos and physiological malfunctions (Nat Rev Dis Primer 2016;2:16080.). Patients with primary mitochondrial disorders (PMD) experience heterogeneous symptoms, typically in multiple organ systems, depending on the tissues affected by mitochondrial dysfunction. Because of this heterogeneity, clinical diagnosis is challenging (Annu Rev Genomics Hum Genet 2017;18:257-75.). Laboratory diagnosis of mitochondrial disease depends on a multipronged analysis that can include biochemical, histopathologic, and genetic testing. Each of these modalities has complementary strengths and limitations in diagnostic utility.

CONTENT

The primary focus of this review is on diagnosis and testing strategies for primary mitochondrial diseases. We review tissue samples utilized for testing, metabolic signatures, histologic findings, and molecular testing approaches. We conclude with future perspectives on mitochondrial testing.

SUMMARY

This review offers an overview of the current biochemical, histologic, and genetic approaches available for mitochondrial testing. For each we review their diagnostic utility including complementary strengths and weaknesses. We identify gaps in current testing and possible future avenues for test development.

2-Methylglutaconic acid as a biomarker in routine urine organic acids leading to the diagnosis of glutaric acidemia type I in a low excretor

GA1 (OMIM# 231670) is an organic aciduria caused by defective Glutaryl-CoA dehydrogenase (GCDH), encoded by GCDH. Early detection of GA1 is crucial to prevent patients from developing acute encephalopathic crisis and subsequent neurologic sequelae. Diagnosis of GA1 relies on elevated glutarylcarnitine (C5DC) in plasma acylcarnitine analysis and hyperexcretion of glutaric acid (GA) and 3-hydroxyglutaric acid (3HG) in urine organic acid (UOA) analysis. Low excretors (LE), however, exhibit subtly elevated or even normal plasma C5DC and urinary GA levels, leading to screening and diagnostic challenges. The measurement of 3HG in UOA is thus often used as the 1st tier test for GA1. We described a case of LE detected via newborn screen with normal excretion of GA, absent of 3HG and increased 2-methylglutaconic acid (2MGA), which was detected at 3 mg/g creatinine (reference interval <1 mg/g creatinine) without appreciable ketones. We retrospectively examined UOA of 8 other GA1 patients and the 2MGA level ranged from 2.5 to 27.39 mg/g creatinine, which is significantly higher than normal controls (0.05-1.61 mg/g creatinine). Although the underlying mechanism of 2MGA formation in GA1 is unclear, our study suggests 2MGA is a biomarker for GA1 and should be monitored by routine UOA to evaluate its diagnostic and prognostic value.

Mitochondrial dysfunction in inflammatory bowel disease alters intestinal epithelial metabolism of hepatic acylcarnitines

As the interface between the gut microbiota and the mucosal immune system, there has been great interest in the maintenance of colonic epithelial integrity through mitochondrial oxidation of butyrate, a short-chain fatty acid produced by the gut microbiota. Herein, we showed that the intestinal epithelium could also oxidize long-chain fatty acids, and that luminally delivered acylcarnitines in bile could be consumed via apical absorption by the intestinal epithelium, resulting in mitochondrial oxidation. Finally, intestinal inflammation led to mitochondrial dysfunction in the apical domain of the surface epithelium that may reduce the consumption of fatty acids, contributing to higher concentrations of fecal acylcarnitines in murine Citrobacter rodentium-induced colitis and human inflammatory bowel disease. These results emphasized the importance of both the gut microbiota and the liver in the delivery of energy substrates for mitochondrial metabolism by the intestinal epithelium.

XPO1 inhibition with selinexor synergizes with proteasome inhibition in neuroblastoma by targeting nuclear export of IkB

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XPO1 is overabundant in high-risk neuroblastoma and correlates with poor survival.

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Neuroblastoma cells are sensitive to XPO1 inhibition with selinexor.

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Use of selinexor results in nuclear retention of IkB, diminishing NF-kB activity.

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Selinexor and bortezomib act synergistically through promotion of apoptosis.

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Synergy is mediated in part, through IkB regulation of NF-kB activity.

Across many cancer types in adults, upregulation of the nuclear-to-cytoplasmic transport protein Exportin-1 (XPO1) correlates with poor outcome and responsiveness to selinexor, an FDA-approved XPO1 inhibitor. Similar data are emerging in childhood cancers, for which selinexor is being evaluated in early phase clinical studies. Using proteomic profiling of primary tumor material from patients with high-risk neuroblastoma, as well as gene expression profiling from independent cohorts, we have demonstrated that XPO1 overexpression correlates with poor patient prognosis. Neuroblastoma cell lines are also sensitive to selinexor in the low nanomolar range. Based on these findings and knowledge that bortezomib, a proteasome inhibitor, blocks degradation of XPO1 cargo proteins, we hypothesized that combination treatment with selinexor and bortezomib would synergistically inhibit neuroblastoma cellular proliferation. We observed that selinexor promoted nuclear retention of IkB and that bortezomib augmented the ability of selinexor to induce cell-cycle arrest and cell death by apoptosis. This synergy was abrogated through siRNA knockdown of IkB. The synergistic effect of combining selinexor and bortezomib in vitro provides rationale for further investigation of this combination treatment for patients with high-risk neuroblastoma.

