Integrative Analysis of the Inflammatory Bowel Disease Serum Metabolome Improves Our Understanding of Genetic Etiology and Points to Novel Putative Therapeutic Targets.

BACKGROUND & AIMS: Polygenic and environmental factors are underlying causes of inflammatory bowel disease (IBD). We hypothesized that integration of the genetic loci controlling a metabolite's abundance, with known IBD genetic susceptibility loci, may help resolve metabolic drivers of IBD. METHODS: We measured the levels of 1300 metabolites in the serum of 484 patients with ulcerative colitis (UC) and 464 patients with Crohn's disease (CD) and 365 controls. Differential metabolite abundance was determined for disease status, subtype, clinical and endoscopic disease activity, as well as IBD phenotype including disease behavior, location, and extent. To inform on the genetic basis underlying metabolic diversity, we integrated metabolite and genomic data. Genetic colocalization and Mendelian randomization analyses were performed using known IBD risk loci to explore whether any metabolite was causally associated with IBD. RESULTS: We found 173 genetically controlled metabolites (metabolite quantitative trait loci, 9 novel) within 63 non-overlapping loci (7 novel). Furthermore, several metabolites significantly associated with IBD disease status and activity as defined using clinical and endoscopic indexes. This constitutes a resource for biomarker discovery and IBD biology insights. Using this resource, we show that a novel metabolite quantitative trait locus for serum butyrate levels containing ACADS was not supported as causal for IBD; replicate the association of serum omega-6 containing lipids with the fatty acid desaturase 1/2 locus and identify these metabolites as causal for CD through Mendelian randomization; and validate a novel association of serum plasmalogen and TMEM229B, which was predicted as causal for CD. CONCLUSIONS: An exploratory analysis combining genetics and unbiased serum metabolome surveys can reveal novel biomarkers of disease activity and potential mediators of pathology in IBD.

Pandora box of BCA assay. Investigation of the accuracy and linearity of the microplate bicinchoninic protein assay: Analytical challenges and method modifications to minimize systematic errors.

Bicinchoninic colorimetric assay is very widely used for total protein quantitative analysis. We report that bicinchoninic (BCA) total protein assay linearity range and the assay sensitivity are counterbalancing factors. BCA assay true linear range may be considerably narrower than the 20-2000 µg/ml and therefore the choice of the assay calibration range should not solely be dictated by the general recommendations of the user guide, however by the test specific needs and subsequent assay quality control. Expanding the BCA assay range up to 2000 µg/ml comes together with unavoidable heavy negative biases at low protein concentrations. The negative bias at low protein concentration only exacerbates with longer incubation time and/or increased sample to working reagent ratio. To minimize the lack of accuracy at low protein concentration of a wide range BCA assay, we proposing an alternative approach: a two-step incubation and calibration. With a minimum of extra work, the two-step incubation/calibration approach is devoid of the standard BCA workflow disadvantages and biases.

Insulin enhances glucose-stimulated insulin secretion in healthy humans.

Islet beta-cells express both insulin receptors and insulin-signaling proteins. Recent evidence from rodents in vivo and from islets isolated from rodents or humans suggests that the insulin signaling pathway is physiologically important for glucose sensing. We evaluated whether insulin regulates beta-cell function in healthy humans in vivo. Glucose-induced insulin secretion was assessed in healthy humans following 4-h saline (low insulin/sham clamp) or isoglycemic-hyperinsulinemic (high insulin) clamps using B28-Asp insulin that could be immunologically distinguished from endogenous insulin. Insulin and C-peptide clearance were evaluated to understand the impact of hyperinsulinemia on estimates of beta-cell function. Preexposure to exogenous insulin increased the endogenous insulin secretory response to glucose by approximately 40%. C-peptide response also increased, although not to the level predicted by insulin. Insulin clearance was not saturated at hyperinsulinemia, but metabolic clearance of C-peptide, assessed by infusion of stable isotope-labeled C-peptide, increased modestly during hyperinsulinemic clamp. These studies demonstrate that insulin potentiates glucose-stimulated insulin secretion in vivo in healthy humans. In addition, hyperinsulinemia increases C-peptide clearance, which may lead to modest underestimation of beta-cell secretory response when using these methods during prolonged dynamic testing.

