Publications

Effect of Parental Adverse Childhood Experiences on Intergenerational DNA methylation Signatures from Peripheral blood mononuclear cells and buccal mucosa.

Mohazzab-Hosseinian S, Garcia E, Wiemels J, Marconett C, Corona K, Howe C, Foley H, Farzan S, Bastain T, Breton C.

Alveolar type I cells can give rise to KRAS-induced lung adenocarcinoma

Minxiao Yang, Hua Shen, Per Flodby, Michael D. Koss, Rania Bassiouni, Yixin Liu, Tea Jashashvili, Aaron Neely, Ezuka Ogbolu,  Theresa R. Stueve, Jonathan Castillo, Daniel J. Mullen, Amy L. Ryan, John Carpten, Alessandra Castaldi, W. Dean Wallace, Beiyun Zhou, Zea Borok, Crystal N. Marconett

Lack of racial and ethnic diversity in lung cancer cell lines contributes to lung cancer health disparities

Leon C, Nanley E, Neely AM, Castillo J, Ramos Correa M, Verlarde DA, Yang M, Puente PE, Romero DI, Ren B, Chai W, Gladstone M, Lamango NS, Huang Y, Offringa IA.

CLOCK'ing differences in DNA methylation signatures to understand the molecular etiology of lung cancer.

Aaron Neely, Minxiao Yang, Crystal Marconett

FOXO1 couples KGF and PI3K/AKT signaling to NKX2.1 regulated differentiation of alveolar epithelial cells

Zhong Q, Yixin Liu, Michele Ramos Correa, Crystal N. Marconett, Parviz Minoo, Changgong Li, DK Ann, Beiyun Zhou, Zea Borok

Development of human alveolar epithelial cell models to study distal lung biology disease

Evelyn Tran, T Shi, X. Li, AY Chowdhury, D Jiang, Yixin Liu, Hongjun Wang, Chunli Yan, W. Dean Wallace, Rongfu Lu, Amy L. Ryan, Crystal N. Marconett, Beiyun Zhou, Zea Borok, Ite. A. Offringa

The sulfotransferase SULT1C2 is epigenetically activated and transcriptionally induced by tobacco exposure and is associated with patient outcome in lung adenocarcinoma

Candace Johnson, Daniel J. Mullen, Suhaida A. Selamat, Mihaela Campan, Ite A. Offringa,  Crystal N. Marconett

Comprehensive epigenomic profiling of human alveolar epithelial differentiation identifies key epigenetic states and transcription factor co-regulatory networks for maintenance of distal lung identity

Beiyun Zhou, Theresa Ryan Stueve,  Evan A. Mihalakakos,  Lin Miao,  Daniel J Mullen,  Yinchong Wang, Yixin Liu, Jiao Luo, Evelyn Tran, Kimberly D. Siegmund, Sean K. Lynch, Amy L. Ryan, Ite A. Offringa,  Zea Borok,  Crystal N. Marconett

The evolutionarily conserved long non-coding RNA LINC00261 drives neuroendocrine prostate cancer proliferation and metastasis via distinct nuclear and cytoplasmic mechanisms

Mather R, Parolia A, Carson S, Venalainen E, Roig-Charles D, Chu SC, Alborelli I, Wu R, Lin D, Nabavi N, Jachetti E, Colombo MP, Xue H, Pucci P, Ci X, Hawkes C, Li Y, Pandha H, Ulitsky I, Crystal N. Marconett, Quagliata L, Jiang W, Romero I, Wang Y, Crea F. 

Molecular Oncology 2021 April 1 (ahead of print)

PMID: 33793068

PEREGRINE: A Genome-Wide Prediction of Enhancer to Gene Relationships Supported by Experimental Evidence

Caitlin Mills, Muruganujan A, Ebert D, Crystal N. Marconett, Juan Pablo Lewinger, Paul D. Thomas, Huaiyu Mi 

Plos One 2020, 15(12):e0243791. 

PMID: 33320871

Integrated Single Cell RNA Sequencing Analysis of Aquaporin-5 expressing Mouse Lung Epithelial Cells Identifies GPRC5A as a Novel Validated Type 1 Cell Surface Marker

Alesandra Castaldi, Masafumi Horie, Mitsuhiro Sunohara, Honjun Wang, Yanbin Ji, Yixin Liu, Li F, Wilkinson TA, Hung L, Hua Shen, Hidenori Kage, Ite A Offringa, Crystal N. Marconett, Per Flodby, Beiyun Zhou, Zea Borok

Cells 2020, 9(11):2460 

PMID: 33187367

TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma

Daniel J Mullen, Chunli Yan, Diane S Kang, Beiyun Zhou, Zea Borok, Crystal N Marconett, Peggy J Farnham, Ite A Offringa, Suhn K Rhie 

PLoS Genetics 2020, 16(9): e1009023. 

