Identifying common and specific microRNAs expressed in peripheral blood mononuclear cell of type 1, type 2, and gestational diabetes mellitus patients

Abstract Background Regardless the regulatory function of microRNAs (miRNA), their differential expression pattern has been used to define miRNA signatures and to disclose disease biomarkers. To address the question of whether patients presenting the different types of diabetes mellitus could be distinguished on the basis of their miRNA and mRNA expression profiling, we obtained peripheral blood mononuclear cell (PBMC) RNAs from 7 type 1 (T1D), 7 type 2 (T2D), and 6 gestational diabetes (GDM) patients, which were hybridized to Agilent miRNA and mRNA microarrays. Data quantification and quality control were obtained using the Feature Extraction software, and data distribution was normalized using quantile function implemented in the Aroma light package. Differentially expressed miRNAs/mRNAs were identified using Rank products, comparing T1DxGDM, T2DxGDM and T1DxT2D. Hierarchical clustering was performed using the average linkage criterion with Pearson uncentered distance as metrics. Results The use of the same microarrays platform permitted the identification of sets of shared or specific miRNAs/mRNA interaction for each type of diabetes. Nine miRNAs (hsa-miR-126, hsa-miR-1307, hsa-miR-142-3p, hsa-miR-142-5p, hsa-miR-144, hsa-miR-199a-5p, hsa-miR-27a, hsa-miR-29b, and hsa-miR-342-3p) were shared among T1D, T2D and GDM, and additional specific miRNAs were identified for T1D (20 miRNAs), T2D (14) and GDM (19) patients. ROC curves allowed the identification of specific and relevant (greater AUC values) miRNAs for each type of diabetes, including: i) hsa-miR-1274a, hsa-miR-1274b and hsa-let-7f for T1D; ii) hsa-miR-222, hsa-miR-30e and hsa-miR-140-3p for T2D, and iii) hsa-miR-181a and hsa-miR-1268 for GDM. Many of these miRNAs targeted mRNAs associated with diabetes pathogenesis. Conclusions These results indicate that PBMC can be used as reporter cells to characterize the miRNA expression profiling disclosed by the different diabetes mellitus manifestations. Shared miRNAs may characterize diabetes as a metabolic and inflammatory disorder, whereas specific miRNAs may represent biological markers for each type of diabetes, deserving further attention.

Anwendung der CE-ICP-MS und RIMS sowie Entwicklung und Anwendung der CE-RIMS auf Umweltproben

