The Role of Long Noncoding Rnas in Cancer and Microbiota
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THE ROLE OF LONG NONCODING RNAS IN CANCER AND MICROBIOTA- DERIVED ARYL HYDROCARBON RECEPTOR LIGANDS A Dissertation by YATING CHENG Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Stephen H. Safe Committee Members, Natalie M. Johnson Timothy D. Phillips Weston W. Porter Yanan Tian Intercollegiate Faculty Chair, Ivan Rusyn December 2016 Major Subject: Toxicology Copyright 2016 Yating Cheng ABSTRACT LncRNAs are a group of non-coding RNAs containing >200 nucleotides and these RNAs have no significant protein coding potential. In the past 10-15 years the role of lncRNAs in cancers have been demonstrated, however, their function in tumors and potential for drug targeting are not well defined. We studied two lncRNAs, HOXA transcript at the distal tip (HOTTIP) and metastasis associated lung adenocarcinoma transcript 1 (MALAT1) in pancreatic cancer using the in vitro cell lines and in vivo xenograft or transgenic mouse models. Our results demonstrated that both lncRNAs are pro-oncogenic in the pancreatic cancer, supported by the observation that knockdown of HOTTIP and MALAT1 decreased cell proliferation, migration/invasion and increased apoptosis. HOTTIP might exhibit some pro-oncogenic functions, via the regulation of HOXA gene clusters in a cis-regulating manner. On the other hand, MALAT1 regulate responses of pancreatic cancer cells in part via polycomb repressive complex 2 (PRC2) dependent and independent pathways. Our transcriptomic results support the important but distinct roles of HOTTIP and MALAT1 in pancreatic cancer and we also show that MALAT1 expression can be targeted by small molecule drugs. In the second part of this dissertation, we studied several microbiota-derived aryl hydrocarbon receptor (AhR) ligands. The AhR is a ligand-activated transcription factor with an evolving role in the normal physiological development and diseases. Gut microbiota metabolites are important for mediating communication between gut microflora and the host. It has recently been shown that the gut microbiota produces several metabolites that are AhR ii ligands. Microbiota-derived tryptophan metabolites and 1,4-dihydroxy-2-napthoic acid (DHNA) and related compounds are reported to be AhR ligands as evidence by their induction of cytochrome P450, family 1, subfamily A, polypeptide 1 (CYP1A1) and other AhR-responsive genes. We hypothesized the microbiota-derived AhR ligands are selective AhR modulators (sAhRMs) and their induction responses are compound, gene and cell context dependent. We have carried out extensive studies on tryptophan metabolites, DHNA and related compounds in both human and mouse colon cancer cell lines, and have observed that some of these compounds exhibited partial agonist/antagonist activities that are both gene and cell context specific. iii DEDICATION To my father who passed away when I was a sophomore. I missed him so much. To my mother for her unconditional love and support. To my husband for his love, patience and support. iv ACKNOWLEDGEMENTS I would like to thank my mentor Dr. Stephen H. Safe for all the support and guidance throughout my Ph.D. studies. He is a great scientist and has taught me how to be a good scientist. Next, I would like to thank my committee members Dr. Natalie M. Johnson, Dr. Timothy D. Phillips, Dr. Weston W. Porter and Dr. Yanan Tian for their precious time and supportive advice. I would like to thank all the people in the Safe lab. I would like to thank the current lab members, Dr. Un-ho Jin, Dr. Xi Li, Dr. Mohankumar Kumaravel, Alexandra Lacey, Erik Hedrick, and Keshav Karki. I also thank past lab members Dr. Indira Jutooru, Dr. Gayathri Chadalapaka, Dr. Sandeep Sreevalsan, and Dr. Vijayalekshmi Vasanthakumari who helped me a lot with my research. I also thank Katherine Mooney, who helped with preparing manuscripts and taught me how to use reference tools. The help from the undergraduate students is also gratefully appreciated. In the end, special thanks to Lorna Safe, who has given me some great advice in life and offered me the chance to train my managing skills in the lab. I also thank all the faculty and staff in the Toxicology program. Special thanks to Kim Daniel, who has helped me a lot since I joined the toxicology program. v Last but not the least, I would like to thank my family and friends for their continuous support. vi CONTRIBUTORS AND FUNDING SOURCES Contributors section Part 1, faculty committee recognition This work was supervised by a dissertation committee consisting of Professors Stephen Safe and Yanan Tian of the Department of Veterinary Physiology and Pharmacology, Professors Western Porter and Timothy Phillips of the Department