Integration of transcriptomes of senescent cell models with multi-tissue patient samples reveals reduced COL6A3 as an inducer of senescence.

Senescent cells are a major contributor to age-dependent cardiovascular tissue dysfunction, but knowledge of their in vivo cell markers and tissue context is lacking. To reveal tissue-relevant senescence biology, we integrate the transcriptomes of 10 experimental senescence cell models with a 224 multi-tissue gene co-expression network based on RNA-seq data of seven tissues biopsies from ∼600 coronary artery disease (CAD) patients. We identify 56 senescence-associated modules, many enriched in CAD GWAS genes and correlated with cardiometabolic traits-which supports universality of senescence gene programs across tissues and in CAD. Cross-tissue network analyses reveal 86 candidate senescence-associated secretory phenotype (SASP) factors, including COL6A3. Experimental knockdown of COL6A3 induces transcriptional changes that overlap the majority of the experimental senescence models, with cell-cycle arrest linked to modulation of DREAM complex-targeted genes. We provide a transcriptomic resource for cellular senescence and identify candidate biomarkers, SASP factors, and potential drivers of senescence in human tissues.

Absolute measurement of internal volume changes inside the pulse damper: discrepancy between delay and dwell volumes.

We have developed a novel technique for the absolute determination of the mobile phase volume stored inside of a variable volume pulse damper at different pressures. Using an Agilent HPLC pulse damper we found a linear volume increase of approximately 1 microL/bar. We found that pump pressurization is a relatively slow process and takes approximately 1 min to reach 90% and takes approximately 2 min to reach 99% equilibration at flow rates below 1 mL/min. During pump pressurization, column flow rate will be less than the pre-set, since part of the mobile phase is retained inside of the pulse damper. During our experiments we observed a discrepancy between data obtained by UV techniques and direct absolute measurements. This difference can be explained by a fundamental difference between the gradient delay volume and dead (dwell) volume.

Reduction in delay time of high-dwell volume pumps in LC-MS applications using short-term low-ratio split flow.

We present a simple hardware design which reduces run time of gradient-based LC/MS applications and improves system equilibration. Our approach does not sacrifice efficiency of chromatographic separation, and does not affect analyte retention time and therefore does not require revalidation. Our technical design is based on a six-port/two-position switching valve and flow splitter installed prior to the LC column. This design minimizes time delays caused by the high-dwell volume of some LC pumps. Implementation of short-term (40-55 s) low-ratio (1:10) flow splitting reduced delay times by over four-fold in our application. This approach allowed hardware-associated time delays to be minimized. Alternative plumbing suggestions are also discussed.

High dead volume pumps: delay time reduction by short-term low-ratio split flow in LC/MS applications.

The aim of our work was to develop a low-cost, simple and reliable solution to reduce LC/MS analysis time by compensating for limitations inherent to high dead volume standard HPLC pumps. In our approach, we utilized a temporary (sub-1 min) low ratio flow split (approximately 1:10) at 5 mL/min pump flow before the column. During this short period, 90% of the entire pump flow is delivered to waste and used for fast pump/system equilibration. Although full-time flow splitting is widely used in capillary/nano applications (usually with high split ratios in the hundreds or thousands), to our knowledge, this is the first time that short-term low-ratio flow splitting has been used in conventional LC/MS applications.

Development of high throughput LC/MS/MS method for analysis of perfluorooctanoic acid from serum, suitable for large-scale human biomonitoring.