Facilitating Test Status Information Communication in the Time of COVID-19

The Coronavirus 2019 pandemic has strained nearly every aspect of pathology practice, including preanalytic, analytic, and postanalytic processes. Much of the challenges result from high demand for limited severe acute respiratory syndrome coronavirus 2 testing capacity, a resource required to facilitate patient flow throughout the hospital system and society at large. At our institution, this led to unprecedented increases in inquiries from providers to laboratory staff relating to the expected time to result for their patients. The demand was great enough to require redeployment of staff to handle the laboratory call volume. Although these data are available in our laboratory information system, the data do not interface to our electronic health record system. We developed systems using the R statistical programming language that abstract the necessary data regarding severe acute respiratory syndrome coronavirus 2 polymerase chain reaction testing from our lab system in real time, store it, and present it to clinicians for on demand querying. These data have been accessed over 2500 times by over 100 distinct users. Median length of each user session is approximately 4.9 minutes. Because our lab information system does not persistently store tracking information while our system does, we have been able to iteratively recalculate time to result values for each tracking stop as workflows have changed over time. Facility with informatics and programming concepts coupled with clinical understanding have allowed us to swiftly develop and iterate on applications which provide efficiency gains, allowing laboratory resources to focus on generating test results for our patients.

Big Data Everywhere: The Impact of Data Disjunction in the Direct-to-Consumer Testing Model

The recent increase in accessible medical and clinical laboratory "Big Data" has led to a corresponding increase in the use of machine-learning tools to develop integrative diagnostic models incorporating both existing and new test data. The rise of direct-to-consumer (DTC) testing paradigms raises the possibility of predictive models that use these new sources. This article discusses several distinct challenges raised by the DTC approach, including issues of centralized data collection, ascertainment bias, linkage to medical outcomes, and standardization/harmonization of results. Several solutions to maximize the promise of machine-learning data analytics for DTC data are suggested.

Advancing Clinicopathologic Diagnosis of High-risk Neuroblastoma Using Computerized Image Analysis and Proteomic Profiling

A subset of patients with neuroblastoma are at extremely high risk for treatment failure, though they are not identifiable at diagnosis and therefore have the highest mortality with conventional treatment approaches. Despite tremendous understanding of clinical and biological features that correlate with prognosis, neuroblastoma at ultra-high risk for treatment failure remains a diagnostic challenge. As a first step towards improving prognostic risk stratification within the high-risk group of patients, we determined the feasibility of using computerized image analysis and proteomic profiling on single slides from diagnostic tissue specimens. After expert pathologist review of tumor sections to ensure quality and representative material input, we evaluated multiple regions of single slides as well as multiple sections from different patients' tumors using computational histologic analysis and semiquantitative proteomic profiling. We found that both approaches determined that intertumor heterogeneity was greater than intratumor heterogeneity. Unbiased clustering of samples was greatest within a tumor, suggesting a single section can be representative of the tumor as a whole. There is expected heterogeneity between tumor samples from different individuals with a high degree of similarity among specimens derived from the same patient. Both techniques are novel to supplement pathologist review of neuroblastoma for refined risk stratification, particularly since we demonstrate these results using only a single slide derived from what is usually a scarce tissue resource. Due to limitations of traditional approaches for upfront stratification, integration of new modalities with data derived from one section of tumor hold promise as tools to improve outcomes.

Evaluation of a research use only luminex based assay for measurement of procalcitonin in serum samples

Research use only (RUO) assays do not undergo a validation process similar to test kits used for clinical purposes. Several studies have suggested that RUO assays need to be validated prior to use in any research studies. We evaluated a research use only Luminex platform based assay for measuring serum procalcitonin levels (Bio-Plex Pro^TM Human Acute Phase Multiplex Assay, Bio-Rad Laboratories, Hercules, CA) for comparability with an FDA cleared assay for procalcitonin (VIDAS B.R.A.H.M.S. PCT Assay, bioMérieux, Durham, NC). We tested 1,072 serum samples collected from patients with suspected sepsis in an intensive care unit setting for the comparison. There was poor correlation of the luminex based assay (r=0.081) with the VIDAS PCT Assay in the clinically relevant measurement range (<10 ng/mL). Additionally the Bio-Plex assay showed poor precision. Mass-spectrometry analysis of material eluted from PCT beads did not reveal any identifiable procalcitonin. The results show that research use only assays need to be validated to determine their suitability for research studies.

