Combined Analysis of Metabolomes, Proteomes, and Transcriptomes of Hepatitis C Virus-Infected Cells and Liver to Identify Pathways Associated With Disease Development

BACKGROUND & AIMS

The mechanisms of hepatitis C virus (HCV) infection, liver disease progression, and hepatocarcinogenesis are only partially understood. We performed genomic, proteomic, and metabolomic analyses of HCV-infected cells and chimeric mice to learn more about these processes.

METHODS

Huh7.5.1dif (hepatocyte-like cells) were infected with culture-derived HCV and used in RNA sequencing, proteomic, metabolomic, and integrative genomic analyses. uPA/SCID (urokinase-type plasminogen activator/severe combined immunodeficiency) mice were injected with serum from HCV-infected patients; 8 weeks later, liver tissues were collected and analyzed by RNA sequencing and proteomics. Using differential expression, gene set enrichment analyses, and protein interaction mapping, we identified pathways that changed in response to HCV infection. We validated our findings in studies of liver tissues from 216 patients with HCV infection and early-stage cirrhosis and paired biopsy specimens from 99 patients with hepatocellular carcinoma, including 17 patients with histologic features of steatohepatitis. Cirrhotic liver tissues from patients with HCV infection were classified into 2 groups based on relative peroxisome function; outcomes assessed included Child-Pugh class, development of hepatocellular carcinoma, survival, and steatohepatitis. Hepatocellular carcinomas were classified according to steatohepatitis; the outcome was relative peroxisomal function.

RESULTS

We quantified 21,950 messenger RNAs (mRNAs) and 8297 proteins in HCV-infected cells. Upon HCV infection of hepatocyte-like cells and chimeric mice, we observed significant changes in levels of mRNAs and proteins involved in metabolism and hepatocarcinogenesis. HCV infection of hepatocyte-like cells significantly increased levels of the mRNAs, but not proteins, that regulate the innate immune response; we believe this was due to the inhibition of translation in these cells. HCV infection of hepatocyte-like cells increased glucose consumption and metabolism and the STAT3 signaling pathway and reduced peroxisome function. Peroxisomes mediate β-oxidation of very long-chain fatty acids; we found intracellular accumulation of very long-chain fatty acids in HCV-infected cells, which is also observed in patients with fatty liver disease. Cells in livers from HCV-infected mice had significant reductions in levels of the mRNAs and proteins associated with peroxisome function, indicating perturbation of peroxisomes. We found that defects in peroxisome function were associated with outcomes and features of HCV-associated cirrhosis, fatty liver disease, and hepatocellular carcinoma in patients.

CONCLUSIONS

We performed combined transcriptome, proteome, and metabolome analyses of liver tissues from HCV-infected hepatocyte-like cells and HCV-infected mice. We found that HCV infection increases glucose metabolism and the STAT3 signaling pathway and thereby reduces peroxisome function; alterations in the expression levels of peroxisome genes were associated with outcomes of patients with liver diseases. These findings provide insights into liver disease pathogenesis and might be used to identify new therapeutic targets.

Sex specific relationships between infants' mental rotation ability and amiotic sex hormones

Sex differences in mental rotation, robust in adults, have recently been reported for infants' looking times although the pattern of results is not completely conclusive. In this context, organizational effects of gonadal steroids affecting the neural circuitry underlying spatial cognition could be (partly) responsible for the early sex difference. In the present study testosterone and estradiol levels measured in amniotic fluid via ultra performance liquid chromatography and tandem mass spectrometry were used to examine the role of prenatal sex hormones on infants' looking times during mental rotation. N = 208 six-month-old infants participated in an expectation of violation task with 3D cube figures. Mental rotation was defined as the difference in looking times for familiar versus mirrored cube figures whereas vigilance was defined as the sum of both looking times. Sex differences were absent for mental rotation as well as for vigilance. Most importantly, however, for boys mental rotation but not vigilance was correlated with prenatal testosterone but not with estradiol. For girls mental rotation but not vigilance was correlated with prenatal estradiol but not with testosterone although it has to be noted that the testosterone values for girls suffered from a floor effect. Only 5% of the within-sex variance was due to prenatal sex hormones indicating small effects. These findings extend our knowledge concerning organizational effects of prenatal sex hormones on the brain circuitry underlying spatial cognition.