A simple method for determination of perfluorooctanoic acid (PFOA) from human serum by liquid chromatography/tandem mass spectrometry (LC/MS/MS) and utilizing high-throughput sample preparation was developed by New York State Public Health Emergency Preparedness Laboratory and used for biomonitoring studies. 50µl of serum was mixed with a 0.4ml of acetonitrile containing isotopically labeled internal standard, followed by phospholipid removal/protein precipitation. The extract was partially dried and analyzed by LC/MS/MS. The linear range of PFOA analysis was 0.5-100ng/ml. LLOQ was selected as 0.5ng/ml. The method was validated following APHL guidelines for LRN-C laboratories and about 6000 specimens were successfully prepared and analyzed using this simple LC/MS method. Due to sample preparation simplicity, the presented method can be used in large-scale clinical testing, such as public health surveillance studies.

Evaluation of matrix effect and chromatography efficiency: new parameters for validation of method development.

From the viewpoint of regulatory guidelines, validation of LC-UV and LC-MS based methods have the same requirements. Matrix effects are not considered for most method validations if they do not influence reproducibility or assay linearity. Since matrix effects can strongly suppress ionizaton efficiency and therefore reduce sensitivity, they must be evaluated (and discussed in the context of method development)--prior to method qualification. The severity of matrix effects is directly dependent upon chromatographic performance. We suggest that evaluation of matrix effects and LC efficiency is essential information for method assessment, optimization and transfer to other mass spectrometers, and should be a mandatory part of routine LC/MS method validation.

Sensitive LC MS quantitative analysis of carbohydrates by Cs+ attachment.

The development of a sensitive assay for the quantitative analysis of carbohydrates from human plasma using LC/MS/MS is described in this paper. After sample preparation, carbohydrates were cationized by Cs(+) after their separation by normal phase liquid chromatography on an amino based column. Cesium is capable of forming a quasi-molecular ion [M + Cs](+) with neutral carbohydrate molecules in the positive ion mode of electrospray ionization mass spectrometry. The mass spectrometer was operated in multiple reaction monitoring mode, and transitions [M + 133] --> 133 were monitored (M, carbohydrate molecular weight). The new method is robust, highly sensitive, rapid, and does not require postcolumn addition or derivatization. It is useful in clinical research for measurement of carbohydrate molecules by isotope dilution assay.

Novel, highly robust method of carbohydrate pre-purification by two-dimensional liquid chromatography prior to liquid chromatography/mass spectrometry or gas chromatography/mass spectrometry.

We describe a novel two-dimensional liquid chromatography (2D-LC) method for fast and robust isolation and concentration of low abundant carbohydrates (sorbitol, glycerol) from biological matrices (plasma and urine). Off-line pre-purified fractions, enriched by analyte of interest, were analyzed by liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS-MS). Initial 2D-LC automated sample pre-purification improved MS detection, eliminated matrix effects, and achieved high sensitivity (picogram detection limit) with a 6 min runtime and increased column lifetime. Using this method we have analyzed more than 1300 samples from biological matrices without column replacement.

Acute elevation of NEFA causes hyperinsulinemia without effect on insulin secretion rate in healthy human subjects.