A clinical measure of DNA methylation predicts outcome in de novo acute myeloid leukemia

BACKGROUND

Variable response to chemotherapy in acute myeloid leukemia (AML) represents a major treatment challenge. Clinical and genetic features incompletely predict outcome. The value of clinical epigenetic assays for risk classification has not been extensively explored. We assess the prognostic implications of a clinical assay for multilocus DNA methylation on adult patients with de novo AML.

METHODS

We performed multilocus DNA methylation assessment using xMELP on samples and calculated a methylation statistic (M-score) for 166 patients from UPENN with de novo AML who received induction chemotherapy. The association of M-score with complete remission (CR) and overall survival (OS) was evaluated. The optimal M-score cut-point for identifying groups with differing survival was used to define a binary M-score classifier. This classifier was validated in an independent cohort of 383 patients from the Eastern Cooperative Oncology Group Trial 1900 (E1900; NCT00049517).

RESULTS

A higher mean M-score was associated with death and failure to achieve CR. Multivariable analysis confirmed that a higher M-score was associated with death (P = 0.011) and failure to achieve CR (P = 0.034). Median survival was 26.6 months versus 10.6 months for low and high M-score groups. The ability of the M-score to perform as a classifier was confirmed in patients ≤ 60 years with intermediate cytogenetics and patients who achieved CR, as well as in the E1900 validation cohort.

CONCLUSION

The M-score represents a valid binary prognostic classifier for patients with de novo AML. The xMELP assay and associated M-score can be used for prognosis and should be further investigated for clinical decision making in AML patients.

Vision Diagnoses Are Common After Concussion in Adolescents

OBJECTIVE

To determine the prevalence of vision diagnoses after concussion in adolescents.

METHODS

Cross-sectional study from July 1, 2013 to February 28, 2014, of patients aged 11 to 17 years with concussion evaluated in a comprehensive concussion program.

RESULTS

A total of 100 adolescents were examined, with a mean age of 14.5 years. Overall, 69% had one or more of the following vision diagnoses: accommodative disorders (51%), convergence insufficiency (49%), and saccadic dysfunction (29%). In all, 46% of patients had more than one vision diagnosis.

CONCLUSIONS

A high prevalence of vision diagnoses (accommodative, binocular convergence, and saccadic eye movement disorders) was found in this sample of adolescents with concussion, with some manifesting more than one vision diagnosis. These data indicate that a comprehensive visual examination may be helpful in the evaluation of a subset of adolescents with concussion. Academic accommodations for students with concussion returning to the classroom setting should account for these vision diagnoses.

Abstract 3290: Limited intra-tumor versus inter-tumor heterogeneity as assessed by proteomic profiling of high-risk neuroblastoma

Introduction: Tumor heterogeneity at a histological and molecular level has been previously described in neuroblastoma (NB) and therefore concern exists about how representative the molecular profile of a single tissue section can be of an entire tumor. We hypothesized that a single tissue section would provide a representative proteomic signature of the whole tumor.

Methods: As part of our effort to assess differential protein expression patterns from two maximally divergent groups with high-risk NB (i.e.: patients with early death from disease versus long-term survivors), we sampled multiple non-adjacent sections from blocks of 5 tumors within our larger cohort of 58 single section tumors. De-identified samples were obtained from the Children's Oncology Group biorepository. Using 5-10μ thick formalin fixed paraffin embedded tumor sections on a glass slide, we extracted 1 microgram of protein, performed tryptic digestion and desalting, and loaded peptides onto a reverse-phase column for separation by nanoflow chromatography. We performed peptide tandem mass spectrometry and protein expression vectors were identified using MaxQuant. The 1,495 most abundant proteins were evaluated across samples. Data were normalized and imputed. Hierarchical clustering analysis was performed using the pvclust R package between subjects with multiple sections and between all samples. We used average clustering criteria, correlation methods for distance, and pairwise covariance measures. Confidence of clusters was measured using approximately unbiased and bootstrap probability (1000 permutations) methods.

Results: Intra-tumor distance was significantly shorter than the inter-tumor distance. When testing only subjects with multiple tumor samples, 4 out of 5 samples from the same subject clustered with &gt;95% confidence. The samples from the remaining subject have a confidence &gt;80% but seem to have differing rates of missing data, suggesting experimental errors. When using all samples available, tumor samples from the same subject still clustered together and had a greater correlation than tumor samples from different subjects. A validation cohort of 7 distinct sections from separate blocks of tumors of 3 high-risk patients confirmed that tumors cluster by protein expression.

Conclusion and Future Directions: Intra-tumor heterogeneity exists but is significantly less than inter-tumor heterogeneity as assessed by proteomic profiling. We provide rationale to use single tissue section proteomics in ongoing research to define biologic drivers of primary refractory NB, a clinically important subgroup of patients who have highly lethal disease.

