Biomarker Discovery and Food Allergy Profiling Distinguishes DOCK8 Deficiency from Atopic Dermatitis
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ResearchOnline@JCU This file is part of the following work: Jacob, Minnie (2019) Biomarker discovery and food allergy profiling distinguishes DOCK8 deficiency from atopic dermatitis. PhD Thesis, James Cook University. Access to this file is available from: https://doi.org/10.25903/myqs%2D6y84 Copyright © 2019 Minnie Jacob. The author has certified to JCU that they have made a reasonable effort to gain permission and acknowledge the owners of any third party copyright material included in this document. If you believe that this is not the case, please email [email protected] BIOMARKER DISCOVERY AND FOOD ALLERGY PROFILING DISTINGUISHES DOCK8 DEFICIENCY FROM ATOPIC DERMATITIS. Thesis submitted by Minnie Jacob M.Sc ( Biochemistry) For the degree of Doctor of Philosophy In the College of Public Health, Medical and Veterinary Sciences James Cook University September 2019 Statement of Contribution STATEMENT OF THE CONTRIBUTION OF OTHERS Nature of Assistance Contribution Name and Affiliation Intellectual Project plan and Dr. Anas Abdel Rahman, King Faisal support development Specialist Hospital and Research Center Editorial support Dr. Anas Abdel Rahman,King Faisal Specialist Hospital and Research Center Prof Andreas Lopata (AL), James Cook University Dr. Majed Aldasouki, King Faisal Specialist Hospital and Research Center Grant proposal Dr. Anas Abdel Rahman, King Faisal writing Specialist Hospital and Research Center Financial Research Department of Genetics, King Faisal Support Specialist Hospital and Research Center College of Public Health, Medical and Veterinary Sciences, James Cook University Conference HDRES Grant rounds-2018,James travel Cook University Dr. Majed Aldasouki, King Faisal Specialist Hospital and Research Center Dr. Anas Abdelrahman,King Faisal Specialist Hospital and Research Center Stipend James Cook University Postgraduate Research Scholarship Write up support Doctoral completion fund, Faculty of Medicine, Health and Molecular Sciences, James Cook University Data Collection Blood sample Dr. Rand Arnout, King Faisal collection Specialist Hospital and Research Center Dr. BanderAlsaud,King Faisal Specialist Hospital and Research Center Dr. Hamoud AlMousa,King Faisal Specialist Hospital and Research Center i Statement of Contribution Targeted Mass Dr. Liang Li, Department of spectrometric Chemistry, University of Alberta, analysis Edmonton, Alberta, Canada. Technical Immunoblotting Dr. Anas M Alazami,King Faisal Support Specialist Hospital and Research Center Tissue culture Ms. Sara Abdulaziz ii Author Contributions CONTRIBUTION OF OTHERS IN PUBLISHED MATERIAL Chapter 1: Minnie Jacob, Andreas L. Lopata, Majed Dasouki, Anas M. Abdel Rahman.Metabolomics toward personalized medicine.Mass Spectrom Rev 2017:1- 18 Name and affiliation MJ and AMAR co-developed the aim of Prof Andreas L Lopata (AL), James the review article. The figures and tables Cook University were generated by MJ, with editorial and Dr. Anas M Abdulrahman (AMAR), technical inputs form AMAR, MAD and KFSH& RC AL. The first draft of the manuscript was Dr.Majed Aldasouki written by MJ with editorial inputs from (MAD),KFSH&RC AMAR, MAD and AL Chapter 2: Minnie Jacob, Duaa Bin Khalaf, Safa Alhissi, Rand Arnout, Bander Alsaud, Hamoud Al-Mousa, Andreas L. Lopata, Anas M Alazami, Majed Dasouki, Anas M. Abdel Rahman. Quantitative profiling of cytokines and chemokines in DOCK8 deficient and Atopic dermatitis patients. Allergy. 2018 Sep 25. doi: 10.1111/all.13610 Name and affiliation Ms. Duaa Bin khalaf (DBF), MJ and AMAR co-developed the KFSH&RC research question. MJ collected the Ms. Safa Alhissi (SA) KFSH&RC. samples, per formed the cytokine Dr. Rand Arnout (RA) KFSH&RC . experiment and ELISA tests, analyzed Dr. Bander Alsaud (BAS) KFSH&RC. the data, compiled the summary tables, Dr. Hamoud AlMousa and drafted the manuscript. DBF (HAM)KFSH&RC, provided technical support for FLEX- Prof. Andreas L Lopata (AL) James MAP 3D. SA and AMAassisted with the Cook University immunoblots. RA, BAS, and HAM Dr. AnasMAlazami (AMA) cared for patients and recruited them for KFSH&RC the study. MJ wrote the first draft that Dr. Majed Aldasouki(MAD), was revised with editorial inputs from KFSH&RC ALL, MAD and AMAR. Dr. Anas M Abdulrahman (AMAR),KFSH&RC iii Author Contributions Chapter 3: Minnie Jacob, Abeer Malkawi, Nour Albast, Salam Al Bougha, Andreas Lopata, Majed Dasouki, Anas M. Abdel Rahman.A targeted metabolomics approach for clinical diagnosis of Inborn Errors of Metabolism.Anal Chim Acta. 2018 Sep 26;1025:141-153 Name and affiliation Ms.Abeer Malkawi (AM), Jordan MJ and AMAR co-developed the research question. University of Science and Technology MJ prepared the standards and tuned the parameters (JUST),Jordan for method development on the LC-MS/MS with Ms. Nour Albast (NA) Al Faisal the assistance of AMAR.MJ also performed the University analysis on tissues, blood, serum