Detection of the designer benzodiazepine metizolam in urine and preliminary data on its metabolism

Designer benzodiazepines provide an attractive alternative to prescribed benzodiazepines for abuse purposes as they are readily available via the Internet without control. Metizolam was ordered via the Internet and a 2 mg blue tablet was orally administered to a 54-year-old man. Urine samples were collected over 6 days in polypropylene tubes. After liquid/liquid extraction at pH 9.5, metizolam was analyzed by ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS) using a standard method devoted to benzodiazepines, and ions transitions, at m/z 328.9 > 275.0 and 328.9 > 300.0. Metizolam was detectable in hydrolyzed urine during the 46-h period, with concentrations always lower than 11 ng/mL. About 0.3% of the initial dose was excreted in urines as total unchanged metizolam during the first 24 h. The most relevant potential CYP- and UGT-dependent metabolites of metizolam were investigated in vitro using human liver microsome incubation and, subsequently, liquid chromatography coupled with quadrupole-time of flight mass spectrometry (UHPLC-Q-TOF-MS) analysis. Three mono-hydroxylated metabolites were produced including a hydroxylation compound at the 2-ethyl moiety of metizolam (M1) as quantitatively main metabolite, and a N-hydroxymetiazolam (M2). The structure of the third metabolite (M3) could not be elucidated because of a too low experimental production rate. Two authentic urine samples were analyzed using the same analytical method to search for metabolites of metizolam. M1, together with its glucuronide (M1-Glu), and M2 were observed in urine at the 8 h mark, whereas only M1 and M1-Glu were still detected in urine at 30 h post administration. Copyright © 2016 John Wiley & Sons, Ltd.

PON3 knockout mice are susceptible to obesity, gallstone formation, and atherosclerosis

We report the engineering and characterization of paraoxonase-3 knockout mice (Pon3KO). The mice were generally healthy but exhibited quantitative alterations in bile acid metabolism and a 37% increased body weight compared to the wild-type mice on a high fat diet. PON3 was enriched in the mitochondria-associated membrane fraction of hepatocytes. PON3 deficiency resulted in impaired mitochondrial respiration, increased mitochondrial superoxide levels, and increased hepatic expression of inflammatory genes. PON3 deficiency did not influence atherosclerosis development on an apolipoprotein E null hyperlipidemic background, but it did lead to a significant 60% increase in atherosclerotic lesion size in Pon3KO mice on the C57BL/6J background when fed a cholate-cholesterol diet. On the diet, the Pon3KO had significantly increased plasma intermediate-density lipoprotein/LDL cholesterol and bile acid levels. They also exhibited significantly elevated levels of hepatotoxicity markers in circulation, a 58% increase in gallstone weight, a 40% increase in hepatic cholesterol level, and increased mortality. Furthermore, Pon3KO mice exhibited decreased hepatic bile acid synthesis and decreased bile acid levels in the small intestine compared with wild-type mice. Our study suggests a role for PON3 in the metabolism of lipid and bile acid as well as protection against atherosclerosis, gallstone disease, and obesity.

Testing for GHB in hair by GC/MS/MS after a single exposure. Application to document sexual assault

Gamma-hydroxybutyric acid, or GHB, is a substance naturally present within mammal species. Properties of neurotransmitter or neuromodulator are generally given to this substance. GHB is therapeutically used as an anesthetic, but can be used for criminal offenses (date-rape drug). It appears that the window of detection of GHB is very short in both blood and urine, and therefore its presence is very difficult to prove after a rape case. In order to document single exposure, we investigated the use of hair. Hair was collected one month after the allegated event in order to sample the corresponding period after regular growing. After rapid (2 min) decontamination with dichloromethane, the hair shaft was cut into 3-mm segments. They were overnight incubated in 0.01 N NaOH in the presence of GHB-d6, followed by neutralization and extraction in ethyl acetate under acidic conditions. GHB (precursor ion m/z 233, product ions m/z 147 and 148) was tested by GC/MS/MS (Finnigan TSQ 700) after derivatization with BSTFA + 1% TMCS. Physiological concentrations (n = 24) were in the range 0.5 to 12.0 ng/mg, with no influence due to hair color. No variation of concentrations was observed along the hair shaft in controlled subjects, except for the proximal segment, due to an incorporation through sweat. This demonstrates that endogenous levels for each single subject are constant during hair growth. A controlled human administration of 25 mg/kg to a volunteer demonstrated that a single exposure to GHB is detectable in hair after segmentation. In a case of rape under influence, a clear increase of the corresponding segment (about 2.4 ng/mg) in time was observed, in comparison with the other segments (0.6 to 0.8 ng/mg). This study demonstrates that a single exposure to GHB in a case of sexual assault can be documented by hair analysis when collected about one month after the crime.

