Biomarker discovery and food allergy profiling distinguishes DOCK8 deficiency from atopic dermatitis

Jacob, Minnie (2019) Biomarker discovery and food allergy profiling distinguishes DOCK8 deficiency from atopic dermatitis. PhD thesis, James Cook University.

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View at Publisher Website: https://doi.org/10.25903/myqs-6y84
 
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Abstract

Metabolomics is metabolites profiling in biological matrices and is a key tool for biomarker discovery. Over the last decade, metabolomics studies have identified several relevant biomarkers involved in complex clinical phenotypes using diverse biological systems. Most diseases result in signature metabolic profiles that reflect the sum of external and internal cellular activities. Metabolomics signature profiles are useful in clinical care, biomarker discovery for several common and rare human diseases, and in understanding disease mechanisms and response to therapy.

Hyper immunoglobulin E (IgE) syndrome [HIES] is characterized by significantly elevated serum IgE levels (>2000UL) and recurrent bacterial infections from infancy involving the skin and the lungs, chronic eczema and eosinophilia. Bi-allelic mutations in dedicator of cytokinesis 8 (DOCK8) are responsible for a form of autosomal recessive type of HIES, characterized by increased IgE levels, atopic dermatitis, food allergies, recurrent severe cutaneous viral infections, autoimmunity and malignancy. Severe atopic dermatitis (AD) and DOCK8 deficiency share some clinical symptoms including eczema, food allergies, increased serum IgE levels and eosinophilia. Increased serum IgE levels are characteristic but not specific for allergic diseases. DOCK8 exhibits an unusual constellation of clinical features, and diagnosis can be confusing and difficult especially during early childhood.The clinical management of patients with moderate-severe AD and DOCK8 deficiency can be challenging and quite complex as they share many clinical features. Deficiency of DOCK8 protein is potentially, life threatening and only curable with bone marrow transplantation. Hence, the diagnosis of DOCK8 deficiency is critical and should be sought at an early stage to initiate definitive therapy.

A detailed review on the analytical methods in metabolomics used for biomarker discovery and workflow for data analysis is provided in Chapter 1. Metabolomics studies have identified several relevant biomarkers involved in complex clinical phenotypes using diverse biological systems. In this review, metabolomics strategies were compared and evaluated, to focus on the discovery of biomarkers that have diagnostic, prognostic, and therapeutic value, validated for monitoring disease progression and responses to various management regimens. The work presented in this PhD thesis provides the development of a comprehensive metabolomics panel for biomarker discovery. Apart from cytokine biomarkers, metabolomics biomarkers differentiating DOCK8-deficient and AD patients were investigated. Furthermore, since these patients have food allergies in common, sensitization patterns were also evaluated.

In Chapter 2, a comprehensive cytokine profile revealed distinctive biomarkers that differentiate between the DOCK8‐deficient and AD patients. The unique expression profile of various inflammatory cytokines in patients with DOCK8 deficiency vs AD likely reflects disease‐specific perturbations in multiple cellular processes and pathways leading to predisposition to infections and allergies seen in these patients. Significant differential expression of the cytokines, CXCL10, CSF3, CCL22, CX3CL1, and TNF‐A were identified in DOCK8 deficiency, which possibly contributes to increased susceptibility to infection and cancer. CXCL10 and TNF-A were up-regulated in DOCK8-deficient patients when compared to AD, possibly contributing towards increased susceptibility to infections and cancer. In contrast, epidermal growth factor (EGF) was significantly down regulated in a subgroup of DOCK8 deficient and AD when compared to the controls. The cytokine IL‐31, is known to be elevated in patients with pruritus and IL-31 expression was found to be elevated in both our cohorts thus contributing toward pruritus common to both groups. The unique expression profile of various inflammatory cytokines in patients with DOCK8 deficiency vs. atopic dermatitis likely reflects upon the disease-specific perturbations in multiple cellular processes and pathways leading to a predisposition to infections and allergies seen in these patients. This data agrees with the role for EGF replacement therapy in EGF deficient individuals with AD as well as DOCK8 deficiency through a potential shared pathway. Hence, CXCL10, TNF-A and EGF were found to be signature cytokine biomarkers, leading to early effective diagnosis and distinction of DOCK8 deficiency from AD.

Chapter 3 describes the development and validation of a comprehensive targeted metabolomics method for a panel of 225 clinically relevant metabolites on Liquid chromatography-tandem mass spectrometry (LC-MS/MS), a powerful analytical technique that combines the separating power of liquid chromatography with highly sensitive and selective mass spectrometry. The potential clinical usefulness of this method was evaluated on different biological matrices such as whole blood, serum, dried blood spots (DBS) and murine tissues. The sensitivity, selectivity, stability and linearity of this method was also studied under defined preparation and analysis conditions. The method was tested and validated on eight different groups of patients with a known diagnosis of Inborn errors of metabolism (IEMs), which are rare genetic or inherited metabolic diseases resulting from an enzyme defect in biochemical and metabolic pathways, presenting with neurologic signs in newborns. The applicability of the method was also tested on various rat tissues to understand the metabolic tissue distribution pattern. The advantages of the developed method are small volume requirement, clinical relevance and cost effectiveness.

