Biomarker-Drug and Liquid Biopsy Co-development for Disease Staging and Targeted Therapy: Cornerstones for Alzheimer's Precision Medicine and Pharmacology.

Systems biology studies have demonstrated that different (epi)genetic and pathophysiological alterations may be mapped onto a single tumor's clinical phenotype thereby revealing commonalities shared by cancers with divergent phenotypes. The success of this approach in cancer based on analyses of traditional and emerging body fluid-based biomarkers has given rise to the concept of liquid biopsy enabling a non-invasive and widely accessible precision medicine approach and a significant paradigm shift in the management of cancer. Serial liquid biopsies offer clues about the evolution of cancer in individual patients across disease stages enabling the application of individualized genetically and biologically guided therapies. Moreover, liquid biopsy is contributing to the transformation of drug research and development strategies as well as supporting clinical practice allowing identification of subsets of patients who may enter pathway-based targeted therapies not dictated by clinical phenotypes alone. A similar liquid biopsy concept is emerging for Alzheimer's disease, in which blood-based biomarkers adaptable to each patient and stage of disease, may be used for positive and negative patient selection to facilitate establishment of high-value drug targets and counter-measures for drug resistance. Going beyond the "one marker, one drug" model, integrated applications of genomics, transcriptomics, proteomics, receptor expression and receptor cell biology and conformational status assessments during biomarker-drug co-development may lead to a new successful era for Alzheimer's disease therapeutics. We argue that the time is now for implementing a liquid biopsy-guided strategy for the development of drugs that precisely target Alzheimer's disease pathophysiology in individual patients

Investigating data mining techniques for extracting information from Alzheimer\u27s disease data

Data mining techniques have been used widely in many areas such as business, science, engineering and more recently in clinical medicine. These techniques allow an enormous amount of high dimensional data to be analysed for extraction of interesting information as well as the construction of models for prediction. One of the foci in health related research is Alzheimer\u27s disease which is currently a non-curable disease where diagnosis can only be confirmed after death via an autopsy. Using multi-dimensional data and the applications of data mining techniques, researchers hope to find biomarkers that will diagnose Alzheimer\u27s disease as early as possible. The primary purpose of this research project is to investigate the application of data mining techniques for finding interesting biomarkers from a set of Alzheimer\u27s disease related data. The findings from this project will help to analyse the data more effectively and contribute to methods of providing earlier diagnosis of the disease

The Zebrafish equivalent of Alzheimer's disease-associated PRESENILIN Isoform PS2V regulates inflammatory and other responses to hypoxic stress

Dominant mutations in the PRESENILIN genes PSEN1 and PSEN2 cause familial Alzheimer's disease (fAD) that usually shows onset before 65 years of age. In contrast, genetic variation at the PSEN1 and PSEN2 loci does not appear to contribute to risk for the sporadic, late onset form of the disease (sAD), leading to doubts that these genes play a role in the majority of AD cases. However, a truncated isoform of PSEN2, PS2V, is upregulated in sAD brains and is induced by hypoxia and high cholesterol intake. PS2V can increase γ-secretase activity and suppress the unfolded protein response (UPR), but detailed analysis of its function has been hindered by lack of a suitable, genetically manipulable animal model since mice and rats lack this PRESENILIN isoform. We recently showed that zebrafish possess an isoform, PS1IV, that is cognate to human PS2V. Using an antisense morpholino oligonucleotide, we can block specifically the induction of PS1IV that normally occurs under hypoxia. Here, we exploit this ability to identify gene regulatory networks that are modulated by PS1IV. When PS1IV is absent under hypoxia-like conditions, we observe changes in expression of genes controlling inflammation (particularly sAD-associated IL1B and CCR5), vascular development, the UPR, protein synthesis, calcium homeostasis, catecholamine biosynthesis, TOR signaling, and cell proliferation. Our results imply an important role for PS2V in sAD as a component of a pathological mechanism that includes hypoxia/oxidative stress and support investigation of the role of PS2V in other diseases, including schizophrenia, when these are implicated in the pathology.Esmaeil Ebrahimie, Seyyed Hani Moussavi Nik, Morgan Newman, Mark Van Der Hoek and Michael Lardell