Doping control for beta-adrenergic compounds through hair analysis

An original procedure was developed to simultaneously test beta2-agonists (salbutamol and clenbuterol) and beta-blockers (atenolol, acebutolol, pindolol, betaxolol, propranolol, timolol, sotalol, metoprolol, tertatolol, bisoprolol, labetalol and oxprenolol) in both human and animal hair. After decontamination with methylene chloride (2 times, 2 min), a 200 mg hair strand is pulverized in a ball mill. Then, a 100 mg portion is incubated overnight in 2 mL 0.1 N HCl, at 56 degrees C, in the presence of carteolol, which was used as an internal standard. After neutralization of the acid phase with 0.1 N NaOH, a 2 mL bicarbonate buffer (pH 8.6) is added to the preparation, which is then purified by solid-phase extraction with Isolute C18 columns. Drugs are derivatized using a mixture of trimethylboroxine-ethyl acetate for 15 min at 80 degrees C to form methaneboronate derivatives. Drugs are detected using GC/MS on an HP 6890-5973 system. A 4 microL portion of the derivatized extract is injected using a pulsed mode in a 30 m HP5 MS capillary column. Linearity was observed for all compounds in the range 25 pg/mg to 10 ng/mg. Limits of detection were in the range 2 to 10 pg/mg. At 1 ng/mg, recoveries were in the range from 37 to 100%, with a within-run precision of 5.9 to 14.1% (n = 8). The application of the method can be documented by the following examples: (1) Hair from asthmatic patients (n - 11), including two cases of asthma deaths, tested positive for salbutamol in the range of 27 to 210 pg/mg. (2) A 24-year-old swimmer who tested positive in urine for salbutamnol denied the results. Hair analysis confirmed salbutamol exposure, with a concentration of 71 pg/mg. (3) A shooting specialist was assumed to chronically use metoprolol (100 mg/daily during some periods). Hair concentration of metoprolol was 8.41 ng/mg. (4) An archery specialist was assumed to chronically use sotalol (80 mg/daily, during some periods). Hair concentration of sotalol was 261 pg/mg. (5) Hair from two calves revealed chronic exposure to clenbuterol, which was used to increase the mass of the animals at a concentration of 30 and 48 pg/mg.

Are cannabinoids detected in hair after washing with Cannabio shampoo?

Today, cannabis plants are used in shampoo preparations, in foodstuffs (e.g., oils, noodles, crackers, etc.), and in beverages (e.g., tea). These products often contain < 1% delta9-tetrahydrocannabinol (THC) in order to eliminate psychoactive effects, but some of them can include 1 to 3% of THC. Gas chromatography-mass spectrometry (GC-MS) analysis of Cannabio shampoo revealed the presence of THC (412 ng/mL) and two constituents of cannabis plants, cannabidiol (CBD, 4079 ng/mL) and cannabinol (CBN, 380 ng/mL). In order to verify if normal hygiene practices with Cannabio shampoo can result in positive tests for cannabinoids in hair, three subjects washed their hair with this shampoo once daily for two weeks. After this period, hair specimens were collected. In the three hair specimens, THC, CBD, and CBN were never detected within their limits of detection, 0.05, 0.02, and 0.01 ng/mg, respectively. We concluded that the use of Cannabio shampoo during normal hygiene practices cannot be considered as a source of potential contamination of hair. In a second experiment, drug-free hair specimens (200 mg) were incubated in 10 mL water/Cannabio shampoo (20:1, v/v) for 30 min, 2 h, and 5 h. After incubation, hair strands were washed with water and separated into two portions. One portion was extracted directly; the second was decontaminated with methylene chloride and then extracted. After an incubation period of 30 min, the analysis of hair by GC-MS did not reveal the presence of THC, CBD, and CBN in hair, regardless of whether the hair was decontaminated. After an incubation period of 2 h, specimens tested positive for CBD (0.11 ng/mg without decontamination and 0.10 ng/mg with decontamination) and CBN (0.02 ng/mg without decontamination and 0.02 ng/mg after decontamination). After an incubation period of 5 h, specimens tested positive for CBD (0.25 ng/mg without decontamination and 0.14 ng/mg after decontamination) and CBN (0.02 ng/mg without decontamination and 0.02 ng/mg after decontamination). In all cases, THC was never detected. Extensive but unrealistic use of Cannabio shampoo can cause drug-free hair to test positive for CBD and CBN but not for the primary psychoactive drug THC.

