Investigating metabolomic biomarkers of hypoxic ischaemic encephalopathy

Background An early objective biomarker to predict the severity of hypoxic-ischaemic encephalopathy (HIE) and identify infants suitable for intervention remains elusive. This thesis aims to progress metabolomic markers of HIE through a pipeline of biomarker discovery and validation by employing a novel untargeted mass spectrometry metabolomic method. Methodology Term infants with perinatal asphyxia were recruited, all having umbilical cord blood (UCB) drawn and biobanked within three hours of birth. HIE was defined by Sarnat score at 24hours and continuous multichannel-EEG. Infant neurodevelopment was assessed at 36-42 months using the Bayley Scales of Infant and Toddler Development Ed. III (BSID-III). Untargeted metabolomic analysis of UCB was performed using direct injection FT-ICR mass spectrometry (DI FT-ICR MS). Putative metabolite annotations and lipid classes were assigned and pathway analysis was performed. Results Untargeted metabolomic analysis: Thirty enrolled infants were diagnosed with HIE, including 17 mild, 8 moderate, and 5 severe cases. Pathway analysis revealed that ΔHIE was associated with a 50% and 75% perturbation of tryptophan and pyrimidine metabolism respectively, alongside alterations in amino acid pathways. Significant metabolite alterations were detected from six putatively identified lipid classes including fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids and prenol lipids. Outcome prediction: Metabolite model scores significantly correlated with outcome R=0.429 (model A) and R=0.549 (model B) respectively. Model B demonstrates the potential to predict both severe outcome (AUROC of 0.915) and intact survival (AUROC of 0.800). The effect of haemolysis: On average 5% of polar and 1.5% of non-polar features were altered between paired haemolysed and clean samples. However unsupervised multivariate analysis concluded that the preanalytical variability introduced by haemolysis was negligible compared with the inherent biological inter-individual variability. Conclusion This research has employed untargeted metabolomics to identify potential early cord blood biomarkers of HIE and has performed the technical validation of previously proposed markers.

Biomarkers in turbidites at ODP Sites 157-951 and 157-952

Free and ester-bound lipid biomarkers were analysed in oxidised and unoxidised parts of four distinct turbidites from the Madeira Abyssal Plain (MAP), which contained 1 to 2% organic carbon homogeneously distributed throughout the turbidites at the time they were deposited. These turbidites are well suited to study the effects of oxic degradation on lipid biomarkers without the complicating influence of varying organic matter sources, sedimentation rates, or bioturbation. One sample from the oxidised turbidite was compared with two samples from the unoxidised part of each turbidite. Postdepositional oxic degradation decreased concentrations of biomarkers by several orders of magnitude. The ester-bound lipids were degraded to a far lesser extent than their free counterparts were. The extent of degradation of different compounds differed substantially. Within a specific class of biomarkers, degradation also took place to a different extent, altering their distributions. This study shows that oxic degradation of the organic matter may have a profound effect on the biomarker fingerprint and may result in a severe bias in, for example, the interpretation of organic matter sources and the estimation of the palaeoproductivity of specific groups of phytoplankton.

Flux of biomarkers and organisms at AWI HAUSGARTEN from two moorings

Time-series sediment traps were deployed at 4 depths in the eastern Fram Strait from July 2007 to June 2008 to investigate variations in the magnitude and composition of the sinking particulate matter from upper waters to the seafloor. Sediment traps were deployed at 196 m in the Atlantic Water layer, at 1296 and 2364 m in the intermediate and deep waters, and at 2430 m on a benthic lander in the near-bottom layer. Fluxes of total particulate matter, particulate organic carbon, particulate organic nitrogen, biogenic matter, lithogenic matter, biogenic particulate silica, calcium carbonate, dominant phytoplankton cells, and zooplankton fecal pellets increased with depth, indicating the importance of lateral advection on fluxes in the deep Fram Strait. The lateral supply of particulate matter was further supported by the constant fluxes of biomarkers such as brassicasterol, alkenones, campesterol, beta-sitosterol, and IP25 at all depths sampled. However, enhanced fluxes of diatoms and appendicularian fecal pellets from the upper waters to the seafloor in the presence of ice during spring indicated the rapid export (15-35 days) of locally-produced large particles that likely contributed most of the food supply to the benthic communities. These results show that lateral supply and downward fluxes are both important processes influencing the transport of particulate matter to the seafloor in the deep eastern Fram Strait, and that particulate matter size dictates the prevailing sinking process.

