Jennifer E. Beane-Ebel, PhD
Associate Professor
Boston University Chobanian & Avedisian School of Medicine
Computational Biomedicine

PhD, Boston University
BE/BEng, Dartmouth College
BA, Dartmouth College

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.

Boston University
BU-BMC Cancer Center

Boston University
Genome Science Institute

The Boston University - UCLA Lung Cancer Biomarker Characterization Center
09/01/2022 - 07/31/2027 (Multi-PI)
PI: Jennifer E. Beane-Ebel, PhD
NIH/National Cancer Institute

Using deep learning to advance lung cancer interception and early detection
01/01/2022 - 12/31/2023 (Multi-PI)
PI: Jennifer E. Beane-Ebel, PhD
Johnson & Johnson Enterprise Innovation, Inc.

PRISTINE: Pre-cancer histology identification of Endobronchial biopsies using deep learning
09/01/2020 - 08/31/2023 (Multi-PI)
PI: Jennifer E. Beane-Ebel, PhD
NIH/National Cancer Institute

Randomized Clinical Trial of Lung Cancer Chemoprevention with Sulforaphane in Former Smokers
01/01/2022 - 05/31/2023 (Subcontract PI)
University of Pittsburgh NIH NCI

Biomarkers of lung squamous premalignant progression using deep learning on pathology images
06/01/2020 - 12/31/2021 (Multi-PI)
PI: Jennifer E. Beane-Ebel, PhD
Johnson & Johnson Enterprise Innovation, Inc.

Clinical Study of Effect of Combined Treatment of Aspirin and Zileuton on Biomarkers on Tobacco-Related Carcinogenesis in Current Smokers
02/07/2018 - 08/31/2021 (Subcontract PI)
Arizona Board of Regents, University of Arizona NIH NCI

Integrated molecular, cellular and imaging characterization of screen-detected lung cancer
09/16/2015 - 08/31/2021 (Co-Investigator of Sub-Project / SP)
PI: Marc Lenburg, PhD
University of California, Los Angeles NIH NCI

Single-cell RNA sequencing of the bronchial epithelium in smokers with lung cancer
07/01/2014 - 06/30/2018 (PI)
Department of Defense/Army Medical Research Acquisition Activity

Quasispecies dynamics in arbovirius emergence persistence and fitness
09/27/2012 - 08/31/2016 (Subcontract PI)
Colorado State University NIH NIAID

Biomarkers of Pre-malignant Disease Progression for Lung Cancer Detection
07/15/2012 - 07/14/2016 (PI)
American Thoracic Society/ LUNGevity Foundation

Showing 10 of 11 results. Show All Results


Yr Title Project-Sub Proj Pubs

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

iCite Analysis       Copy PMIDs To Clipboard

  1. 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.View Related Profiles. PMID: 34601489; PMCID: PMC8487426; DOI: 10.1038/s41398-021-01635-w;
  2. 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.View Related Profiles. PMID: 31061400; PMCID: PMC6502805; DOI: 10.1038/s41598-019-43295-3;
  3. 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.View Related Profiles. PMID: 31015447; PMCID: PMC6478943; DOI: 10.1038/s41467-019-09834-2;
  4. 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.View Related Profiles. PMID: 30664780; PMCID: PMC7614970; DOI: 10.1038/s41591-018-0323-0;
  5. Beane J, Campbell JD, Lel J, Vick J, Spira A. Genomic approaches to accelerate cancer interception. Lancet Oncol. 2017 Aug; 18(8):e494-e502.View Related Profiles. PMID: 28759388; PMCID: PMC6020676; DOI: 10.1016/S1470-2045(17)30373-X;
  6. 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.View Related Profiles. PMID: 28533227; PMCID: PMC7404813; DOI: 10.1158/1078-0432.CCR-16-2540;
  7. 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.View Related Profiles. PMID: 27882349; PMCID: PMC5111517; DOI: 10.1172/jci.insight.88814;
  8. 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.View Related Profiles. PMID: 27104832; PMCID: PMC5067817; DOI: 10.1164/rccm.201510-2026OC;
  9. 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.View Related Profiles. PMID: 27658890; PMCID: PMC5136333; DOI: 10.1158/1940-6207.CAPR-15-0254;
  10. 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.View Related Profiles. PMID: 26839336; DOI: 10.1158/1940-6207.CAPR-16-0024;
Showing 10 of 29 results. Show More

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 29 publications over 15 distinct years, with a maximum of 5 publications in 2004

In addition to these self-described keywords below, a list of MeSH based concepts is available here.

Lung cancer
Computational Biology
Lung Disease
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