Evaluation of acetylcodeine as a specific marker of illicit heroin in human hair

In addition to acetylmorphine (6-AM), acetylcodeine (AC) has been suggested as a marker for the use of illicit heroin. Because no procedure was available for AC testing in hair, a new method was developed for the simultaneous identification and quantitation of morphine (MOR), codeine (COD), 6-AM, and AC. After decontamination, each hair specimen was cut into 1-mm pieces. A 50-mg aliquot was incubated overnight at 50 degrees C in 1 mL Soerensen buffer (pH 7.6) in presence of 200 ng of MOR-d3, COD-d3, 6-AM-d3, and AC-d3. After pH adjustment to 8.4, the analytes were extracted in 5 mL of chloroform/isopropanol/n-heptane (25:10:65, v/v/v). The organic phase was removed and evaporated to dryness, and the residue was derivatized by silylation (BSTFA + 1% TMCS). Drugs were analyzed by gas chromatography-mass spectrometry in electron impact mode. Limits of quantitation were set to 0.1 ng/mg. Fifty hair specimens obtained from subjects who died from fatal opiate overdose were analyzed. AC was detected in 22 samples in concentrations ranging from 0.17 to 5.60 ng/mg with a mean value of 1.04 ng/mg. 6-AM was also present in these samples at concentrations ranging from 1.35 to 41.10 ng/mg with a mean value of 7.79 ng/mg. Of the 28 specimens negative for AC, 21 were positive for 6-AM at concentrations ranging from 0.18 to 7.13 ng/mg. When detected, the AC concentrations were an average of 15.5% (2.8 to 32.6%) of the 6-AM concentrations. There was a positive relationship between AC concentrations and 6-AM concentrations (r = 0.915, p = 0.001). Neither AC nor COD was identified in hair specimens collected from 20 subjects taking part in a heroin-maintenance program in Switzerland and receiving pure pharmaceutical heroin hydrochloride daily. Although it is indicative of illicit heroin use, AC would not make a suitable biomarker in place of 6-AM because of its low concentration in hair compared with that of 6-AM and its absence in about 50% of the specimens that tested positive for 6-AM.

Colchicine poisoning: report of a fatal case and presentation of an HPLC procedure for body fluid and tissue analyses

A case involving a suicidal overdose resulting from the ingestion of colchicine tablets is presented. The drug was quantitated using liquid chromatography. The femoral blood level was 62 ng/mL, and the maximum concentration found in bile was 2921 ng/mL. Therefore, bile appears to be the sample of choice for toxicological analysis when a poisoning case involving colchicine is suspected.

Acute fatal poisoning with dichlorophen

A case is presented involving an acute fatality resulting from self-administered dichlorophen, a chlorophenol fungicide. The compound was quantified using gas chromatography/mass spectrometry after extraction with methyl-tert-butyl ether, derivatization by methylation and separation on a HP5-MS capillary column. The blood concentration was 9.77 mg/l and other drugs, including ethanol, were not detected.

Trichloroethanol is not a metabolite of alpha chloralose

Head space capillary gas chromatography was used to detect alpha chloralose and its potent metabolite, trichloroethanol in clinical and forensic cases. Although alpha chloralose was identified in blood and urine in all cases, trichloroethanol was never detected. In a fatal case the alpha chloralose concentration in blood was 151.3 mg/l. It was concluded that trichloroethanol is not a metabolite of alpha chloralose.

Detection of codeine and phenobarbital in sweat collected with a sweat patch

Six male and two female subjects participated in a clinical study to determine the time course, the cumulative excretion, the intrasubject variability, the influence of site application, and the concentrations of codeine or phenobarbital in sweat following administration of a single dose of the drug. The doses of codeine and phenobarbital were 90 and 100 mg. respectively. Sweat was collected by means of a Sudormed sweat patch. Patches were removed at specified times over 1 week, and the drug content was determined by gas chromatography-mass spectrometry using deuterated internal standards. Codeine was detectable at 1 h following the administration, and a plateau concentration was observed on the third day. The peak codeine concentration was observed during the 12-24-h period. Morphine was never detected in sweat. In contrast, phenobarbital was first observed 3 h after administration, and cumulative excretion was continual throughout the week. Intersubject variability was enormous, as the concentrations for the same dose were in a magnitude of 1-5. Concentrations were in the range of 2-127 and 0.5-33 ng per patch for codeine and phenobarbital, respectively. The influence of the site of patch application was evaluated by analysis of six patches, all removed at the same time (24 h) in two subjects receiving 90 mg codeine. Codeine concentrations differed by a magnitude of 1-3 according to the area of application: the upper arm, the back, and the ribs. These data suggest that the sweat patch technology can be useful for documenting drug use over a 1-week period of surveillance.