PMID: 32925947

Genome-wide integration of microRNA and transcriptomic profiles of differentiating human alveolar epithelial cells

Alessandra Castaldi, Masafumi Horie M, Megan E Rieger, Mickael Dubourd, Mitsuhiro Sunohara, Kusum Pandit, Beiyun Zhou, Ite A Offringa, Crystal N Marconett, Zea Borok  

American Journal of Physiology Lung Cell Molecular Physiology 2020,

PMID: 32432919

Tuberculosis infection and lung adenocarcinoma: Mendelian randomization and pathway analysis of genome-wide association study data from never-smoking Asian women

Wong JYY, Zhang H, Hsiung CA, Shiraishi K, Yu K, Matsuo K, Wong MP, Hong YC, Wang J, Seow WJ, Wang Z, Song M, Kim HN, Chang IS, Chatterjee N, Hu W, Wu C, Mitsudomi T, Zheng W, Kim JH, Seow A, Caporaso NE, et al., Laird-Offringa IA, Marconett CN, Rieswijk L, Chao A, Yang PC, Shu XO, Wu T, Wu YL, Lin D, Chen K, Zhou B, Huang YC, Kohno T, Shen H, Chanock SJ, Rothman N, Lan Q. 

Genomics 2019 S0888-7543 (19)30112-0. 

PMID: 31306748

LINC00261 Is an Epigenetically Regulated Tumor Suppressor Essential for Activation of the DNA Damage Response

Shandy Shahabi, Vishaly Kumaran, Jonathan Castillo, Zhengmin Cong, Gopika Nandagopal, Danie J Mullen, Alex Alvarado, Michele Ramos Correa, Autumn Saizan, Riya Goel, Amrita Bhat, Sean K. Lynch, Beiyun Zhou, Zea Borok, & Crystal N. Marconett.

Cancer Research 2019 (79) 3050–3062.

PMID: 30796052

Positional integration of lung adenocarcinoma susceptibility loci with primary human alveolar epithelial cell genomes

Chenchen Yang, Theresa Ryan Stueve, Chunli L. Yan, Suhn K. Rhie, Jiao Luo, Beiyun Zhou, Zea Borok, Crystal N. Marconett, Ite A. Offringa 

Epigenomics 2018 Sept; 10(9):1167-1187. 

PMID:30212242

Tight junction protein CLDN18.1 attenuates malignant properties and related signaling pathways of human lung adenocarcinoma in vivo and in vitro

Jiao Luo, Nyam O Chimge, Beiyun Zhou, Per Flodby, Alessandra Castaldi, Amy L Firth, Yixin Liu, Hongjun Wang, Chenchen Yang, Crystal N. Marconett, Edward D. Crandall, Ite A Offringa, Baruch Frenkel, Zea Borok

International Journal of Cancer 2018 Dec 15; 143(12):3169-3180. 

PMID:30325015

Claudin-18 regulates lung stem/progenitor cells homeostasis, YAP activity, and tumorigenesis

Beiyun Zhou, Per Flodby, Jiao Luo, Castillo D, Yixin Liu, Yu FX, McConnell A, Bino Varghese, Guanglei Li, Nyam O Chimge, Mitsuhiro Sunohara, Michael Koss, Wafaa Elatre, Peter Conti, Janice Leibler, Chenchen Yang, Crystal N. Marconett, Ite A Laird-Offringa, Parviz Minoo, Guan KL, Barry R. Stripp, Edward D. Crandall , Zea Borok. 

Journal of Clinical Investigation 2018 128(3): 970-984. 

PMID:29400695

Epigenome-wide association study of normal lung tissues identified hypomethylation of multiple CpG sites associated with cigarette smoking

Theresa R Stueve*, Li WQ*, Jianxin Shi, Crystal N. Marconett, W Wheeler, Neil E Caporaso, Pesatori AC, Ite A Laird-Offringa, Maria T. Landi 

Human Molecular Genetics 2017 Aug1;26(15):3014-3027. 

PMID: 28854564

Association between GWAS-identified lung adenocarcinoma susceptibility loci and EGFR mutations in never-smoking Asian women, a comparison with findings from Western populations

Seow WJ, Matsuo K, Hsiung CA, Shiraishi K, Song M, Kim HN, Wong MP, Hong YC, Dean Hosgood H 3rd, Wang Z, Chang IS, Wang JC, Chatterjee N, et al., Laird-Offringa IA, Marconett CN, Lin D, Chen K, Wu YL, Landi MT, Shen H, Rothman N, Kohno T, Chanock SJ, Lan Q. 

Human Molecular Genetics 2017 Jan 15;26(2):454-465. 

PMID:28025329

Intersecting transcriptomic profiling technologies and long non-coding RNA function in lung adenocarcinoma: discovery, mechanisms, and therapeutic applications. 

Jonathan Castillo, Theresa Ryan Stueve, Crystal N. Marconett. 

Oncotarget 2017 Jun 9;8(46):81538-81557.