Die vorliegende Arbeit wurde im Rahmen des Verbundprojektes „Wechselwirkung und Transport von Actiniden im natürlichen Tongestein unter Berücksichtigung von Huminstoffen und Tonorganika – Wechselwirkung von Neptunium und Plutonium mit natürlichem Tongestein“ durchgeführt. Diese Untersuchungen sollen die thermodynamische Datenbasis für Actiniden erweitern sowie Informationen zur Ableitung von Bewertungskriterien für die Endlagerung radioaktiver Abfälle in Ton als Wirtsgestein, insbesondere über das Rückhaltevermögen von Tongestein gegenüber Radionukliden, liefern. Dabei stand die Anwendung verschiedener Speziationstechniken wie CE-ICP-MS, UV/VIS und die apparative Entwicklung der CE-RIMS im Vordergrund. Es sollte das Verhalten von Plutonium in umweltrelevanten Medien und Konzentrationen, im Ultraspurenbereich, untersucht werden. Unabhängig davon sollten Uranproben aus dem 2. Weltkrieg und Umweltproben des Landesamts für Umwelt und Forsten Rheinland-Pfalz auf ihren Plutoniumgehalt analysiert werden. Dazu wurde zunächst ein neues ICP-MS-Gerät Agilent 7500ce in Betrieb genommen und auf die Verwendung in Kombination mit der Kapillarelektrophorese optimiert. Die erreichte Nachweisgrenze für die vier Oxidationsstufen des Pu beträgt 0,05 ppb des gesamten Plutoniums in Lösung. Mit Hilfe der CE-ICP-MS wurde die Redoxstabilität einer Mischung aus verschiedenen Oxidationszuständen des Plutoniums in Opalinus-Ton-Porenwasser und Vergleichsmedien unter aeroben und anaeroben Bedingungen mit der CE untersucht. Die Untersuchungen zeigen das Pu(III) bis zu 40 min im verwendeten Elektrolytsystem stabil ist und dann oxidiert wird. In Porenwasser wurde als vorherrschende Spezies Pu(V) bestimmt. Die Redoxstabilität von Pu(VI) wurde untersucht, dabei wurde festgestellt, dass sich Pu(VI) bereits durch einfaches Verdünnen reduzieren lässt. Weiterhin wurden die Kd-Werte für die Sorption von Plutonium an Opalinuston unter aeroben und anaeroben Bedingungen für Pu(III) und Pu(IV) im System Porenwasser/Opalinuston von Kd(aerob) Pu(III) ≈ 53 m3/kg, Kd(aerob) Pu(IV) ≈ 14 m3/kg, Kd(anaerob) Pu(III) ≈ 114 m3/kg, Kd(anaerob) Pu(IV) ≈ 178 m3/kg bestimmt. Ein weiterer Schwerpunkt der Arbeit war die Entwicklung, Optimierung und Anwendung der Kopplung CE-RIMS zur Speziation des Plutoniums im Ultraspurenbereich. Dies konnte erfolgreich in mehreren Schritten durchgeführt und an den Proben aus den Batchversuchen zur Kd-Wert Bestimmung angewandt werden. Der Memory-Effekt des an den Kapillarwänden sorbierenden Pu(IV) konnte mit der empfindlichen Kopplung CE-RIMS ebenfalls nachgewiesen werden.

Entwicklung eines Screeningverfahrens zum simultanen Nachweis von Opioiden in menschlichen Körperflüssigkeiten, Geweben und Haaren für forensisch-toxikologische und klinische Untersuchungen