and DBS Ms.SalamBougha(SAB) Faisal samples.AM and NA assisted in analysis of DBS University samples and building of reference range. MJ wrote Prof.Andreas L Lopata (AL)James the first draft with assistance from AMAR, and was Cook University revised with editorial inputs from AL, MAD. MJ Dr.Majed Aldasouki and AMAR jointly developed the figures and (MAD),KFSH&RC tables. Dr.Anas AbdulRahman(AMAR), KFSH&RC Chapter 4 Minnie Jacob, Xinyun Gu, Xian Luo, Hamoud Al-Mousa, Rand Arnaout, Bandar Al Saud, Andreas L. Lopata, PhD, Liang Li, PhD, Majed Dasouki, MD and Anas M. Abdel Rahman: Metabolomics distinguishes DOCK8 deficiency from atopic dermatitis:Towards a biomarker discovery.Metabolites.2019 Nov 12,9 (11),doi: 10.3390/metabo9110274. Name and affiliation Xinyun Gu (XG) University of Alberta, Canada Xian Luo (XL) University of Alberta, MJ and AMAR co-developed the Canada research question. MJ collected the Dr.Rand Arnout (RA) KFSH&RC samples and analyzed the data, compiled Dr.Bander Alsaud (BAS) KFSH&RC the summary tables, and drafted the Dr.Hamoud AlMousa manuscript. LL, XG and XL performed (HAM)KFSH&RC Mass spectrometric experiment. RA, Prof.Andreas L Lopata(AL) James BAS, and HAM cared for patients and Cook University recruited them for the study. MJ wrote Dr.Liang Li(LL) University of Alberta, the first draft which was revised with Canada editorial inputs from ALL, MD and Dr.Majed Aldasouki (MAD), AMAR KFSH&RC Dr. Anas M Abdulrahman (AMAR), KFSH&RC iv Author Contributions Chapter 5 Minnie Jacob, Xian Luo, Rand Arnout, Bander Alsaud, Hamoud Al-Mousa, Liang Li,Majed Dasouki,Andreas L Lopata ,Anas M. Abdel Rahman: Distinct IgE based allergen array, metabolomics and cytokine profiles in DOCK8-deficient and atopic dermatitis patients (Submission to Allergy in process) Name and affiliation Xian Luo (XL) University of Alberta,Canada MJ and AMAR co-developed the Dr. RandArnout (RA) KFSH&RC . research question. MJ collected the Dr. Bander Alsaud (BAS) KFSH&RC samples and analyzed the data, compiled Dr. HamoudAlMousa the summary tables, and drafted the (HAM)KFSH&RC manuscript. LL and XL performed the Prof. Andreas L Lopata (AL) James mass spectrometric experiments. RA, Cook University BAS, and HAM cared for patients and Dr. Liang Li (LL) University of recruited them for the study. MJ wrote Alberta,Canada the first draft which was revised with Dr. Majed Aldasouki editorial inputs from ALL, MD and (MAD),KFSH&RC AMAR Dr. Anas M AbdulRahman (AMAR),KFSH&RC v Acknowledgments Acknowledgments Accomplishing this PhD has been a truly life-changing experience for me, and it would not have been possible to do without the time, support and guidance that I received from many people involved personally and professionally. This section is meant to acknowledge some of them. I am immensely grateful to all of you. First, I thank God, for shepherding me through this journey. Thank you, Lord. I would like to express my deepest thanks to my two advisors, Dr. Anas Abdulrahman and Professor Andreas L Lopata: your patience, encouragement, and immense knowledge were key motivations throughout my PhD. Dr. Anas’s enthusiasm supported my academic developments and he gave me the freedom and sense of ownership of my research project. My heartfelt appreciation and thanks to, Professor Andreas for encouragingly supporting me throughout this journey. Your advice on both research as well as on my career have been invaluable. I would also like to extend my gratitude to Dr. Majed Dasouki for his expertise and grooming me during my PhD. I am very grateful to Dr. Ali Odaib for his encouragement and support especially in attending courses and presenting my work at conferences. A special appreciation to Dr. Faiqa Imtiaz Ahmad for her great help with proof reading my thesis and. I am deeply thankful to Dr. Brian Meyer, for promoting my research and for allowing me to grow as a research scientist. I gratefully acknowledge the funding received towards my PhD from the JCUPRS scholarship and thank my thesis committee members. I am fortunate to be a part of an amazing team at Molecular and Immunology group: thanks to Dr. Sandip Kamath, Dr. Roni Nugraha Dr. Elecia Johnston, Dr. Aya Taki, Mr. Thimo Ruethers and Ms. Thu Le for all the help and support you gave me. I have very fond memories of my time there. I am thankful to Dr.Liz Tynan, for supporting me in this journey. I am indebted to all my lab mates, especially Ms. Lujane Alhaidib, Mr. Mohammed Alamoudi, Ms Samia Hagos and Ms Najat Mazhar for cheering me up when I felt like giving up and filling my life with fun and excitement. I am wholeheartfully thankful to Ms. Sara Abdulaziz for providing me with training at tissue culture lab and Ms. Samia for setting up my experimental work and helping me technically. I am very greatful to Ms. Anwar Alotaibi for her computational skills I could keep going through this herculean journey only because of the support and prayers of St. Mary’s group members who always cheered me and encouraged me. My warmest gratitude goes to the fruit of my womb, Dr.