of Veterinary Integrative Biosciences, and Professor Natalie Johnson of the School of Public Health. Part 2, student/collaborator contributions The work presented in Section 2 is the reprinted from Cheng et al. “The long non-coding RNA HOTTIP enhances pancreatic cancer cell proliferation, survival and migration” published in May 2015 with permission from Oncotarget. All work was completed by the student, under the supervision of Dr. Stephen Safe, in collaboration with Drs. Indira Jutooru, Gayathri Chadalapaka from Department of Veterinary Physiology and Pharmacology, Dr. J. Christopher Corton of Integrated Systems Toxicology Division, US-EPA. We would like to thank the help from Drs. Susan Hester and Brian Chorley for reviewing this manuscript. The work presented in Section 3 is a version of Cheng et al “Role of metastasis- associated lung adenocarcinoma transcript-1 (MALAT-1) in pancreatic cancer” which is under review at Carcinogenesis. All work was completed by the student, under the vii supervision of Dr. Stephen Safe, in collaboration with Drs. Parisa Imanirad, Indira Jutooru, Erik Hedrick, Un-ho Jin of Department of Veterinary Physiology and Pharmacology, Dr. Aline Rodriguez-Hoffman of the Department of Veterinary Pathobiology, Drs. Ben Morpurgo, Andrei Golovko of Institute for Genomic Medicine. The work presented in Section 4 is reprinted from Cheng et al. “Aryl hydrocarbon receptor activity of tryptophan metabolites in young adult mouse colonocytes” published in October 2015 with the permission from Drug metabolism and Disposition. All work was completed by the student, under the supervision of Dr. Stephen Safe, in collaboration with Dr. Unho Jin of Department of Veterinary Physiology and Pharmacology, Drs. Clint D. Allred, Robert S. Chapkin of Department of Nutrition and Food Science, Dr. Arul Jayraman of Department of Chemical Engineering. The work presented in Section 5 is reprinted from Cheng et al “Microbial-derived 1,4- dihydroxy-2-naphthoic acid and related compounds as aryl hydrocarbon receptor agonists/antagonists: structure-activity relationships and receptor modeling” which was accepted in November 2016. All work was completed by the student, under the supervision of Dr. Stephen Safe, in collaboration with Dr. Un-ho Jin of Department of Veterinary Physiology and Pharmacology; Drs. Clint Allred, Laurie A. Davidson, Robert S. Chapkin of Department of Nutrition and Food Science; Drs. Arul Jayraman, Phanourios Tamamis, Mr. Asuka Orr of Department of Chemical Engineering; Evelyn viii Weaver of Department of Animal Science; and Drs. Michael S. Denison, Anatoly Soshilov of Department of Environmental Toxicology at University of California. Funding sources The financial assistance from the National Institutes of Health (P30-ES023512) and Texas AgriLife Research is gratefully appreciated for the work in Section 2. The financial assistance from the National Institutes of Health National Institute of Environmental Health Sciences [P30-ES023512], Texas AgriLife Research, Sid Kyle Chair Endowmentis and TAMU-CVM graduate student core facility experiential learning program funds is gratefully appreciated for the work in Section 3. This work in Section 4 was supported by the National Institutes of Health National Institute of Environmental Health Sciences [P30-ES023512], Texas AgriLife Research, the Sid Kyle Chair Endowment and TAMU-CVM graduate student trainee research grant. The work in Section 5 was supported by National Institutes of Health [R01-ES025713, R01-ES007685, P30-ES023512, R35-CA19707 and R01-CA202697]; Cancer Prevention Research Institute of Texas; Texas AgriLife Research; the Office of Graduate and Professional Studies and the Artie McFerrin Department of Chemical Engineering at Texas A&M University; and the Sid Kyle Endowment. ix TABLE OF CONTENTS Page ABSTRACT .......................................................................................................................ii DEDICATION .................................................................................................................. iv ACKNOWLEDGEMENTS ............................................................................................... v CONTRIBUTORS AND FUNDING SOURCES ............................................................vii TABLE OF CONTENTS ................................................................................................... x LIST OF FIGURES ..........................................................................................................xii LIST OF TABLES .......................................................................................................... xiv 1. INTRODUCTION AND LITERATURE REVIEW ...................................................... 1 1.1