Bacteriohopanepolyol biomarkers of sediments from the Congo fan

The transport and deposition of terrestrially derived organic matter (TOM) into the ocean is an important but poorly constrained aspect of the modern global carbon cycle. A preliminary study of Late Quaternary sediments from the Congo deep sea fan (ODP leg 175, site 1075, 2 km water depth) and four surface samples from associated cores has confirmed the presence of proposed soil-specific bacteriohopanepolyol biomarkers (BHPs) including adenosylhopane, in samples to a depth of 89 m. Concentrations of soil marker BHPs are high in the upper sediment section (to 49 m) and the closest related surface sample (4913), supporting the case for these molecular markers as novel proxies for soil organic carbon (SOC) supply via riverine transport and subsequent burial. Distinct peaks for the markers at about 21, 34 and 60 m below surface level tentatively imply that the rate of TOM discharge from tropical Africa significantly increased at these times, possibly associated with periods of reduced soil stability in the Congo catchment.

Terrigenous input and marine productivity for the Pacific sector of the Southern Ocean based on lipid biomarkers

In this study, we present a new multiproxy data set of terrigenous input, marine productivity and sea surface temperature (SST) from 52 surface sediment samples collected along E-W transects in the Pacific sector of the Southern Ocean. Allochtonous terrigenous input was characterized by the distribution of plant wax n-alkanes and soil-derived branched glycerol dialkyl glycerol tetraethers (brGDGTs). 230Th-normalized burial rates of both compound groups were highest close to the potential sources in Australia and New Zealand and are strongly related to lithogenic contents, indicating common sources and transport. Detection of both long-chain n-alkanes and brGDGTs at the most remote sites in the open ocean strongly suggests a primarily eolian transport mechanism to at least 110°W, i.e. by prevailing westerly winds. Two independent organic SST proxies were used, the UK'37 based on long-chain alkenones, and the TEX86 based on isoprenoid GDGTs. Both, UK'37 and TEX86 indices show robust relationships with temperature over a temperature range between 0.5 and 20°C, likely implying different seasonal and regional imprints on the temperature signal. While alkenone-based temperature estimates reliably reflect modern SST even at the low temperature end, large temperature residuals are observed for the polar ocean using the TEX86 index. 230Th-normalized burial rates of alkenones are highest close to the Subtropical Front and are positively related to lithogenic fluxes throughout the study area. In contrast, highest isoGDGT burial south of the Antarctic Polar Front is not related with dust flux but may be largely controlled by diatom blooms, and thus high opal fluxes during austral summer.

(Table 1) Lipid biomarkers in surface sediments from the Gulf of Genoa

A series of molecular organic markers were determined in surface sediments from the Gulf of Genoa (Ligurian Sea) in order to evaluate their potential for palaeo-environmental reconstructions. Allochthonous input can be characterized by the distributions of n-C29 and n-C31 alkanes, n-C26 and n-C28 alkanols and branched glycerol dialkyl glycerol tetraethers (GDGTs), whose concentrations are generally highest near the river mouths. In the open basin however, terrestrial n-alkanes and n-alkanols may have an additional, aeolian source. Autochthonous input is represented by crenarchaeol and isoprenoid GDGTs. Their concentrations are highest in the open basin showing the preference of Thaumarchaeota for oligotrophic waters. Indications of a significant degradation of sterols and C37 alkenones exclude these lipids as reliable productivity proxies. Using terrestrial and aquatic lipids as end-members allows estimating the percentage of terrestrial organic matter between 20% and 58% in the coastal area decreasing to 1 to 30% in the deep basin. The spatial distribution of sea surface temperature (SST) estimates using the alkenone-based UK'37 index is very similar to the autumnal (November) mean satellite-based SST distribution. Conversely, TEXH86-derived SST estimates are close to winter SSTs in the coastal area and summer SSTs in the open basin. This pattern reflects presumably a shift in the main production of Thaumarchaeota from the coastal area in winter to the open basin in summer. This study represents a major prerequisite for the future application of lipid biomarkers on sediment cores from the Gulf of Genoa.

