Jennifer E. Beane-Ebel PhD

Associate Professor, Computational Biomedicine

Member, Genome Science Institute

72 East Concord Street | (617) 501-5184
Jennifer Beane-Ebel

Computational Biomedicine


BU-BMC Cancer Center


Smoking Effects on Airway Epithelial Gene Expression.
Given the burden of lung disease created by cigarette smoking, surprisingly few studies had been done in humans to determine how smoking affects the epithelial cells of the pulmonary airways that are exposed to the highest concentrations of cigarette smoke. My research described changes in the airway transcriptome in response to cigarette smoke exposure and smoking cessation. The work represents global molecular characterization of the airway response to smoking and provided insights into the mechanisms leading to reversible and persistent effects of tobacco smoke. We are currently using single cell technologies to understand how smoking alters the cellular architecture of the bronchial epithelium and the immune microenvironment.

Gene Expression-Based Diagnostic for Lung Cancer.
Lung cancer is the leading cause of death from cancer in the US and the world and the mortality rate remains high due to lack of effective tools to diagnose the disease at an early stage. Histologically normal airway epithelial cells obtained from smokers undergoing bronchoscopy for suspicion of lung cancer were profiled using microarrays, and the data was used to develop a biomarker for the diagnosis of lung cancer. The biomarker has been commercialized by Veracyte and is marketed under the name PERCEPTATM. We continue to develop genomic biomarkers to predict the presence and outcome of bronchial premalignant lesions and early aggressive lung tumors.

Lung Cancer Chemoprevention and Understanding Biology Associated with the Development of Lung Squamous Premalignant Lesions.
Lung squamous cell cancer (LUSC) arises in the epithelial layer of the bronchial airways and is often preceded by the development of premalignant lesions. The molecular events involved in the progression of premalignant lesions to LUSC are not clearly understood as not all premalignant lesions go on to form carcinoma. Molecular characterization of premalignant lesions and non-lesion areas in the airway of individuals with premalignant lesions (i.e. the “field of injury”) is identifying early events in the process of lung carcinogenesis that can be leverage for lung cancer interception. As part of a large consortium, we are creating a Lung Pre-Cancer Atlas that includes bulk and single cell multi-omic profiling of a large number of lung premalignant lesions. Our goals are to understand mechanisms of premalignant lesion progression and persistence and to identify therapies to reverse or delay the onset of invasive lung cancer.


BU Profile


Health Administration/Informatics, PhD, Boston University

Biochemical Engineering, BE/BEng, Dartmouth College

Science Engineering, BA, Dartmouth College


Published on 10/2/2021

Lim Y, Beane-Ebel JE, Tanaka Y, Ning B, Husted CR, Henderson DC, Xiang Y, Park IH, Farrer LA, Zhang H. Exploration of alcohol use disorder-associated brain miRNA-mRNA regulatory networks. Transl Psychiatry. 2021 10 02; 11(1):504. PMID: 34601489.

Published on 5/6/2019

Hijazi K, Malyszko B, Steiling K, Xiao X, Liu G, Alekseyev YO, Dumas YM, Hertsgaard L, Jensen J, Hatsukami D, Brooks DR, O'Connor G, Beane J, Lenburg ME, Spira A. Tobacco-Related Alterations in Airway Gene Expression are Rapidly Reversed Within Weeks Following Smoking-Cessation. Sci Rep. 2019 05 06; 9(1):6978. PMID: 31061400.

Published on 4/23/2019

Beane JE, Mazzilli SA, Campbell JD, Duclos G, Krysan K, Moy C, Perdomo C, Schaffer M, Liu G, Zhang S, Liu H, Vick J, Dhillon SS, Platero SJ, Dubinett SM, Stevenson C, Reid ME, Lenburg ME, Spira AE. Molecular subtyping reveals immune alterations associated with progression of bronchial premalignant lesions. Nat Commun. 2019 04 23; 10(1):1856. PMID: 31015447.

Published on 1/21/2019

Teixeira VH, Pipinikas CP, Pennycuick A, Lee-Six H, Chandrasekharan D, Beane J, Morris TJ, Karpathakis A, Feber A, Breeze CE, Ntolios P, Hynds RE, Falzon M, Capitanio A, Carroll B, Durrenberger PF, Hardavella G, Brown JM, Lynch AG, Farmery H, Paul DS, Chambers RC, McGranahan N, Navani N, Thakrar RM, Swanton C, Beck S, George PJ, Spira A, Campbell PJ, Thirlwell C, Janes SM. Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions. Nat Med. 2019 03; 25(3):517-525. PMID: 30664780.

Published on 7/26/2017

Beane J, Campbell JD, Lel J, Vick J, Spira A. Genomic approaches to accelerate cancer interception. Lancet Oncol. 2017 Aug; 18(8):e494-e502. PMID: 28759388.

Published on 5/22/2017

Beane J, Mazzilli SA, Tassinari AM, Liu G, Zhang X, Liu H, Buncio AD, Dhillon SS, Platero SJ, Lenburg ME, Reid ME, Lam S, Spira AE. Detecting the Presence and Progression of Premalignant Lung Lesions via Airway Gene Expression. Clin Cancer Res. 2017 Sep 01; 23(17):5091-5100. PMID: 28533227.

Published on 11/17/2016

Rahman SM, Ji X, Zimmerman LJ, Li M, Harris BK, Hoeksema MD, Trenary IA, Zou Y, Qian J, Slebos RJ, Beane J, Spira A, Shyr Y, Eisenberg R, Liebler DC, Young JD, Massion PP. The airway epithelium undergoes metabolic reprogramming in individuals at high risk for lung cancer. JCI Insight. 2016 11 17; 1(19):e88814. PMID: 27882349.

Published on 10/15/2016

Kusko RL, Brothers JF, Tedrow J, Pandit K, Huleihel L, Perdomo C, Liu G, Juan-Guardela B, Kass D, Zhang S, Lenburg M, Martinez F, Quackenbush J, Sciurba F, Limper A, Geraci M, Yang I, Schwartz DA, Beane J, Spira A, Kaminski N. Integrated Genomics Reveals Convergent Transcriptomic Networks Underlying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2016 Oct 15; 194(8):948-960. PMID: 27104832.

Published on 9/22/2016

Lam S, Mandrekar SJ, Gesthalter Y, Allen Ziegler KL, Seisler DK, Midthun DE, Mao JT, Aubry MC, McWilliams A, Sin DD, Shaipanich T, Liu G, Johnson E, Bild A, Lenburg ME, Ionescu DN, Mayo J, Yi JE, Tazelaar H, Harmsen WS, Smith J, Spira AE, Beane J, Limburg PJ, Szabo E. A Randomized Phase IIb Trial of myo-Inositol in Smokers with Bronchial Dysplasia. Cancer Prev Res (Phila). 2016 Dec; 9(12):906-914. PMID: 27658890.

Published on 2/1/2016

Campbell JD, Mazzilli SA, Reid ME, Dhillon SS, Platero S, Beane J, Spira AE. The Case for a Pre-Cancer Genome Atlas (PCGA). Cancer Prev Res (Phila). 2016 Feb; 9(2):119-24. PMID: 26839336.

View full list of 29 publications.