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Identification and Clinical Validation of Novel Please do not remove this page Identification and Clinical Validation of Novel Prostate Cancer Biomarkers Filamin A (flna), Filamin B (flnb), and Keratin 19 (krt19) Using Patient-Derived Omics and Bayesian Artificial Intelligence Narain, Niven Rajin https://scholarship.miami.edu/discovery/delivery/01UOML_INST:ResearchRepository/12355380470002976?l#13355517950002976 Narain, N. R. (2018). Identification and Clinical Validation of Novel Prostate Cancer Biomarkers Filamin A (flna), Filamin B (flnb), and Keratin 19 (krt19) Using Patient-Derived Omics and Bayesian Artificial Intelligence [University of Miami]. https://scholarship.miami.edu/discovery/fulldisplay/alma991031447635902976/01UOML_INST:ResearchR epository Open Downloaded On 2021/09/27 20:00:52 -0400 Please do not remove this page UNIVERSITY OF MIAMI IDENTIFICATION AND CLINICAL VALIDATION OF NOVEL PROSTATE CANCER BIOMARKERS FILAMIN A (FLNA), FILAMIN B (FLNB), AND KERATIN 19 (KRT19) USING PATIENT-DERIVED OMICS AND BAYESIAN ARTIFICIAL INTELLIGENCE By Niven Rajin Narain A DISSERTATION Submitted to the Faculty of the University of Miami in partial fulfillment of the requirements for the degree of Doctor of Philosophy Coral Gables, Florida December 2018 ©2018 Niven Rajin Narain All Rights Reserved UNIVERSITY OF MIAMI A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy IDENTIFICATION AND CLINICAL VALIDATION OF NOVEL PROSTATE CANCER BIOMARKERS FILAMIN A (FLNA), FILAMIN B (FLNB), AND KERATIN 19 (KRT19) USING PATIENT-DERIVED OMICS AND BAYESIAN ARTIFICIAL INTELLIGENCE Niven Rajin Narain Approved: ________________________ ________________________ Stephen Lee, Ph.D. Shanta Dhar, Ph.D. Professor of Biochemistry Associate Professor of Biochemistry and Molecular Biology and Molecular Biology ________________________ ________________________ Feng- Chun Yang, M.D., Ph.D. Guillermo Prado, Ph.D. Professor of Biochemistry Dean of the Graduate School and Molecular Biology ________________________ Feng Gong, Ph.D. Associate Professor of Biochemistry and Molecular Biology ________________________ Brian Berman, M.D, Ph.D. Emeritus Professor of Dermatology and Cutaneous Surgery NARAIN, NIVEN RAJIN (Ph.D., Biochemistry and Molecular Biology) Identification and Clinical Validation of Novel (December 2018) Prostate Cancer Biomarkers Filamin A (Flna), Filamin B (Flnb) and Keratin 19 (KRT19) Using Patient-Derived Omics and Bayesian Artificial Intelligence. Abstract of dissertation at the University of Miami. Dissertation supervised by Professor Stephen Lee No. of pages in text (88) This dissertation herein describes a novel strategy for Prostate Cancer (PCa) biomarker discovery employing use of systems biology causal modeling using omics, molecular phenotyping, and Bayesian artificial intelligence. Three studies were conducted towards this goal. In Study 1, a novel strategy that combines biological outputs with Bayesian network learning to identify potential biomarkers for prostate cancer was utilized. This methodology identified two proteins, filamin B (FLNB) and keratin-19, as potential biomarkers for prostate cancer. The network map also identified a direct linkage between FLNB and filamin A (FLNA), a protein previously identified as playing a role in prostate cancer etiology. The proteins identified from the in silico network model were then biologically validated by examining their levels in a panel of prostate cancer cell lines and in human plasma samples. Given the roles FLNA, FLNB, and KRT19 play in prostate cancer and their identification and validation in Study 1, a novel panel of serum biomarkers was developed in Study 2, using a multi-omic approach that defined FLNA, FLNB, and KRT19 in the panel. New ELISAs for FLNA and FLNB, and IPMRM for FLNA were developed and analytically validated by quantitative measurements of the biomarkers in serum. Retrospectively collected and clinically annotated serum samples with PSA values and Gleason scores from subjects who underwent prostate biopsy, and showed no evidence of cancer, with or without indication of prostatic hyperplasia, or had a definitive pathology diagnosis of prostatic adenocarcinoma were analyzed. Probit linear regression models were used to combine the analytes into score functions to address the following clinical questions. Does the biomarker test augment PSA for population screening? Can aggressive disease be differentiated from lower risk disease, and finally can the panel discriminate between prostate cancer and benign prostate hyperplasia? Modeling of the data showed that the new prostate biomarkers and PSA in combination were better than PSA alone in identifying prostate cancer, improved the prediction of high and low risk disease, and improved prediction of cancer