Diatoms and biomarkers in sediments from the Antarctic Peninsula

The Antarctic Peninsula (AP) has been identified as one of the most rapidly warming region on Earth. Satellite monitoring currently allows for a detailed understanding of the relationship between sea ice extent and duration and atmospheric and oceanic circulations in this region. However, our knowledge on ocean-ice-atmosphere interactions is still relatively poor for the period extending beyond the last 30 years. Here, we describe environmental conditions in Northwestern and Northeastern Antarctic Peninsula areas over the last century using diatom census counts and diatom specific biomarkers (HBIs) in two marine sediment multicores (MTC-38C and -18A, respectively). Diatom census counts and HBIs show abrupt changes between 1935 and 1950, marked by ocean warming and sea ice retreat in both sides of the AP. Since 1950, inferred environmental conditions do not provide evidence for any trend related to the recent warming but demonstrate a pronounced variability on pluri-annual to decadal time scale. We propose that multi-decadal sea ice variations over the last century are forced by the recent warming, while the annual-to-decadal variability is mainly governed by synoptic and regional wind fields in relation with the position and intensity of the atmospheric low-pressure trough around the AP. However, the positive shift of the SAM since the last two decades cannot explain the regional trend observed in this study, probably due to the effect of local processes on the response of our biological proxies.

Computational models for improved diagnosis and prognosis of stroke using robot-based biomarkers

Stroke is a leading cause of death and permanent disability worldwide, affecting millions of individuals. Traditional clinical scores for assessment of stroke-related impairments are inherently subjective and limited by inter-rater and intra-rater reliability, as well as floor and ceiling effects. In contrast, robotic technologies provide objective, highly repeatable tools for quantification of neurological impairments following stroke. KINARM is an exoskeleton robotic device that provides objective, reliable tools for assessment of sensorimotor, proprioceptive and cognitive brain function by means of a battery of behavioral tasks. As such, KINARM is particularly useful for assessment of neurological impairments following stroke. This thesis introduces a computational framework for assessment of neurological impairments using the data provided by KINARM. This is done by achieving two main objectives. First, to investigate how robotic measurements can be used to estimate current and future abilities to perform daily activities for subjects with stroke. We are able to predict clinical scores related to activities of daily living at present and future time points using a set of robotic biomarkers. The findings of this analysis provide a proof of principle that robotic evaluation can be an effective tool for clinical decision support and target-based rehabilitation therapy. The second main objective of this thesis is to address the emerging problem of long assessment time, which can potentially lead to fatigue when assessing subjects with stroke. To address this issue, we examine two time reduction strategies. The first strategy focuses on task selection, whereby KINARM tasks are arranged in a hierarchical structure so that an earlier task in the assessment procedure can be used to decide whether or not subsequent tasks should be performed. The second strategy focuses on time reduction on the longest two individual KINARM tasks. Both reduction strategies are shown to provide significant time savings, ranging from 30% to 90% using task selection and 50% using individual task reductions, thereby establishing a framework for reduction of assessment time on a broader set of KINARM tasks. All in all, findings of this thesis establish an improved platform for diagnosis and prognosis of stroke using robot-based biomarkers.

The Comparative Effectiveness of EEG Biomarkers in Antidepressant Response and Illness Prediction in Major Depressive Disorder

Background: There is growing evidence that individual EEG differences may aid in classifying patients with major depressive disorder (MDD) and also help predict clinical response to antidepressant treatment. This study aims to compare the effectiveness of EEG frequency band power, alpha asymmetry and prefrontal theta cordance towards escitalopram response prediction and MDD diagnosis, in a multi-site initiative. Methods: Resting EEG (eyes open and closed) was recorded from 64 electrodes in 44 depressed patients and 20 healthy controls at baseline, 2 weeks post-treatment and 8 weeks post-treatment. Clinical response was measured as change from baseline MADRS of 50% or more. EEG measures were analyzed (1) at baseline (2) at 2 weeks post-treatment and (3) as an ‘‘early change” variable defined as change in EEG from baseline to 2 weeks post-treatment. Results: At baseline, responders exhibited greater absolute alpha power in the left hemisphere versus the right while non-responders showed the opposite. Responders further exhibited a cortical asymmetry of greater right relative to left activity in parietal areas. Groups also differed in baseline relative delta power with responders showing greater power in the right hemisphere versus the left while non-responders showed the opposite. At 2 weeks post-treatment, responders exhibited greater absolute beta power in the left hemisphere relative to right and the opposite was noted for non-responders. The opposite pattern was noted for absolute and relative delta power at 2 weeks post-treatment. Responders exhibited early reduction in relative alpha power and early increments in relative theta power. Non-responders showed a significant early increase in prefrontal theta cordance. Absolute delta power helped distinguish MDD patients from healthy controls. Conclusions: Hemispheric asymmetries in the alpha and delta bands at pre-treatment baseline and at 2 weeks post-treatment have moderate to moderately strong predictive utility towards antidepressant treatment response. These findings have significant potential for improving clinical practice in psychiatry by eventually guiding clinical choice of treatments. This would greatly benefit patients awaiting relief from depressive symptoms as treatment optimization would help overcome problems associated with delayed recovery. Our results also indicate that resting EEG activity may have clinical utility in predicting MDD diagnosis.