Citation Format: Raquel Castellanos, Katherine Heaton-Johnson, Jonathan Chung, Edward Nieves, Michael Fremed, Stephen R. Master, Daniel Weiser. Limited intra-tumor versus inter-tumor heterogeneity as assessed by proteomic profiling of high-risk neuroblastoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3290. doi:10.1158/1538-7445.AM2015-3290

Serum Fractalkine (CX3CL1) and Cardiovascular Outcomes and Diabetes: Findings From the Chronic Renal Insufficiency Cohort (CRIC) Study

BACKGROUND

Cardiometabolic disease is a major cause of morbidity and mortality in persons with chronic kidney disease (CKD). Fractalkine (CX3CL1) is a potential mediator of both atherosclerosis and metabolic disease. Studies of the relationship of CX3CL1 with risk of cardiovascular disease (CVD) events and metabolic traits are lacking, particularly in the high-risk setting of CKD.

STUDY DESIGN

Cross-sectional and longitudinal observational analysis.

SETTING & PARTICIPANTS

Adults with CKD from 7 US sites participating in the Chronic Renal Insufficiency Cohort (CRIC) Study.

PREDICTOR

Quartiles of plasma CX3CL1 levels at baseline.

OUTCOMES

Baseline estimated glomerular filtration rate from a creatinine and cystatin C-based equation, prevalent and incident CVD, diabetes, metabolic syndrome and its criteria, homeostatic model assessment of insulin resistance, hemoglobin A1c level, myocardial infarction, all-cause mortality, and the composite outcome of myocardial infarction/all-cause mortality.

RESULTS

Among 3,687 participants, baseline CX3CL1 levels were associated positively with several CVD risk factors and metabolic traits, lower estimated glomerular filtration rate, and higher levels of inflammatory cytokines, as well as prevalent CVD (OR, 1.09; 95% CI, 1.01-1.19; P=0.03). Higher CX3CL1 level also was associated with prevalent diabetes (OR, 1.26; 95% CI, 1.16-1.38; P<0.001) in adjusted models. During a mean follow-up of 6 years, there were 352 deaths, 176 myocardial infarctions, and 484 composite outcomes. In fully adjusted models, 1-SD higher CX3CL1 level increased the hazard for all-cause mortality (1.11; 95% CI, 1.00-1.22; P=0.02) and the composite outcome (1.09; 95% CI, 1.00-1.19; P=0.04).

LIMITATIONS

Study design did not allow evaluation of changes over time, correlation with progression of phenotypes, or determination of causality of effect.

CONCLUSIONS

Circulating CX3CL1 level may contribute to both atherosclerotic CVD and diabetes in a CKD cohort. Further studies are required to establish mechanisms through which CX3CL1 affects the pathogenesis of atherosclerosis and diabetes.

Higher Expression of miR-182 in Cytology Specimens of High-Grade Urothelial Cell Carcinoma: A Potential Diagnostic Marker

OBJECTIVE

MicroRNAs (miRs) are short noncoding RNA molecules that posttranscriptionally modulate protein expression. There are distinct miR alterations characterizing urothelial cell carcinoma (UCC) of the urinary bladder.

STUDY DESIGN

In this study, we investigate the possibility of using miR as a noninvasive marker in the screening of UCC. The total RNA was extracted from 75 cytology specimens including bladder or renal washings and voided urines. Cases comprise UCC (21 high grade and 6 low grade), 25 normal controls and 23 cases with a history of UCC but negative at the time of testing (negative with a positive history). The expressions of miR-96, miR-182, miR-183, miR-200c, miR-21, miR-141 and miR-30b were determined using quantitative TaqMan real-time PCR.

RESULTS AND CONCLUSION

This study shows that the level of miR-182 is higher in cytology specimens from high-grade UCC patients as compared to normal controls. Measuring miR-182 may provide a potential alternative or adjunct approach for screening high-grade UCC.

Identification of prolyl hydroxylation modifications in mammalian cell proteins

Prolyl hydroxylation is a PTM that plays an important role in the formation of collagen fibrils and in the oxygen-dependent regulation of hypoxia inducible factor-α (HIF-α). While this modification has been well characterized in the context of these proteins, it remains unclear to what extent it occurs in the remaining mammalian proteome. We explored this question using MS to analyze cellular extracts subjected to various fractionation strategies. In one strategy, we employed the von Hippel Lindau tumor suppressor protein, which recognizes prolyl hydroxylated HIF-α, as a scaffold for generating hydroxyproline capture reagents. We report novel sites of prolyl hydroxylation within five proteins: FK506-binding protein 10, myosin heavy chain 10, hexokinase 2, pyruvate kinase, and C-1 Tetrahydrofolate synthase. Furthermore, we show that identification of prolyl hydroxylation presents a significant technical challenge owing to widespread isobaric methionine oxidation, and that manual inspection of spectra of modified peptides in this context is critical for validation.