In den letzten Jahren stieg in Deutschland der Gebrauch bzw. Missbrauch von Opioid-Analgetika zunehmend an. Das entwickelte Verfahren sollte unter Einbeziehung neuer Substanzen möglichst viele verschiedene Opioide und auch ihre pharmakologisch aktiven Stoffwechselprodukte berücksichtigen.rnVor Analyse wurden Blut-, Serum- oder Urinproben mit Phosphatpuffer versetzt und mittels Festphasenextraktion an C18-Säulenmaterial aufgearbeitet. Post-Mortem-Gewebematerial wurde mit isotonischer Kochsalzlösung versetzt, homogenisiert und anschließend durch eine Festphasenextraktion aufgereinigt. Haarproben wurden nach Zerkleinerung mit Methanol unter Ultrabeschallung extrahiert. Die Flüssigchromatographie gekoppelt mit Tandem-Massenspektrometrie (Elektrosprayionisation im positiven Modus) erwies sich als geeignetes Verfahren für die simultane Bestimmung der Opioide in biologischem Probenmaterial (Körperflüssigkeiten, Gewebe und Haaren). Der Multi-Analyt Assay erlaubt die quantitative Analyse von 35 verschiedenen Opioiden. Die Analyten wurden durch eine Phenyl-Hexyl Säule und einen Wasser/Acetonitril Gradienten durch eine UPLC 1290 Infinity gekoppelt mit einem 6490 Triple Quadrupol von Agilent Technologies separiert.rnDie LC/MS Methode zur simultanen Bestimmung von 35 Opioiden in Serum und Haaren wurde nach den Richtlinien der Gesellschaft für Toxikologische und Forensische Chemie (GTFCh) validiert. Im Fall der Serumvalidierung lagen die Nachweisgrenzen zwischen 0.02 und 0.6 ng/ml und die Bestimmungsgrenzen im Bereich von 0.1 bis 2.0 ng/ml. Die Kalibrationskurven waren für die Kalibrationslevel 1 bis 6 linear. Wiederfindungsraten lagen für alle Verbindungen zwischen 51 und 88 %, außer für Alfentanil, Bisnortiliidn, Pethidin und Morphin-3-Glucuronid. Der Matrixeffekt lag zwischen 86 % (Ethylmorphin) und 105 % (Desomorphin). Für fast alle Analyten konnten akzeptable Werte bei der Bestimmung der Genauigkeit und Richtigkeit nach den Richtlinien der GTFCh erhalten werden. Im Fall der Validierung der Haarproben lagen die Nachweisgrenzen zwischen 0.004 und 0.6 ng/Probe und die Bestimmungsgrenzen zwischen 0.1 ng/Probe und 2.0 ng/Probe. Für die Kalibrationslevel 1 bis 6 waren alle Kalibrationsgeraden linear. Die Wiederfindungsraten lagen für die Opioide im Bereich von 73.5 % (Morphin-6-Glucuronid) und 114.1 % (Hydrocodon). Die Werte für die Bestimmung der Richtigkeit lagen zwischen - 6.6 % (Methadon) und + 11.7 % (Pholcodin). Präzisionsdaten wurden zwischen 1.0 % für Dextromethorphan und 11.5 % für Methadon ermittelt. Die Kriterien der GTFCh konnten bei Ermittlung des Matrixeffekts für alle Substanzen erfüllt werden, außer für 6-Monoacetylmorphin, Bisnortilidin, Meperidin, Methadon, Morphin-3-glucuronid, Morphin-6-glucuronid, Normeperidin, Nortilidin und Tramadol.rnZum Test des Verfahrens an authentischem Probenmaterial wurden 206 Proben von Körperflüssigkeiten mit Hilfe der simultanen LC/MS Screening Methode untersucht. Über 150 Proben wurden im Rahmen von forensisch-toxikologischen Untersuchungen am Instituts für Rechtsmedizin Mainz analysiert. Dabei konnten 23 der 35 Opioide in den realen Proben nachgewiesen werden. Zur Untersuchung der Pharmakokinetik von Opioiden bei Patienten der anästhesiologischen Intensivstation mit Sepsis wurden über 50 Blutproben untersucht. Den Patienten wurde im Rahmen einer klinischen Studie einmal täglich vier Tage lang Blut abgenommen. In den Serumproben wurde hauptsächlich Sufentanil (0.2 – 0.8 ng/ml in 58 Fällen) und Piritramid (0.4 – 11 ng/ml in 56 Fällen) gefunden. Außerdem wurden die Proben von Körperflüssigkeiten und Gewebe von 13 verschiedenen Autopsiefällen mit Hilfe des Multi-Analyt Assays auf Opioide untersucht.rnIn einem zweiten Schritt wurde die Extraktions- und Messmethode zur Quantifizierung der 35 Opioide am Forensic Medicine Center in Ho Chi Minh City (Vietnam) etabliert. Insgesamt wurden 85 Herzblutproben von Obduktionsfällen mit Verdacht auf Opiatintoxikation näher untersucht. Der überwiegende Teil der untersuchten Fälle konnte auf eine Heroin- bzw. Morphin-Vergiftung zurückgeführt werden. Morphin wurde in 68 Fällen im Konzentrationsbereich 1.7 – 1400 ng/ml und der Heroinmetabolit 6-Monoactetylmorphin in 34 Fällen (0.3 – 160 ng/ml) nachgewiesen werden.rnSchließlich wurden noch 15 Haarproben von Patienten einer psychiatrischen Klinik, die illegale Rauschmittel konsumiert hatten, mit Hilfe der simultanen Opioid-LC/MS Screeningmethode gemessen. Die Ergebnisse der Untersuchung wurden mit früheren Auswertungen von gaschromatographischen Analysen verglichen. Es zeigte sich eine weitgehende Übereinstimmung der Untersuchungsergebnisse für die Opioide 6-Monoacetylmorphin, Morphin, Codein, Dihydrocodein und Methadon. Mit der LC/MS Methode konnten weitere Substanzen, wie zum Beispiel Bisnortilidin, Dextromethorphan und Tramadol in den Haarproben gefunden werden, die bislang nicht entdeckt worden waren.rn