Extracellular cathepsin S and intracellular caspase 1 activation are surrogate biomarkers of particulate-induced lysosomal disruption in macrophages

BACKGROUND: Particulate matter has been shown to stimulate the innate immune system and induce acute inflammation. Therefore, while nanotechnology has the potential to provide therapeutic formulations with improved efficacy, there are concerns such pharmaceutical preparations could induce unwanted inflammatory side effects. Accordingly, we aim to examine the utility of using the proteolytic activity signatures of cysteine proteases, caspase 1 and cathepsin S (CTSS), as biomarkers to assess particulate-induced inflammation.

METHODS: Primary peritoneal macrophages and bone marrow-derived macrophages from C57BL/6 mice and ctss(-/-) mice were exposed to micro- and nanoparticulates and also the lysosomotropic agent, L-leucyl-L-leucine methyl ester (LLOME). ELISA and immunoblot analyses were used to measure the IL-1β response in cells, generated by lysosomal rupture. Affinity-binding probes (ABPs), which irreversibly bind to the active site thiol of cysteine proteases, were then used to detect active caspase 1 and CTSS following lysosomal rupture. Reporter substrates were also used to quantify the proteolytic activity of these enzymes, as measured by substrate turnover.

RESULTS: We demonstrate that exposure to silica, alum and polystyrene particulates induces IL-1β release from macrophages, through lysosomal destabilization. IL-1β secretion positively correlated with an increase in the proteolytic activity signatures of intracellular caspase 1 and extracellular CTSS, which were detected using ABPs and reporter substrates. Interestingly IL-1β release was significantly reduced in primary macrophages from ctss(-/-) mice.

CONCLUSIONS: This study supports the emerging significance of CTSS as a regulator of the innate immune response, highlighting its role in regulating IL-1β release. Crucially, the results demonstrate the utility of intracellular caspase 1 and extracellular CTSS proteolytic activities as surrogate biomarkers of lysosomal rupture and acute inflammation. In the future, activity-based detection of these enzymes may prove useful for the real-time assessment of particle-induced inflammation and toxicity assessment during the development of nanotherapeutics.

Can emerging biomarkers of myocardial remodelling identify asymptomatic hypertensive patients at risk for diastolic dysfunction and diastolic heart failure?

AIMS: Hypertension is one of the main drivers of the heart failure (HF) epidemic. The aims of this study were to profile fibro-inflammatory biomarkers across stages of the hypertensive heart disease (HHD) spectrum and to examine whether particular biochemical profiles in asymptomatic patients identify a higher risk of evolution to HF.

METHODS AND RESULTS: This was a cross-sectional observational study involving a population of 275 stable hypertensive patients divided into two different cohorts: Group 1, asymptomatic hypertension (AH) (n= 94); Group 2, HF with preserved ejection fraction (n= 181). Asymptomatic hypertension patients were further subdivided according to left atrial volume index ≥34 mL/m(2) (n= 30) and <34 mL/m(2) (n= 64). Study assays involved inflammatory markers [interleukin 6 (IL6), interleukin 8 (IL8), monocyte chemoattractant protein 1 (MCP1), and tumour necrosis factor α], collagen 1 and 3 metabolic markers [carboxy-terminal propeptide of collagen 1, amino-terminal propeptide of collagen 1, amino-terminal propeptide of collagen 3 (PIIINP), and carboxy-terminal telopeptide of collagen 1 (CITP)], extra-cellular matrix turnover markers [matrix metalloproteinase 2 (MMP2), matrix metalloproteinase 9 (MMP9), and tissue inhibitor of metalloproteinase 1 (TIMP1)], and the brain natriuretic peptide. Data were adjusted for age, sex, systolic blood pressure, and creatinine. Heart failure with preserved ejection fraction was associated with an increased inflammatory signal (IL6, IL8, and MCP1), an increased fibrotic signal (PIIINP and CITP), and an increased matrix turnover signal (MMP2 and MMP9). Alterations in MMP and TIMP enzymes were found to be significant indicators of greater degrees of asymptomatic left ventricular diastolic dysfunction.