Supervised multi-view canonical correlation analysis (sMVCCA): integrating histologic and proteomic features for predicting recurrent prostate cancer

In this work, we present a new methodology to facilitate prediction of recurrent prostate cancer (CaP) following radical prostatectomy (RP) via the integration of quantitative image features and protein expression in the excised prostate. Creating a fused predictor from high-dimensional data streams is challenging because the classifier must 1) account for the "curse of dimensionality" problem, which hinders classifier performance when the number of features exceeds the number of patient studies and 2) balance potential mismatches in the number of features across different channels to avoid classifier bias towards channels with more features. Our new data integration methodology, supervised Multi-view Canonical Correlation Analysis (sMVCCA), aims to integrate infinite views of highdimensional data to provide more amenable data representations for disease classification. Additionally, we demonstrate sMVCCA using Spearman's rank correlation which, unlike Pearson's correlation, can account for nonlinear correlations and outliers. Forty CaP patients with pathological Gleason scores 6-8 were considered for this study. 21 of these men revealed biochemical recurrence (BCR) following RP, while 19 did not. For each patient, 189 quantitative histomorphometric attributes and 650 protein expression levels were extracted from the primary tumor nodule. The fused histomorphometric/proteomic representation via sMVCCA combined with a random forest classifier predicted BCR with a mean AUC of 0.74 and a maximum AUC of 0.9286. We found sMVCCA to perform statistically significantly (p < 0.05) better than comparative state-of-the-art data fusion strategies for predicting BCR. Furthermore, Kaplan-Meier analysis demonstrated improved BCR-free survival prediction for the sMVCCA-fused classifier as compared to histology or proteomic features alone.

Validation of DNA methylation to predict outcome in acute myeloid leukemia by use of xMELP

BACKGROUND

Epigenetic dysregulation involving alterations in DNA methylation is a hallmark of various types of cancer, including acute myeloid leukemia (AML). Although specific cancer types and clinical aggressiveness of tumors can be determined by DNA methylation status, the assessment of DNA methylation at multiple loci is not routinely performed in the clinical laboratory.

METHODS

We recently described a novel microsphere-based assay for multiplex evaluation of DNA methylation. In the current study, we validated and used an improved assay [termed expedited microsphere HpaII small fragment Enrichment by Ligation-mediated PCR (xMELP)] that can be performed with appropriate clinical turnaround time.

RESULTS

Using the xMELP assay in conjunction with a new 17-locus random forest classifier that has been trained using 344 AML samples, we were able to segregate an independent cohort of 70 primary AML patients into methylation-determined subgroups with significantly distinct mortality risk (P = 0.009). We also evaluated precision, QC parameters, and preanalytic variables of the xMELP assay and determined the sensitivity of the random forest classifier score to failure at 1 or more loci.

CONCLUSIONS

Our results demonstrate that xMELP performance is suitable for implementation in the clinical laboratory and predicts AML outcome in an independent patient cohort.

Urine neutrophil gelatinase-associated lipocalin and risk of cardiovascular disease and death in CKD: results from the Chronic Renal Insufficiency Cohort (CRIC) Study

BACKGROUND

Chronic kidney disease is common and is associated with increased cardiovascular disease risk. Currently, markers of renal tubular injury are not used routinely to describe kidney health and little is known about the risk of cardiovascular events and death associated with these biomarkers independent of glomerular filtration-based markers (such as serum creatinine or albuminuria).

STUDY DESIGN

Cohort study, CRIC (Chronic Renal Insufficiency Cohort) Study.

SETTING & PARTICIPANTS

3,386 participants with estimated glomerular filtration rate of 20 to 70mL/min/1.73m(2) enrolled from June 2003 through August 2008.

PREDICTOR

Urine neutrophil gelatinase-associated lipocalin (NGAL) concentration.

OUTCOMES

Adjudicated heart failure event, ischemic atherosclerotic event (myocardial infarction, ischemic stroke, or peripheral artery disease), and death through March 2011.

MEASUREMENTS

Urine NGAL measured at baseline with a 2-step assay using chemiluminescent microparticle immunoassay technology on an ARCHITECT i2000SR (Abbott Laboratories).

RESULTS

There were 428 heart failure events (during 16,383 person-years of follow-up), 361 ischemic atherosclerotic events (during 16,584 person-years of follow-up), and 522 deaths (during 18,214 person-years of follow-up). In Cox regression models adjusted for estimated glomerular filtration rate, albuminuria, demographics, traditional cardiovascular disease risk factors, and cardiac medications, higher urine NGAL levels remained associated independently with ischemic atherosclerotic events (adjusted HR for the highest [>49.5ng/mL] vs lowest [≤6.9ng/mL] quintile, 1.83 [95% CI, 1.20-2.81]; HR per 0.1-unit increase in log urine NGAL, 1.012 [95% CI, 1.001-1.023]), but not heart failure events or deaths.

LIMITATIONS

Urine NGAL was measured only once.

CONCLUSIONS

Among patients with chronic kidney disease, urine levels of NGAL, a marker of renal tubular injury, were associated independently with future ischemic atherosclerotic events, but not with heart failure events or deaths.