In Chapter 4, metabolomics based biomarkers were investigated using chemical isotope labeling liquid chromatography-mass spectrometry (CIL LC-MS) that is capable of distinguishing DOCK8-deficient from AD patients. The metabolomics profiles revealed seven positively identified metabolites through binary comparisons between DOCK8-deficient and AD patients. Aspartic and 3-hydroxyanthranillic acids were up-regulated in DOCK8 deficiency, whereas hypotaurine, guanosine and the dipeptides leucyl-phenylalanine and glycyl-phenylalanine were down-regulated. Hypotaurine, 3-hydroxyanthranillic acid and glycyl-phenyalanine were identified as potential biomarkers specific for DOCK8 deficiency.

In Chapter 5, In chapter 5 a comparative analysis of food and inhalant allergens, metabolomics and cytokines profiles was conducted in allergic patients with DOCK8-deficiency and AD. Serum samples from DOCK8-deficient and AD patients showed different and overlapping sensitization patterns; in particular, the cat allergen (rFel d1) was significantly up-regulated in AD patients when compared to DOCK8-deficient patients. LC-MS, followed by multivariate analysis revealed distinct signature profiles of dysregulated metabolites in the DOCK8-deficient and AD patient groups. Both cohorts commonly showed altered amino acid metabolism and taurine & hypotaurine metabolism pathways. DOCK8-deficient patients demonstrated perturbed tryptophan metabolism pathways whereas in AD patient’s caffeine metabolism pathways was altered. Food and inhalant sensitization in DOCK8 deficiency and atopic dermatitis induce distinct metabolomic and cytokine profiles suggesting both shared as well as unique mechanisms mediating these disorders.

In summary, the newly developed metabolomics method shows a great potential to discover novel biomarkers for various diseases. Chemokines, CXCL10, TNF-A and EGF were identified to be signature cytokine biomarkers differentiating DOCK8 deficient and atopic dermatitis patients.DOCK8 deficiencies appear to have a distinctive metabolomics profile characterized by significant differential over expression of 3-hydroxyanthranillic acid, aspartic acid and hyptotaurine. The work presented in this thesis provides an important contribution towards the development of biomarkers that have diagnostic, prognostic and therapeutic values for monitoring disease progression and responses to various management regimes. The complex nature of these diseases suggests that no single biomarker will be sufficient to meet the clinical needs of such patients. Future work involving the evaluation and validation of these biomarkers in larger cohorts involving other Omics will be essential before their clinical application is accepted.

Item ID: 64106
Item Type: Thesis (PhD)
Keywords: 3-hydroxyanthranilic acid, atopic dermatitis, biomarker discovery, cancer metabolomics, clinical metabolomics, CXCL10, Dansylation, Dedicator of cytokinesis, DOCK8, dried blood spot, epidermal growth factor, genetic disorder, hyper-IgE syndrome, Hypotaurine, inborn errors of metabolism, inherited disease, liquid chromatography-mass spectrometry, mass spectrometry, metabolomics, targeted metabolomics
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Copyright Information: Copyright © 2019 Minnie Jacob.
Additional Information:

Four publications arising from this thesis are stored in ResearchOnline@JCU, at the time of processing. Please see the Related URLs. The publications are:

Chapter 1: Jacob, Minnie, Lopata, Andreas L., Dasouki, Majed, and Abdel Rahman, Anas M. (2019) Metabolomics toward personalized medicine. Mass Spectrometry Reviews, 38 (3). pp. 221-238.

Chapter 2: Jacob, Minnie, Bin Khalaf, Duaa, Alhissi, Safa, Arnout, Rand, Alsaud, Bander, Al-Mousa, Hamoud, Lopata, Andreas L., Alazami, Anas M., Dasouki, Majed, and Rahman, Anas M. Abdel (2019) Quantitative profiling of cytokines and chemokines in DOCK8-deficient and atopic dermatitis patients. Allergy, 74 (2). pp. 370-379.

Chapter 3: Jacob, Minnie, Malkawi, Abeer, Albast, Nour, Al Bougha, Salam, Lopata, Andreas, Dasouki, Majed, and Rahman, Anas M. Abdel (2018) A targeted metabolomics approach for clinical diagnosis of inborn errors of metabolism. Analytica Chimica Acta, 1025. pp. 141-153.

Chapter 4: Jacob, Minnie, Gu, Xinyun, Luo, Xian, Al-Mousa, Hamoud, Arnaout, Rand, Al-Saud, Bandar, Lopata, Andreas L., Li, Liang, Dasouki, Majed, and Abdel Rahman, Anas M. (2019) Metabolomics distinguishes DOCK8 deficiency from atopic dermatitis: towards a biomarker discovery. Metabolites, 9 (11). 274.

Date Deposited: 17 Aug 2020 00:05
FoR Codes: 11 MEDICAL AND HEALTH SCIENCES > 1101 Medical Biochemistry and Metabolomics > 110101 Medical Biochemistry: Amino Acids and Metabolites @ 35%
11 MEDICAL AND HEALTH SCIENCES > 1107 Immunology > 110701 Allergy @ 30%
11 MEDICAL AND HEALTH SCIENCES > 1107 Immunology > 110703 Autoimmunity @ 35%
SEO Codes: 92 HEALTH > 9201 Clinical Health (Organs, Diseases and Abnormal Conditions) > 920108 Immune System and Allergy @ 35%
92 HEALTH > 9201 Clinical Health (Organs, Diseases and Abnormal Conditions) > 920110 Inherited Diseases (incl. Gene Therapy) @ 35%
92 HEALTH > 9202 Health and Support Services > 920203 Diagnostic Methods @ 30%
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