CONCLUSION: These data define varying fibro-inflammatory profiles throughout different stages of HHD. In particular, the observations on MMP9 and TIMP1 raise the possibility of earlier detection of those at risk of evolution to HF which may help focus effective preventative strategies.

Risk factors and biomarkers of age-related macular degeneration

A biomarker can be a substance or structure measured in body parts, fluids or products that can affect or predict disease incidence. As age-related macular degeneration (AMD) is the leading cause of blindness in the developed world, much research and effort has been invested in the identification of different biomarkers to predict disease incidence, identify at risk individuals, elucidate causative pathophysiological etiologies, guide screening, monitoring and treatment parameters, and predict disease outcomes. To date, a host of genetic, environmental, proteomic, and cellular targets have been identified as both risk factors and potential biomarkers for AMD. Despite this, their use has been confined to research settings and has not yet crossed into the clinical arena. A greater understanding of these factors and their use as potential biomarkers for AMD can guide future research and clinical practice. This article will discuss known risk factors and novel, potential biomarkers of AMD in addition to their application in both academic and clinical settings.

Biostratigraphic Evidence Relating to the Age-Old Question of Hannibal's Invasion of Italy, II: Chemical Biomarkers and Microbial Signatures

As discussed in Part I, a large accumulation of mammalian faeces at the mire site in the upper Guil Valley near Mt. Viso, dated to 2168cal ¹⁴C yr., provides the first evidence of the passage of substantial but indeterminate numbers of mammals within the time frame of the Punic invasion of Italia. Specialized organic biomarkers bound up in a highly convoluted and bioturbated bed constitute an unusual anomaly in a histosol comprised of fibric and hemist horizons that are usually expected to display horizontal bedding. The presence of deoxycholic acid and ethylcoprostanol derived from faecal matter, coupled with high relative numbers of Clostridia 16S rRNA genes, suggests a substantial accumulation of mammalian faeces at the site over 2000years ago. The results reported here constitute the first chemical and biological evidence of the passage of large numbers of mammals, possibly indicating the route of the Hannibalic army at this time. Combined with the geological analysis reported in Part I, these data provide a background supporting the need for further historical archaeological exploration in this area.

Circulating miRNAs: Potential Novel Biomarkers for Hepatopathology Progression and Diagnosis of Schistosomiasis Japonica in Two Murine Models

BACKGROUND: Schistosomiasis remains a major public health issue, with an estimated 230 million people infected worldwide. Novel tools for early diagnosis and surveillance of schistosomiasis are currently needed. Elevated levels of circulating microRNAs (miRNAs) are commonly associated with the initiation and progression of human disease pathology. Hence, serum miRNAs are emerging as promising biomarkers for the diagnosis of a variety of human diseases. This study investigated circulating host miRNAs commonly associated with liver diseases and schistosome parasite-derived miRNAs during the progression of hepatic schistosomiasis japonica in two murine models.

METHODOLOGY/PRINCIPAL FINDINGS: Two mouse strains (C57BL/6 and BALB/c) were infected with a low dosage of Schistosoma japonicum cercariae. The dynamic patterns of hepatopathology, the serum levels of liver injury-related enzymes and the serum circulating miRNAs (both host and parasite-derived) levels were then assessed in the progression of schistosomiasis japonica. For the first time, an inverse correlation between the severity of hepatocyte necrosis and the level of liver fibrosis was revealed during S. japonicum infection in BALB/c, but not in C57BL/6 mice. The inconsistent levels of the host circulating miRNAs, miR-122, miR-21 and miR-34a in serum were confirmed in the two murine models during infection, which limits their potential value as individual diagnostic biomarkers for schistosomiasis. However, their serum levels in combination may serve as a novel biomarker to mirror the hepatic immune responses induced in the mammalian host during schistosome infection and the degree of hepatopathology. Further, two circulating parasite-specific miRNAs, sja-miR-277 and sja-miR-3479-3p, were shown to have potential as diagnostic markers for schistosomiasis japonica.

CONCLUSIONS/SIGNIFICANCE: We provide the first evidence for the potential of utilizing circulating host miRNAs to indicate different immune responses and the severity of hepatopathology outcomes induced in two murine strains infected with S. japonicum. This study also establishes a basis for the early and cell-free diagnosis of schistosomiasis by targeting circulating schistosome parasite-derived miRNAs.