ALTERNATING CURRENT DIELECTROPHORETIC MANIPULATION OF ERYTHROCYTES IN MEDICAL MICRODEVICE TECHNOLOGY

Medical microdevices have gained popularity in the past few decades because they allow the medical laboratory to be taken out into the field and for disease diagnostics to happen with a smaller sample volume, at a lower cost and much faster. Blood is the human body's most readily available and informative diagnostic fluid because of the wealth of information it provides about the body's general health including enzymatic, proteomic and immunological states. The purpose of this project is to optimize operating conditions and study ABO-Rh erythrocytes dielectrophoretic responses to alternating current electric signals. The end goal of this project is the creation of a relatively inexpensive microfluidic device, which can be used for the ABO-Rh typing of a blood sample. This dissertation presents results showing how blood samples of a known ABO- Rh blood type exhibit differing behavior to the same electrical stimulus based on their blood type. The first panel of donors and experiments, presented in Chapter 4 occurred when a sample of known blood type was injected into a microdevice with a T-shaped electrode configuration and the erythorcytes were found to rupture at a rate specific to their ABO-Rh blood type. The second set of experiments, presented in Chapter 5, were originally published in Electrophoresis in 20111. Novel in this work was the discovery that treatment of human erythrocytes with β-galactosidase successfully removed ABO surface antigens such that native A and B blood no longer agglutinated with the proper antibodies. This work was performed in a medium of conductivity 0.9S/m which is close to the measured conductivity of pooled plasma (~1.1S/m). The ability to perform dielectrophoresis experiments at physiological conductivities conditions is advantageous for future portable devices because the device/instrument would not need to store dilution buffers. The final results of this project, presented in Chapter 6, explore the entire dielectrophoretic spectra of the ABO-Rh erythrocytes including the cross-over frequency and the magnitudes of the positive or negative dielectrophoretic response. These were completed at lower medium conductivities of 0.1S/m and 0.01-0.04S/m. These results show that by using the sweep function built into the Agilent alternating current generator it is possible to explore how a single group of blood cells will react to rapid changes in frequency and will provide the user with curve that can be matched the theoretical dielectrophoretic response curves. As a whole this project shows that it is possible to distinguish human erythrocytes by their ABO-Rh blood type via three different dielectrophoretic methods. This work builds on the foundation of that it is possible to distinguish healthy from infected cells2-7, similar cell types1,7-14 and other work regarding the dielectrophoresis of human erythrocytes1,10,11. This work has implications in both medical diagnostics and future dielectrophoretic work because it has shown that ABO-Rh blood type is now a factor, which must be identified when working with a human blood sample. It also shows that the creation of a microfluidic device that subjects human erythrocytes to a dielectrophoretic impulse and then exports an ABO-Rh blood type is a near future possibility.

Time Dependence of Elimination of Different PEth Homologues in Alcoholics in Comparison with Social Drinkers

BACKGROUND: Phosphatidylethanol (PEth) is a direct marker of alcohol consumption, which has been known for almost 30 years. Each PEth molecule carries 2 fatty acids, which differ in chain length and degree of unsaturation. It is formed by means of phospholipase D in the presence of ethanol. Usually, this marker was used by quantification of the PEth homologue 16:0/18:1. The intention of this work was to get more information about the distribution and the quantity of the different PEth homologues. METHODS: Blood samples from 12 alcohol-dependent subjects were collected and analyzed during withdrawal therapy. For comparison, blood from 78 healthy social drinkers was also analyzed. PEth analysis was performed as follows: after liquid-liquid extraction, the homologues were separated on a Luna Phenyl Hexyl column, injected to an HPLC system (1100 system; Agilent) and identified by ESI-MS/MS (QTrap 2000; AB Sciex) using multiple reaction monitoring. RESULTS: PEth 16:0/18:1 is the major homologue comparing the area ratios of PEth homologues in blood samples from alcoholics. Additional prevalent homologues were PEth 16:0/18:2, 18:0/18:2, and 18:0/18:1. The homologues occurring in blood samples from alcoholics as well as from social drinkers were mostly the same, but differences among their distribution pattern were observed. CONCLUSIONS: In addition to the approach to quantitate the PEth homologue 16:0/18:1, this is a new and alternative proceeding for the differentiation between alcoholics and social drinkers using this alcohol consumption marker.