Blood-based molecular biomarkers for Alzheimer\u27s disease

A major barrier to the effective conduct of clinical trials of new drug candidates against Alzheimer\u27s disease (AD) and to identifying patients for receiving future disease-modifying treatments is the limited capacity of the current health system to find and diagnose patients with early AD pathology. This may be related in part to the limited capacity of the current health systems to select those people likely to have AD pathology in order to confirm the diagnosis with available cerebrospinal fluid and imaging biomarkers at memory clinics. In the current narrative review, we summarize the literature on candidate blood tests for AD that could be implemented in primary care settings and used for the effective identification of individuals at increased risk of AD pathology, who could be referred for potential inclusion in clinical trials or future approved treatments following additional testing. We give an updated account of blood-based candidate biomarkers and biomarker panels for AD-related brain changes. Our analysis centres on biomarker candidates that have been replicated in more than one study and discusses the need of further studies to achieve the goal of a primary care-based screening algorithm for AD

Neuroinflammation and its resolution in Alzheimer's disease

Alzheimer's disease (AD) is the most common dementia with high prevalence among an increasing aged population. Despite the existence of symptom-reliving drugs for AD, the clinical trials performed until now have failed to find drugs that cure or stop the progression of AD. New perspectives and strategies for treatments are therefore direly needed. Chronic inflammation as indicated by persistent activation of microglia and increased proinflammatory mediators is one of the major characteristics for AD, together with pathological accumulation of β-amyloid (Aβ), hyperphosphorylated tau proteins and neuronal loss. In normal physiological conditions, inflammation is ended by resolution, an active process associated with restoration and regeneration mediated by specialised pro-resolving lipid mediators (SPMs). Previous studies have shown that there are alterations in the resolution of inflammation in AD that can cause neurodegeneration by impairment in neuroprotective signalling, control of inflammation, and in the removal of the pathogenic Aβ peptide. The current studies focus on the impairment of pro-resolving mechanisms in the context of AD. The prospect of reducing harmful inflammation while at the same time increasing protective and pro-homeostatic activities present a promising strategy for treating AD. In Paper I and II, we focused on answering the fundamental question, whether and how the neuroinflammation (Paper I) and its resolution (Paper II) are altered in AD patients. We aimed to identify dissimilar inflammation-related protein mediators (Paper I) and SPMs (Paper II) profiles in the cerebrospinal fluid (CSF) of patients diagnosed with subjective cognitive impairment (SCI), mild cognitive impairment (MCI) or AD. We found an inflammatory pattern in the CSF that could differentiate SCI and AD. Comorbidities have an influence on the inflammatory pattern. SPMs were decreased in the CSF of AD patients and were associated with AD pathologies and cognition, suggesting that SPMs have potential to be novel biomarkers for AD. In Paper III and IV, the aim of the studies was to explore the pro-resolving role of maresin 1 (MaR1) in the context of Aβ42-induced inflammation in human microglial cell models. In Paper III, AD-like neuroinflammation was induced exposure to Ab42 monomers in both human monocyte-derived microglia (MdM) and a differentiated human monocyte cell line (THP-1 cells). We showed that one of the SPMs MaR1 reduced Aβ42-induced elevation in pro-inflammatory activation and stimulated the Aβ42 uptake. In Paper IV, RNA-Sequencing (RNA-Seq) was used to study the effects of MaR1 on the transcriptome of Aβ42-treated MdM to obtain a broader view regarding the pro-resolving roles of MaR1. We found that Aβ42 up-regulated inflammatory pathways and that co-incubation with MaR1 down-regulated some of these pathways. Proteomics confirmed the finding. In conclusion, the inflammation-related protein mediator profile and SPMs in CSF have a potential to contribute to the diagnosis of AD and are correlated to AD pathologies and cognition. SPM MaR1 attenuates AD-like neuroinflammation and supports the hypothesis that stimulating the resolution of inflammation could be a new therapeutic strategy in A

Network-driven plasma proteomics expose molecular changes in the Alzheimer’s brain