Somatic Genomic Landscape of Lung Adenocarcinoma and its Association with Clinical Features

Shi J, Hua X, Zhu B, Ravichandran S, Wang M, Nguyen C, Brodie S, Palleschi A, Alloisio M, Pariscenti et al., Crystal N. Marconett, Ite A. Laird-Offringa, Mills I, Caporaso N, Gail M, Pesatori A, Consonni D, Bertazzi PA, Chanock S, Lanti MT. 

PLoS Medicine 2016 13(12):e1002162. 

PMID:27923066

Cross-species transcriptome profiling identifies new alveolar epithelial type I cell-specific genes

Crystal N. Marconett, Beiyun Zhou, Mitsuhiro Sunohara, Tiffany M Pouldar, Hongjun Wang, Yixin Liu, Megan E Rieger, Ite A Laird-Offringa, Zea Borok. 

American Journal of Respiratory Cell and Molecular Biology 2016 56(3):310-321

PMID: 27749084

Multi-trait pleiotropic analysis of genetic risk uncovers a pan-tissue functional variant for lung cancer

Zuber V, Marconett CN, Shi J, Laplana M, Risch A, Witolaer A, Thompson WK, Schork AJ, Bettella F, Wang Y, Djurovic S, TRICL Consortium, GAME-ON Consortium, Dale AM, Andreassen OA, Laird-Offringa IA, Landi MT, Mills IG

Journal of the National Cancer Institute2016 Aug 26; 108(12). 

PMID: 27565901

The importance of detailed epigenomic profiling of different cell types within organs 

Theresa Ryan Stueve, Crystal N. Marconett, Beiyun Zhou, Zea Borok, Ite A Laird-Offringa. 

Epigenomics 2016.  8(6):817-29. 

PMID: 27305639

The 78-kD glucose-regulated protein regulates endoplasmic reticulum homeostasis and distal epithelial cell survival during lung development 

Per Flodby, Yixin Liu, Hongjun Wang, Crystal N. Marconett, Ite A Laird-Offringa, Parviz Minoo, Amy S Lee, Beiyun Zhou 

American Journal of Respiratory Cell & Molecular Biology 2016  55(1):135-49

PMID: 26816051                                                                   

Combinations of differentiation markers distinguish subpopulations of alveolar epithelial cells in adult lung

Janice Liebler, Crystal N. Marconett, Juul N, Hongjun Wang, Yixin Liu, Per Flodby, Ite A Laird-Offringa, Beiyun Zhou 

American Journal of Physiology - Lung Cellular and Molecular Physiology 2016 310(2) LL114-20. 

PMID: 26545903                                                    

Transcriptomic profiling of primary alveolar epithelial cell differentiation in human and rat

Marconett CN, Zhou B, Siegmund KM, Borok Z, Laird-Offringa IA.

Genomics Data May 2014 (2):105-109. 

PMID: 25343132      

Characterizing the genetic basis of methylome diversity in histologically normal lung tissue 

Shi J, Marconett CN, Duan J, Hyland PL, Li P, Wang Z, Wheeler W, Zhou B, Campan M, Lee DS, Huang J, Zhou W, Triche T, Amundadottir L, Warner A, Hutchinson A, Chen PH, Chung B, Pesatori AC, Consonni D, Bertazzi PA, Bergen AQ, Freedman M, Siegmund KD, Berman BP, Borok Z, Chatterjee N, Tucker MA, Caporaso NE, Chanock SJ, Laird-Offringa IA, Landi MT. 

Nature Communications 2014; 5:3365

PMID: 24572595     

Claudin 4 knockout mice: normal physiologic phenotype with increased susceptibility to lung injury

Kage H, Flodby P, Gao D, Kim YH, Marconett CN, DeMaio L, Kim KJ, Crandall ED, Borok Z. 

American Journal Lung Molecular Physiology 2014 307(7):L524-36

PMID: 25106430

Knockout mice reveal key roles for claudin 18 in alveolar barrier properties and fluid homeostasis

Li G*, Flodby P*, Luo J, Kage H, Spios A, Gao D, Beard L, Marconett CN, DeMaio L, Kim YH, Kim KJ, Laird-Offringa IA, Minoo P, Liebler J, Zhou B, Crandall ED

American Journal of Respiratory Cell & Molecular Biology 2014 51(2):210-22

PMID: 24588076

Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation

Crystal N. Marconett, Beiyun Zhou, Megan E Rieger, Suhaida A Selamat, Mickael Dubourd M, Theresa Ryan Stueve, Fang X, Sean K. Lynch, Kimberly D Siegmund, Benjamin P Berman, Zea Borok*, Ite A Laird-Offringa 

PLoS Genetics 2013; 9(6):e1003513. 

PMID: 23818859

CDKN2A/p16 inactivation methods and their relationship to smoke exposure and molecular features in non-small cell lung cancer

Tam KW, Zhang W, Soh J, Stastny V, Chen M, Sun H, Thu K, Lam W, Yang C, Marconett CN, Selamat SA, Laird-Offringa IA, Taguchi A, Hanash S, Gazdar A. –J of Thoracic Oncology 

PMID: 24077454