Increased circulating levels of nonesterified free fatty acids (NEFA) have been observed in such hyperinsulinemic states as obesity, impaired glucose tolerance, diabetes, and dyslipidemia where they have been causally linked to the development of insulin resistance and hyperinsulinemia. The concentration of NEFA in plasma is believed to have direct modifying effects on insulin secretion and clearance. It remains controversial whether acute increases in NEFA potentiate insulin secretion in human subjects. We studied the effect of an acute elevation of NEFA during lipid-heparin infusion compared to a glycerol-only control on glucose-stimulated insulin secretion and clearance during a 120-min hyperglycemic (10 mM) clamp in 7 healthy normoglucose-tolerant volunteers. The metabolic clearance rate of C-peptide (MCR(CP)) was measured in each subject during the study by simultaneous infusion of C-peptide. Insulin secretion rate (ISR) was calculated from deconvolution of C-peptide data after correction for the rate of C-peptide infusion. Clearance rate of insulin (MCR(INS)) was calculated based upon endogenous ISR. Plasma glucose (mg/dL): basal (90-115 min) 90.2 +/- 2.8 vs. 90.2 +/- 2.3; clamp (150-240 min) 180.5 +/- 2.8 vs. 180.9 +/- 1.3. Plasma insulin (pmol/L): prebasal (fasting) 29.6 +/- 10.0 vs. 29.8 +/- 10.6; basal (90-115 min) 30.1 +/- 9.2 vs. 34.5 +/- 12.1; second phase clamp (210-240 min) 127.6 +/- 18.2 vs. 182.5 +/- 17.3*. Plasma NEFA (mM): prebasal 0.47 +/- 0.08 vs. 0.52 +/- 0.09; basal 0.35 +/- 0.05 vs. 0.98 +/- 0.02*; clamp (122-240 min) 0.06 +/- 0.02 vs. 0.77 +/- 0.06*. ISR (pmol/min): prebasal 72.7 +/- 7.5 vs. 72.0 +/- 7.9; second phase clamp (210-240 min) 268.5 +/- 27.2 vs. 200.2 +/- 23.7. MCR(INS) (mL/min): prebasal 3393 +/- 488 vs. 3370 +/- 511; clamp 2284 +/- 505 vs. 1214 +/- 153* (*p < 0.05 glycerol vs. intralipid/heparin). This study demonstrates that acute NEFA elevation causes hyperinsulinemia due to a significant decrease in systemic insulin clearance without increasing rates of insulin secretion.

Human C-peptide Quantitation by LC-MS Isotope-Dilution Assay in Serum or Urine Samples.

In this communication we report a simple and efficient approach to C-peptide quantitation using isotope dilution mass-spectrometry analysis. The method facilitates quantitation of C-peptide levels at least one order of magnitude lower compared to concentration levels achieved with an IDA method reported previously. The improvement was due to more intensive sample preparation procedure that, in turn, makes it possible to increase the sample load without a corresponding increase in matrix effects. We also show the results of a comparison study with a second laboratory using a similar previously reported method for C-peptide quantitation.

Isotope dilution assay in peptide quantification: the challenge of microheterogeneity of internal standard.

Isotope dilution analysis allows quantitation of elements and different compounds in complex mixtures. The quantitation is based on a known amount of reference material (internal standard, IS) added to a sample that makes the result critically dependent on the value assigned to the standard. In the case of peptides, IS concentration is determined by nitrogen and amino acid analysis while purity is normally assessed by methods such as chromatography or electrophoresis that might not be able to detect many possible amino acid modifications, either naturally occurring or chemically induced. Microheterogeneity of the IS, if it is not accounted for when assigning a reference value to the standard, results in highly overestimated values in target analyte quantitation. In this viewpoint article, we illustrate the problem of internal standard microheterogeneity by analyzing synthetic human C-peptide labeled analogs.

Flow inconsistency: the evil twin of column switching--hardware aspects.

Solvent flow, generated by HPLC pumps is consistent and accurate. This statement, while true for single column (one dimensional) liquid chromatography applications, may not apply to column switching applications. Connection of pumps and/or columns to one flow path may cause substantial pressure changes. Immediate post valve switch pressure differences between pumps can cause backflow where the mobile phase stored at higher pressure will temporary flow into the lower pressure area. A more common side effect of column switching is flow inconsistency during pump pressurization. For the duration of pump pressurization, liquid flow through the column will be smaller than expected since the HPLC column acts like a flow restrictor.

Standardization of C-peptide measurements.

BACKGROUND: C-peptide is a marker of insulin secretion in diabetic patients. We assessed within- and between-laboratory imprecision of C-peptide assays and determined whether serum calibrators with values assigned by mass spectrometry could be used to harmonize C-peptide results. METHODS: We sent 40 different serum samples to 15 laboratories, which used 9 different routine C-peptide assay methods. We also sent matched plasma samples to another laboratory for C-peptide analysis with a reference mass spectrometry method. Each laboratory analyzed 8 of these samples in duplicate on each of 4 days to evaluate within- and between-day imprecision. The same 8 samples were also used to normalize the results for the remaining samples to the mass spectrometry reference method. RESULTS: Within- and between-run CVs ranged from <2% to >10% and from <2% to >18%, respectively. Normalizing the results with serum samples significantly improved the comparability among laboratories and methods. After normalization, the differences among laboratories in mean response were no longer statistically significant (P = 0.24), with least-squares means of 0.93-1.02. CONCLUSIONS: C-peptide results generated by different methods and laboratories do not always agree, especially at higher C-peptide concentrations. Within-laboratory imprecision also varied, with some methods giving much more consistent results than others. These data show that calibrating C-peptide measurement to a reference method can increase comparability between laboratories.