Defective Tibetan PHD2 binding to p23 links high altitude adaption to altered oxygen sensing

The Tibetan population has adapted to the chronic hypoxia of high altitude. Tibetans bear a genetic signature in the prolyl hydroxylase domain protein 2 (PHD2/EGLN1) gene, which encodes for the central oxygen sensor of the hypoxia-inducible factor (HIF) pathway. Recent studies have focused attention on two nonsynonymous coding region substitutions, D4E and C127S, both of which are markedly enriched in the Tibetan population. These amino acids reside in a region of PHD2 that harbors a zinc finger, which we have previously discovered binds to a Pro-Xaa-Leu-Glu (PXLE) motif in the HSP90 cochaperone p23, thereby recruiting PHD2 to the HSP90 pathway to facilitate HIF-α hydroxylation. We herein report that the Tibetan PHD2 haplotype (D4E/C127S) strikingly diminishes the interaction of PHD2 with p23, resulting in impaired PHD2 down-regulation of the HIF pathway. The defective binding to p23 depends on both the D4E and C127S substitutions. We also identify a PXLE motif in HSP90 itself that can mediate binding to PHD2 but find that this interaction is maintained with the D4E/C127S PHD2 haplotype. We propose that the Tibetan PHD2 variant is a loss of function (hypomorphic) allele, leading to augmented HIF activation to facilitate adaptation to high altitude.

Race modifies the association between adiposity and inflammation in patients with chronic kidney disease: findings from the chronic renal insufficiency cohort study

OBJECTIVE

The race-specific association of inflammation with adiposity and muscle mass in subjects with chronic kidney disease (CKD) was examined.

METHODS

Plasma concentration of interleukin (IL)-1β, IL-1 receptor antagonist (IL-1RA), IL-6, IL-10, tumor necrosis factor (TNF)-α, TGF-β, high-sensitivity C-reactive protein (hs-CRP), fibrinogen, and serum albumin was measured in 3,939 Chronic Renal Insufficiency Cohort study participants. Bioelectric impedance analysis was used to determine body fat mass (BFM) and fat-free mass (FFM).

RESULTS

Plasma levels of hs-CRP, fibrinogen, IL-1RA, IL-6, and TNF-α increased and serum albumin decreased across the quartiles of body mass index. In multivariable analysis, BFM and FFM were positively associated with hs-CRP, fibrinogen, IL-1β, IL-1RA, and IL-6. One standard deviation (SD) increase in BFM and FFM was associated with 0.36 (95% confidence interval [CI] = 0.33, 0.39) and 0.26 (95% CI = 0.22, 0.30) SD increase in log-transformed hs-CRP, respectively (P < 0.001). Race stratified analysis showed that the association between biomarkers and BFM and FFM differed by race, with Caucasians, demonstrating a stronger association with markers of inflammation than African Americans.

CONCLUSIONS

BFA and FFM are positively associated with markers of inflammation in patients with CKD. Race stratified analysis showed that Caucasians have a stronger association with markers of inflammation compared to African Americans.

Automated screening for myelodysplastic syndromes through analysis of complete blood count and cell population data parameters

The diagnosis of myelodysplastic syndromes (MDS) requires a high clinical index of suspicion to prompt bone marrow studies as well as subjective assessment of dysplastic morphology. We sought to determine if data collected by automated hematology analyzers during complete blood count (CBC) analysis might help to identify MDS in a routine clinical setting. We collected CBC parameters (including those for research use only and cell population data) and demographic information in a large (>5,000), unselected sequential cohort of outpatients. The cohort was divided into independent training and test groups to develop and validate a random forest classifier that identifies MDS. The classifier effectively identified MDS and had a receiver operating characteristic area under the curve (AUC) of 0.942. Platelet distribution width and the standard deviation of red blood cell distribution width were the most discriminating variables within the classifier. Additionally, a similar classifier was validated with an additional, independent set of >200 patients from a second institution with an AUC of 0.93. This retrospective study demonstrates the feasibility of identifying MDS in an unselected outpatient population using data routinely collected during CBC analysis with a classifier that has been validated using two independent data sets from different institutions.

Microsphere-based multiplex analysis of DNA methylation in acute myeloid leukemia

Aberrant regulation of DNA methylation is characteristic of cancer cells and clearly influences phenotypes of various malignancies. Despite clear correlations between DNA methylation and patient outcome, tests that directly measure multiple-locus DNA methylation are typically expensive and technically challenging. Previous studies have demonstrated that the prognosis of patients with acute myeloid leukemia can be predicted by the DNA methylation pattern of 18 loci. We have developed a novel strategy, termed microsphere HpaII tiny fragment enrichment by ligation-mediated PCR (MELP), to simultaneously analyze the DNA methylation pattern at these loci using methylation-specific DNA digestion, fluorescently labeled microspheres, and branched DNA hybridization. The method uses techniques that are inexpensive and easily performed in a molecular laboratory. MELP accurately reflects the methylation levels at each locus analyzed and segregates patients with acute myeloid leukemia into prognostic subgroups. Our results demonstrate the usefulness of MELP as a platform for simultaneous evaluation of DNA methylation of multiple loci.