versus benign prostate hyperplasia. Building upon Study 2, in Study 3 the utility of a Prostate Cancer Biomarker panel test on the analysis of 777 patients assessed the combinatorial power of filamin-A (FLNA), age, and prostate volume in predicting clinical segregation of BPH versus PCa. Retrospective analysis of biobank samples from patients with LUTS/BPH and patients with PCa was conducted with results indicating a diagnostic performance that is improved over that of PSA alone in discriminating patients with LUTS/BPH from patients with PCa. Use of this panel as a diagnostic test may reduce the number of unnecessary biopsies performed while providing physicians enhanced clinical decision support in addition to more definitive treatment clarity for patients in the future. Keywords: Bayesian artificial intelligence, Systems biology, Omics, Biomarkers, FLNA, FLNB, KRT19, Prostate Cancer, keratin-19, filamin-A, filamin- B, Benign prostate hypertrophy, ELISA, multiple reaction monitoring, PSA, BPH. DEDICATION This humble body of science and dissertation produced to further the understanding of cancer and efforts to employ novel technologies to detect prostate cancer more effectively is firstly dedicated to God for his choice to use me as a vessel to shed light onto the mysteries of cancer. The passion and energy instilled in me continues to navigate the cognitive chasm of blind faith of belief of a Supreme Being juxtaposed against the need to observe and understand the casual elements of disease pathophysiology. Secondly, I have been immensely Blessed to have educators as parents, Toolsie Ram Narain and Leela Narain who instilled in me the love of learning, the rejection of fear in the unknown, and the will power to have an indefatigable spirit to be unashamedly curious in my attempt to unmask the mysteries in medicine. For my brother Stephen R. Narain, my greatest critic and healthy competitor who has exposed me to the marvels of the world of literature and the arts, galvanizing an appreciation for the value in emotions of the fight but most importantly, the result. Most affectionately and with deepest love and appreciation to my life partner and endearing wife, Paula Patricia Narain for allowing me to be who I am and supporting a bold cause to make medicine better. Many nights holding my hands and wiping my tears on this path would have created a bond of truth and legacy. iii Saving my most fervent dedication to my 2 sons Paul Rajendra Narain and Philip Rajin Narain and if further Blessed other children to be. It is for you that this body of work which seeks truth and understanding shall propel a legacy that embraces the strength of being a servant while boldly carrying the necessary burdens of being a great leader. Professionally dedicated to the late Dr. Sung L. Hsia (Miller School of Medicine) and Dr. Rajendra S. Rana (St. John’s University, NY) who handed me their illustrious batons of science. iv ACKNOWLEDGEMENTS I would like to thank my mentor Stephen Lee who so poignantly yet gracefully reminds me of the sanctity and purity of the scientific process, the mark of greatness not created by the idea but what the data suggestions lead to. To other faculty at the Miller School of Medicine who molded my path either in research or clinical practice, Chairwoman of Biochemistry & Molecular Biology, Dr. Sylvia Daunert whose fire for science is infective and Chairman of Dermatology & Cutaneous Surgery, Dr. Robert Kirsner whose humility in patient care is ineffable. A special acknowledgement to Dr. Joaquin J. Jimenez who taught me the importance of translational science in truly validating clinical phenotypes. Also, to Dr. Sapna Deo who instilled in me the discipline and adherence to the academic process while engaging data-driven learning as the fuel for innovation. I would especially like to thank Carl E. Berg and Mitch Gray from Berg, LLC who have served as beacons to the opportunity to build an ecosystem of academic, industry, and government partners to advance the mission of creating better medicines and diagnostics. Their stark concentration and commitment to translating novel science into useful products for patients correlates to my passion and vision and for funding all of the research. To leadership and employees at Berg, LLC who over the years have emboldened my vision and passion for translational medicine, namely Drs. Rangaprasad Sarangarajan, Michael Kiebish, Viatschelav Akmaev, Stephane Gesta, and Vivek Vishnudas. v To key institutions and collaborators such as Maj. General (Ret.) USA, Dr. Elder Granger from the US Department of Defense, Walter Reed National Military Medical Center, leadership at the DoD/Center for Prostate Disease Research, Cleveland Clinic, Mt. Sinai Hospital, University of Toronto,
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