Circulating microRNA profiling in patients with advanced non-squamous NSCLC receiving bevacizumab/erlotinib followed by platinum-based chemotherapy at progression (SAKK 19/05).

OBJECTIVES Molecular subclassification of non small-cell lung cancer (NSCLC) is essential to improve clinical outcome. This study assessed the prognostic and predictive value of circulating micro-RNA (miRNA) in patients with non-squamous NSCLC enrolled in the phase II SAKK (Swiss Group for Clinical Cancer Research) trial 19/05, receiving uniform treatment with first-line bevacizumab and erlotinib followed by platinum-based chemotherapy at progression. MATERIALS AND METHODS Fifty patients with baseline and 24 h blood samples were included from SAKK 19/05. The primary study endpoint was to identify prognostic (overall survival, OS) miRNA's. Patient samples were analyzed with Agilent human miRNA 8x60K microarrays, each glass slide formatted with eight high-definition 60K arrays. Each array contained 40 probes targeting each of the 1347 miRNA. Data preprocessing included quantile normalization using robust multi-array average (RMA) algorithm. Prognostic and predictive miRNA expression profiles were identified by Spearman's rank correlation test (percentage tumor shrinkage) or log-rank testing (for time-to-event endpoints). RESULTS Data preprocessing kept 49 patients and 424 miRNA for further analysis. Ten miRNA's were significantly associated with OS, with hsa-miR-29a being the strongest prognostic marker (HR=6.44, 95%-CI 2.39-17.33). Patients with high has-miR-29a expression had a significantly lower survival at 10 months compared to patients with a low expression (54% versus 83%). Six out of the 10 miRNA's (hsa-miRN-29a, hsa-miR-542-5p, hsa-miR-502-3p, hsa-miR-376a, hsa-miR-500a, hsa-miR-424) were insensitive to perturbations according to jackknife cross-validation on their HR for OS. The respective principal component analysis (PCA) defined a meta-miRNA signature including the same 6 miRNA's, resulting in a HR of 0.66 (95%-CI 0.53-0.82). CONCLUSION Cell-free circulating miRNA-profiling successfully identified a highly prognostic 6-gene signature in patients with advanced non-squamous NSCLC. Circulating miRNA profiling should further be validated in external cohorts for the selection and monitoring of systemic treatment in patients with advanced NSCLC.

The search for the primary tumor in metastasized gastroenteropancreatic neuroendocrine neoplasm.

Gastroenteropancreatic neuroendocrine tumors (NETs) often present as liver metastasis from a carcinoma of unknown primary. We recently showed that primary NETs from the pancreas, small intestine and stomach as well as their respective liver metastases differ from each other by the expression profile of the three genes CD302, PPWD1 and ABHB14B. The gene and protein expression of CD302, PPWD1, and ABHB14B was studied in abdominal NET metastases to identify the site of the respective primary tumors. Cryopreserved tissue from NET metastases collected in different institutions (group A: 29, group B: 50, group C: 132 specimens) were examined by comparative genomic hybridization (Agilent 105 K), gene expression analysis (Agilent 44 K) (groups A and B) and immunohistochemistry (group C). The data were blindly evaluated, i.e. without knowing the site of the primary. Gene expression analysis correctly revealed the primary in the ileum in 94 % of the cases of group A and in 58 % of group B. A pancreatic primary was predicted in 83 % (group A) and 20 % (group B), respectively. The combined sensitivity of group A and B was 75 % for ileal NETs and 38 % for pancreatic NETs. Immunohistochemical analysis of group C revealed an overall sensitivity of 80 %. Gene and protein expression analysis of CD302 and PPWD1 in NET metastases correctly identifies the primary in the pancreas or the ileum in 80 % of the cases, provided that the tissue is well preserved. Immunohistochemical profiling revealed CD302 as the best marker for ileal and PPWD1 for pancreatic detection.