Background Biological pathways that significantly contribute to sporadic Alzheimer’s disease are largely unknown and cannot be observed directly. Cognitive symptoms appear only decades after the molecular disease onset, further complicating analyses. As a consequence, molecular research is often restricted to late-stage post-mortem studies of brain tissue. However, the disease process is expected to trigger numerous cellular signaling pathways and modulate the local and systemic environment, and resulting changes in secreted signaling molecules carry information about otherwise inaccessible pathological processes. Results To access this information we probed relative levels of close to 600 secreted signaling proteins from patients’ blood samples using antibody microarrays and mapped disease-specific molecular networks. Using these networks as seeds we then employed independent genome and transcriptome data sets to corroborate potential pathogenic pathways. Conclusions We identified Growth-Differentiation Factor (GDF) signaling as a novel Alzheimer’s disease-relevant pathway supported by in vivo and in vitro follow-up experiments, demonstrating the existence of a highly informative link between cellular pathology and changes in circulatory signaling proteins

Computational methods toward early detection of neuronal deterioration

In today's world, because of developments in medical sciences, people are living longer, particularly in the advanced countries. This increasing of the lifespan has caused the prevalence of age-related diseases like Alzheimer’s and dementia. Researches show that ion channel disruptions, especially the formation of permeable pores to cations by Aβ plaques, play an important role in the occurrence of these types of diseases. Therefore, early detection of such diseases, particularly using non-invasive tools can aid both patients and those scientists searching for a cure. To achieve the goal toward early detection, the computational analysis of ion channels, ion imbalances in the presence of Aβ pores in neurons and fault detection is done. Any disruption in the membrane of the neuron, like the formation of permeable pores to cations by Aβ plaques, causes ionic imbalance and, as a result, faults occur in the signalling of the neuron.The first part of this research concentrates on ion channels, ion imbalances and their impacts on the signalling behaviour of the neuron. This includes investigating the role of Aβ channels in the development of neurodegenerative diseases. Results revealed that these types of diseases can lead to ionic imbalances in the neuron. Ion imbalances can change the behaviour of neuronal signalling. Therefore, by identifying the pattern of these changes, the disease can be detected in the very early stages. Then the role of coupling and synchronisation effects in such diseases were studied. After that, a novel method to define minimum requirements for synchronicity between two coupled neurons is proposed. Further, a new computational model of Aβ channels is proposed and developed which mimics the behaviour of a neuron in the course of Alzheimer's disease. Finally, both fault computation and disease detection are carried out using a residual generation method, where the residuals from two observers are compared to assess their performance

Network-Driven Plasma Proteomics Expose Molecular Changes in the Alzheimer\u27s Brain

Background: Biological pathways that significantly contribute to sporadic Alzheimer’s disease are largely unknown and cannot be observed directly. Cognitive symptoms appear only decades after the molecular disease onset, further complicating analyses. As a consequence, molecular research is often restricted to late-stage post-mortem studies of brain tissue. However, the disease process is expected to trigger numerous cellular signaling pathways and modulate the local and systemic environment, and resulting changes in secreted signaling molecules carry information about otherwise inaccessible pathological processes. Results: To access this information we probed relative levels of close to 600 secreted signaling proteins from patients’ blood samples using antibody microarrays and mapped disease-specific molecular networks. Using these networks as seeds we then employed independent genome and transcriptome data sets to corroborate potential pathogenic pathways. Conclusions: We identified Growth-Differentiation Factor (GDF) signaling as a novel Alzheimer’s disease-relevant pathway supported by in vivo and in vitro follow-up experiments, demonstrating the existence of a highly informative link between cellular pathology and changes in circulatory signaling proteins