Higher plasma CXCL12 levels predict incident myocardial infarction and death in chronic kidney disease: findings from the Chronic Renal Insufficiency Cohort study

AIMS

Genome-wide association studies revealed an association between a locus at 10q11, downstream from CXCL12, and myocardial infarction (MI). However, the relationship among plasma CXCL12, cardiovascular disease (CVD) risk factors, incident MI, and death is unknown.

METHODS AND RESULTS

We analysed study-entry plasma CXCL12 levels in 3687 participants of the Chronic Renal Insufficiency Cohort (CRIC) Study, a prospective study of cardiovascular and kidney outcomes in chronic kidney disease (CKD) patients. Mean follow-up was 6 years for incident MI or death. Plasma CXCL12 levels were positively associated with several cardiovascular risk factors (age, hypertension, diabetes, hypercholesterolaemia), lower estimated glomerular filtration rate (eGFR), and higher inflammatory cytokine levels (P < 0.05). In fully adjusted models, higher study-entry CXCL12 was associated with increased odds of prevalent CVD (OR 1.23; 95% confidence interval 1.14, 1.33, P < 0.001) for one standard deviation (SD) increase in CXCL12. Similarly, one SD higher CXCL12 increased the hazard of incident MI (1.26; 1.09,1.45, P < 0.001), death (1.20; 1.09,1.33, P < 0.001), and combined MI/death (1.23; 1.13-1.34, P < 0.001) adjusting for demographic factors, known CVD risk factors, and inflammatory markers and remained significant for MI (1.19; 1.03,1.39, P = 0.01) and the combined MI/death (1.13; 1.03,1.24, P = 0.01) after further controlling for eGFR and urinary albumin:creatinine ratio.

CONCLUSIONS

In CKD, higher plasma CXCL12 was associated with CVD risk factors and prevalent CVD as well as the hazard of incident MI and death. Further studies are required to establish if plasma CXCL12 reflect causal actions at the vessel wall and is a tool for genomic and therapeutic trials.

Interference From Anti-Streptavidin Antibody

Immunoassays are commonly used for clinical diagnosis, although interferences have been well documented. The streptavidin-biotin interaction provides an efficient and convenient method to manipulate assay components and is currently used in several immunoassay platforms. To date, there has been no report in the literature of interference from endogenous anti-streptavidin antibodies; however, such antibodies would potentially affect multiple diagnostic platforms. We report results from a patient being treated for thyroid dysfunction who demonstrated a T-uptake result of less than 0.2 and a nonlinear thyroid stimulating hormone dilution that suggested an immunoassay interference. Protein-A sepharose pretreatment corrected the nonlinear dilution and revealed an interference trend of falsely decreased results, as measured by sandwich assay, and falsely elevated results, as measured by competitive assay. The results of streptavidin-agarose adsorption were comparable to adsorption with protein-A sepharose. To our knowledge, this is the first published description of an endogenous anti-streptavidin antibody interfering with clinical laboratory assays.

Rap1 relocalization contributes to the chromatin-mediated gene expression profile and pace of cell senescence

Cellular senescence is accompanied by dramatic changes in chromatin structure and gene expression. Using Saccharomyces cerevisiae mutants lacking telomerase (tlc1Δ) to model senescence, we found that with critical telomere shortening, the telomere-binding protein Rap1 (repressor activator protein 1) relocalizes to the upstream promoter regions of hundreds of new target genes. The set of new Rap1 targets at senescence (NRTS) is preferentially activated at senescence, and experimental manipulations of Rap1 levels indicate that it contributes directly to NRTS activation. A notable subset of NRTS includes the core histone-encoding genes; we found that Rap1 contributes to their repression and that histone protein levels decline at senescence. Rap1 and histones also display a target site-specific antagonism that leads to diminished nucleosome occupancy at the promoters of up-regulated NRTS. This antagonism apparently impacts the rate of senescence because underexpression of Rap1 or overexpression of the core histones delays senescence. Rap1 relocalization is not a simple consequence of lost telomere-binding sites, but rather depends on the Mec1 checkpoint kinase. Rap1 relocalization is thus a novel mechanism connecting DNA damage responses (DDRs) at telomeres to global changes in chromatin and gene expression while driving the pace of senescence.