LC/MS quantitative study of glucose by iodine attachment.

We explored the potential of iodine attachment to improve the sensitivity of glucose measurement by LC/MS. After sample preparation, glucose was separated by normal phase chromatography, followed by anionization by I(-)-attachment prior to MS by post-column addition of a methanolic solution of iodoform. Iodine is capable of forming an anionic adduct with neutral monosaccharides in negative ion mode electrospray mass spectrometry. Quasi-molecular ions [M+I]- of glucose, and [6,6-(2)H2]glucose (abbreviated d2-glucose) internal standard were quantitated in selected ion monitoring (SIM) mode. Iodine attachment LC/MS analysis provided high sensitivity, superior to GC/MS. It greatly simplified sample preparation and increased throughput. The advantages of iodine attachment can be realized even on old mass spectrometers. A LOD of 50 pg glucose on column was achieved. Due to iodine's predisposition to sublimate, the iodoform concentration must be minimized, which adds complexity to method development. To optimize reagent concentration we developed an efficient and flexible gradient-based delivery platform. Strategy for method development with iodoform is given.

Nondigest liberation of biomarkers from plasma: a novel two-stage ultrafiltration approach.

A simple procedure for sample preparation of human plasma by two stages of ultrafiltration using one device is described. Our approach is useful for nondigest liberation of biomarkers bound to albumin and other plasma proteins. The analyte contained in the ultrafiltrate can be directly analyzed without additional sample preparation, and quantified by 2-D RP-RP LC/MS.

Calculating glucose fluxes during meal tolerance test: a new computational approach.

A new calculation method is proposed to quantify the endogenous glucose production (EGP), the glucose appearance rate due to meal ingestion (R(a meal)), and the glucose disposal (R(d)) during a three-tracer study design. The method utilizes the maximum likelihood theory combined with a regularization method to achieve a theoretically coherent computational framework. The method uses the two-compartment formulation of the glucose kinetics. Instead of assuming smoothness of unlabeled and labeled glucose concentrations, the method assumes that the EGP, the R(a meal), and the fractional glucose clearance are smooth, increasing plausibility of their individual estimates. The method avoids transformation of the measurement errors, which may skew the estimates of the EGP, R(a meal), and R(d) with the traditional approach. Finally, the sequential nature of the calculations is replaced by calculating the EGP, R(a meal), and R(d) in "one go" to avoid the propagation of the errors from the EGP and R(a meal) into R(d). An example study is shown demonstrating the utility of the approach. A better performance of the new method is demonstrated in a simulation study.

Trace LC/MS quantitative analysis of polypeptide biomarkers: impact of 1-D and 2-D chromatography on matrix effects and sensitivity.

We investigated the impact of one dimension (single reverse phase (RP) column) and two dimension (two different RP columns) chromatographic methods on SIM (MS) and multiple reaction monitoring (MRM; MS/MS) performance from human plasma. We find that MRM analysis is clearly preferable for 1-D applications; however, implementation of SIM detection in conjunction with 2-D separation technique resulted in an over 60-fold increase in analyte peak area and improved S/N compared to MRM for our analyte, human C-peptide. Implementation of a 2-D RP-RP technique with SIM detection is capable of eliminating matrix effects and greatly increases signal response and data quality. For two large peptides in complex biological samples, we found that a 2-D approach performed better than high quality sample preparation together with 1-D chromatography and MRM, even on a high-end mass spectrometer.