Identification of plasma lipid biomarkers in Alzheimer\u27s disease

Alzheimer’s disease (AD), the commonest form of dementia, is a chronic, progressive neurodegenerative disease which manifests clinically as a slow global decline in cognitive function, including deterioration of memory, reasoning, abstraction, language and emotional stability, culminating in a patient with end-stage disease, totally dependent on custodial care. With an ageing population, there is predicted to be a marked increase in the number of people diagnosed with AD in the coming decades, making this a significant challenge to socio-economic policy and aged care. Currently there is no cure for AD and while current therapies may temporarily ameliorate symptoms, death usually occurs approximately 8 years after diagnosis. Attention is now being directed to the discovery of biomarkers that may not only facilitate pre-symptomatic diagnosis but provide an insight into aberrant biochemical pathways that may reveal potential therapeutic targets. AD pathogenesis develops over many years before clinical symptoms appear, providing the opportunity to develop therapy that could slow or stop disease progression well before any clinical manifestations develop. Research and understanding of AD pathology has been driven in recent years by advances in technologies, enabling the precise investigation of the lipidome; the repertoire of lipid species present in cells and tissues that reflect the net effect of gene and protein expression, which in turn are influenced by the cellular environment. Lipidomic studies have identified abnormal lipid metabolism as a key component of the pathological processes which lead to the development of AD. Therefore, lipidomic studies are crucial for advancing the understanding of AD pathology and for identifying potential therapeutic targets; these studies may also facilitate biomarker discovery. Many studies have reported abnormal lipid profiles in both AD plasma and brain tissue. This thesis investigated plasma lipid species using a “shotgun” lipidomics approach by electrospray ionisation tandem mass spectrometry (ESI/MS/MS). Additionally, Phospholipid Transfer Protein (PLTP); a protein involved in lipid metabolism was assayed using a commercial kit. The utility of these analytes as potential AD biomarkers was investigated by testing plasma samples from the highly characterised Australian Imaging, Biomarkers and Lifestyle (AIBL) study. The study cohort comprised over 1000 participants at inception who were classified as either healthy control (n=733), mild cognitive impairment (MCI, n=125) or AD (n=204): Samples from the baseline and 18 month follow-up time points were utilised. Plasma PLTP activity levels were measured in a subset of the baseline samples (n=259). Lipid and PLTP measurements were analysed in conjunction with supplementary neuroimaging and blood biomarker data collected as part of the AIBL study. The thesis identified significant differences in several plasma lipids between clinical classification groups, including several ceramide, sphingomyelin (SM), phosphatidylethanolamine (PE), phosphatidylcholine (PC) and plasmalogen species. Additionally, a panel of lipids was identified which could distinguish AD participants from healthy controls with a sensitivity and specificity of 80%. Plasma PLTP activity was significantly lower in AD and MCI groups compared to healthy controls, and levels correlated with plasma Aβ in all groups and cerebral Aβ in the healthy controls. The results of this thesis validate and extend previous findings reported in the literature. The current findings provide evidence to indicate that several lipid species and PLTP show promise as potential blood biomarkers of AD. Further investigation using a targeted lipidomics platform and prospective longitudinal follow-up is warranted

Differences in AD astrocyte phenotypes and responses to microglial-derived cytokines

Dysregulated cross-talk between activated glia and neurons, mediated by exosomal trafficking, is a key mechanism in the spreading of neuroinflammation and in the exacerbation of the Alzheimer’s disease (AD) pathology. In AD patients, A1 reactive astrocytes are found in brain regions affected by neurodegeneration, and display a neurotoxic profile that is crucial for the disease progression. Despite its pivotal role in AD progression, the astroglial population remains strikingly under-investigated, mainly due to the lack of reliable experimental biological platforms to study glial cell function in a disease context. In this thesis, our goal was to develop a human model able to recapitulate the pathological potential of AD astrocytes, thus surpassing species-specific differences in the study of neurodegenerative mechanisms. For that we differentiated astrocytes from iPSCs generated from the fibroblasts of AD patients and healthy matched controls. After a time-consuming process of differentiation, iPSCs-derived astrocytes from AD patients with PSEN1ΔE9 mutation showed a decrease in cellular HMGB1, S100B and microRNA (miR)-155 expression, together with a reduction in the number of GFAP-positive cells, a finding sustained after A1 induction for 48 h exposure to microglial cytokines (C1q/IL-1α/TNF-α), relatively to matched controls. Such treatment decreased cell arborisation leading to polarization as fibroblast-like and rounded cells, with increased mean surface area, and triggered the release of sAPPβ. A1 stimulation increased miR-155 in cells and exosomes, while diminished the cellular increase in miR-21 and miR-125b by inducing their package in exosomes, thus favouring the dissemination of inflammation to far and near cells. As observed in vivo, our cell population showed astrocyte heterogeneity, mainly for alarmins and miRNAs. In sum, astrocytic atrophy and abnormal distribution of inflammatory-miRNA in iPSCs-derived astrocytes carrying the PSEN1ΔE9 mutation and in their exosomes may provide important tools in targeting discovery, therapeutic development and personalised medicine for AD intervention