Fibroblast growth factor 23 is not associated with and does not induce arterial calcification

Elevated fibroblast growth factor 23 (FGF23) is associated with cardiovascular disease in patients with chronic kidney disease. As a potential mediating mechanism, FGF23 induces left ventricular hypertrophy; however, its role in arterial calcification is less clear. In order to study this, we quantified coronary artery and thoracic aorta calcium by computed tomography in 1501 patients from the Chronic Renal Insufficiency Cohort (CRIC) study within a median of 376 days (interquartile range 331-420 days) of baseline. Baseline plasma FGF23 was not associated with the prevalence or severity of coronary artery calcium after multivariable adjustment. In contrast, higher serum phosphate levels were associated with prevalence and severity of coronary artery calcium, even after adjustment for FGF23. Neither FGF23 nor serum phosphate were consistently associated with thoracic aorta calcium. We could not detect mRNA expression of FGF23 or its coreceptor, klotho, in human or mouse vascular smooth muscle cells, or normal or calcified mouse aorta. Whereas elevated phosphate concentrations induced calcification in vitro, FGF23 had no effect on phosphate uptake or phosphate-induced calcification regardless of phosphate concentration or even in the presence of soluble klotho. Thus, in contrast to serum phosphate, FGF23 is not associated with arterial calcification and does not promote calcification experimentally. Hence, phosphate and FGF23 promote cardiovascular disease through distinct mechanisms.

Candidate gene association study of coronary artery calcification in chronic kidney disease: findings from the CRIC study (Chronic Renal Insufficiency Cohort)

OBJECTIVES

This study sought to identify loci for coronary artery calcification (CAC) in patients with chronic kidney disease (CKD).

BACKGROUND

CKD is associated with increased CAC and subsequent coronary heart disease (CHD), but the mechanisms remain poorly defined. Genetic studies of CAC in CKD may provide a useful strategy for identifying novel pathways in CHD.

METHODS

We performed a candidate gene study (∼2,100 genes; ∼50,000 single nucleotide polymorphisms [SNPs]) of CAC within the CRIC (Chronic Renal Insufficiency Cohort) study (N = 1,509; 57% European, 43% African ancestry). SNPs with preliminary evidence of association with CAC in CRIC were examined for association with CAC in the PennCAC (Penn Coronary Artery Calcification) (N = 2,560) and AFCS (Amish Family Calcification Study) (N = 784) samples. SNPs with suggestive replication were further analyzed for association with myocardial infarction (MI) in the PROMIS (Pakistan Risk of Myocardial Infarction Study) (N = 14,885).

RESULTS

Of 268 SNPs reaching p < 5 × 10(-4) for CAC in CRIC, 28 SNPs in 23 loci had nominal support (p < 0.05 and in same direction) for CAC in PennCAC or AFCS. Besides chr9p21 and COL4A1, known loci for CHD, these included SNPs having reported genome-wide association study association with hypertension (e.g., ATP2B1). In PROMIS, 4 of the 23 suggestive CAC loci (chr9p21, COL4A1, ATP2B1, and ABCA4) had significant associations with MI, consistent with their direction of effect on CAC.

CONCLUSIONS

We identified several loci associated with CAC in CKD that also relate to MI in a general population sample. CKD imparts a high risk of CHD and may provide a useful setting for discovery of novel CHD genes and pathways.

Race and gender variation in response to evoked inflammation

BACKGROUND

Race- and gender-variation in innate immunity may contribute to demographic differences in inflammatory and cardiometabolic disease; yet their influence on dynamic responses during inflammatory stress is poorly understood. Our objective was to examine race and gender influence on the response to experimental endotoxemia.

METHODS

The Genetics of Evoked Responses to Niacin and Endotoxemia (GENE) study was designed to investigate regulation of inflammatory and metabolic responses during low-grade endotoxemia (LPS 1 ng/kg intravenously) in healthy individuals (median age 24, IQR=7) of European (EA; n=193, 47% female) and African ancestry (AA; n=101, 59% female).

RESULTS

Baseline clinical, metabolic, and inflammatory biomarkers by race and gender were consistent with epidemiological literature; pre-LPS cytokines (e.g. median (IQR) IL-6, 2.7 (2) vs.2.1 (2) pg/ml, P=0.001) were higher in AA than EA. In contrast, acute cytokine responses during endotoxemia were lower in AA than EA (e.g. median (IQR) peak IL-1RA, 30 (38) vs.43 (45) ng/ml P=0.002) as was the induction of hepatic acute-phase proteins (e.g. median (IQR) peak CRP 12.9 (9) vs.17.4 (12) mg/L P=0.005). Further, baseline levels of cytokines were only weakly correlated with peak inflammatory responses (all r(s) <0.2) both in AA and in EA. There were less pronounced and less consistent differences in the response by gender, with males having a higher AUC for CRP response compared to females (median (IQR) AUC: 185 (112) vs. 155 (118), P=0.02).

CONCLUSIONS

We observed lower levels of evoked inflammation in response to endotoxin in AA compared with EA, despite similar or higher baseline levels of inflammatory markers in AA. Our data also suggest that levels of inflammatory biomarkers measured in epidemiological settings might not predict the degree of acute stress-response or risk of diseases characterized by activation of innate immunity.

TRIAL REGISTRATION

FDA clinicaltrials.gov registration number NCT00953667.