Comparison between GC-MS and the EMIT II, Abbott ADx, and Roche OnLine immunoassays for the determination of THCCOOH

Gas chromatography-mass spectrometry (GC-MS) and immunological methods, including the Syva enzyme multiplied immunoassay technique, the Abbott fluorescence polarization immunoassay, and the Roche OnLine immunoassay, were compared for the determination of 11-nor-delta 9-tetrahydrocannabinol-9- carboxylic acid (THCCOOH). The results of all three immunoassays were not in accordance with the GC-MS results in three cases of a 72-specimen panel. Only one false negative was observed using the OnLine immunoassay. The immunological methods compared favorably and are acceptable for detecting the presence of cannabis metabolites in urine. These results support the concept that all immunoassays for cannabinoids should be considered as screening procedures. No concentration correlation between GC-MS and the immunoassays could be established because of the different cross-reactivities of the metabolites.

The detection of opiate drugs in nontraditional specimens (clothing): a report of ten cases

We present a series of 10 fatalities involving opiate overdosage, in which morphine, codeine, and 6-monoacetylmorphine were identified and quantified, not only in postmortem biological samples, but also in pieces of underwear taken from the bodies. Small tissue samples (about 1 g) were cut off from several parts of the underwear, stored at ambient temperature until analysis, then extracted by agitation in a mixture of chloroform/2-propanol/n-heptane (60:14:26, v/v/v) and assayed using GC/MS in the single ion monitoring mode. Morphine, codeine and 6-monoacetylmorphine concentrations were in the range 0.02 to 9.27 micrograms/g. These results indicate that the impregnation of underwear by sweat and sebaceous secretions and/or urine provides detectable levels of the drugs excreted by these ways. Even in the absence of biological samples, assaying pieces of clothing may bring some evidence about the drug abuser status of their owner.

Hair analysis for buprenorphine and its dealkylated metabolite by RIA and confirmation by LC/ECD

Hair samples were obtained from 14 subjects admitted 2 or 3 months previously to a detoxification center. All reported an history of intravenous heroin abuse. After decontamination by two dichloromethane washes, about 50 mg hair were pulverized in a ball mill and incubated at 56 degrees C overnight in 1 mL 0.1 HCl. After neutralization, buprenorphine analyzed by RIA was in the range of 0.01 to 0.47 ng/mg. To confirm buprenorphine, liquid chromatography was used. After neutralization, drugs were extracted with toluene at pH 8.5 during a 3-step extraction procedure. A portion of the reconstituted residue was injected into a Lichrosorb CN column, with a mobile phase of phosphate buffer (pH 4.0)-acetonitrile-1-heptane sulfonic acid-butylamine (85:17:2:0.01, v/v). Detection was achieved by coulometry, and the potential of the electrodes was 0.15 and 0.50 V, respectively. Linear calibration curves were obtained from 0.02 to 2.0 ng/mg with a correlation coefficient r > 0.99 for both drugs. The detection limit for the major metabolite was about 0.01 ng/mg and 0.02 ng/mg for buprenorphine, using a 50 mg hair sample. Recovery (at 0.2 ng/mg) was 54 and 62% for norbuprenorphine and buprenorphine, respectively. Drugs concentrations in hair were in the range 0.02-0.59 and not detected--0.15 ng/mg for buprenorphine and norbuprenorphine, respectively. Results suggest that a dose-response relationship exists between the concentration of buprenorphine in hair and the administered dose.

Ethylmorphine concentrations in human samples in an overdose case

Capillary gas chromatography coupled to mass spectrometry was employed to quantify ethylmorphine in biological fluids and tissues in a death attributed to oral ethylmorphine ingestion. The femoral blood concentration of the drug was 488 ng/ml. Hair analysis revealed the individual's drug abuse pattern, particularly the switching from heroin to ethylmorphine.

Toxicological data in a fatality involving cyamemazine

A fatality involving cyamemazine, a phenothiazine derivative, is presented. Cyamemazine was formally identified in postmortem blood using an HPLC-DAD screening procedure, and then quantified in some postmortem samples by means of a specific HPLC method. The blood concentration of cyamemazine was 9.8 micrograms/mL. Tissue distribution of cyamemazine is discussed in light of the existing literature.