New insights into the performance of human whole-exome capture platforms.

Whole exome sequencing (WES) is increasingly used in research and diagnostics. WES users expect coverage of the entire coding region of known genes as well as sufficient read depth for the covered regions. It is, however, unknown which recent WES platform is most suitable to meet these expectations. We present insights into the performance of the most recent standard exome enrichment platforms from Agilent, NimbleGen and Illumina applied to six different DNA samples by two sequencing vendors per platform. Our results suggest that both Agilent and NimbleGen overall perform better than Illumina and that the high enrichment performance of Agilent is stable among samples and between vendors, whereas NimbleGen is only able to achieve vendor- and sample-specific best exome coverage. Moreover, the recent Agilent platform overall captures more coding exons with sufficient read depth than NimbleGen and Illumina. Due to considerable gaps in effective exome coverage, however, the three platforms cannot capture all known coding exons alone or in combination, requiring improvement. Our data emphasize the importance of evaluation of updated platform versions and suggest that enrichment-free whole genome sequencing can overcome the limitations of WES in sufficiently covering coding exons, especially GC-rich regions, and in characterizing structural variants.

Molecular dissolved organic matter composition and environmental parameters from a laboratory incubation study

Dissolved organic matter (DOM) in the oceans constitutes a major carbon pool involved in global biogeochemical cycles. More than 96% of the marine DOM resists microbial degradation for thousands of years. The composition of this refractory DOM (RDOM) exhibits a molecular signature which is ubiquitously detected in the deep oceans. Surprisingly efficient microbial transformation of labile into RDOM was shown experimentally, implying that microorganisms produce far more RDOM than needed to sustain the global pool. By assessing the microbial formation and transformation of DOM in unprecedented molecular detail for 3 years, we show that most of the newly formed RDOM is molecularly different from deep sea RDOM. Only <0.4% of the net community production was channeled into RDOM molecularly undistinguishable from deep sea DOM. Our study provides novel experimentally derived molecular evidence and data for global models on the production, turnover and accumulation of marine DOM.

Oxygen isotopes and Sr/Ca ratios of fossil corals from Bonaire

Explanations for the demise of the Classic Maya civilization on the Yucatán Peninsula during the Terminal Classic Period (TCP; CE 750-1050) are controversial. Multiyear droughts are one likely cause, but the role of the Caribbean Sea, the dominant moisture source for Mesoamerica, remains largely unknown. Here we present bimonthly resolved snapshots of reconstructed sea surface temperature (SST) and salinity (SSS) variability in the southern Caribbean from precisely dated fossil corals. Our fossil coral results from Bonaire indicate strong interannual to decadal SST and SSS variability in the southern Caribbean Sea during the TCP with multiyear extremes of high SSS and high SST that coincide with droughts on the Yucatán Peninsula. The results are best explained by changed Caribbean SST gradients affecting the Caribbean low-level atmospheric jet with consequences for Mesoamerican precipitation, possibly linked to changes in Atlantic Meridional Overturning Circulation strength. Our findings provide a new perspective on the anomalous hydrological changes on the Yucatán Peninsula during the TCP that complement the often-suggested southward displacement of the Intertropical Convergence Zone. We advocate for a strong role of ocean-atmosphere interactions in the Caribbean Sea related to the multiyear variations in Caribbean Sea surface conditions as an important driver of the spatially complex pattern of hydrological anomalies during the TCP.