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

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

Pronouns: she/her/hers



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. Recent single cell RNA sequencing on airway epithelial cells from current and never smokers attributes many of these previously described changes to smoking-associated changes in the abundance of different cell types and the existence of a previously uncharacterized cell type expressing genes persistently altered by smoking.

Early Detection of Lung Cancer via a 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. I was subsequently able to show that the gene expression biomarker added predictive value above clinical risk variables and maintained high performance among subjects with intermediate risk for lung cancer. The biomarker was patented and commercialized by Veracyte. We continue to develop lung cancer detection biomarkers derived from the bronchial and nasal epithelium and explore their efficacy in combination with CT image and blood based biomarkrers.

Development and Progression 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 and chemoprevention.

Pathology Image Analysis. Many lung-related studies involve that pathologic evaluation of lung resection tissues or lung biopsies to determine disease severity. The rich data present in pathology slides is rarely incorporated into analyses to identify determinants of disease progression. To address this shortcoming, I am involved in developing methods that utilize H&E-stained digitized whole slide images alone or in combination with molecular data to understand the pathologic and molecular features associated with the early development of lung cancer. These methods complement our analyses of spatial transcriptomic and proteomic data to understand mechanisms of cancer initiation.

Member
Boston University
BU-BMC Cancer Center


Member
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
5U2CCA271898-03

Analysis of Genes and Products in Tumor and Normal Issue and Biomarkers of Lichen Scelrosus
01/23/2024 - 01/22/2025 (PI)
Lahey Clinic, Inc.


PRISTINE: Pre-cancer histology identification of Endobronchial biopsies using deep learning
09/01/2020 - 08/31/2024 (Multi-PI)
PI: Jennifer E. Beane-Ebel, PhD
NIH/National Cancer Institute
1R21CA253498-01

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.


Randomized Clinical Trial of Lung Cancer Chemoprevention with Sulforaphane in Former Smokers
01/01/2022 - 05/31/2023 (Subcontract PI)
The University of Pittsburgh NIH NCI
5R01CA213123-05

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 (PI of Sub-Project / SP)
PI: Marc Lenburg, PhD
University of California, Los Angeles NIH NCI
3U01CA196408-05S1

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
5R01AI067380-09

Showing 10 of 12 results. Show All Results


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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. Sousa A, Besong OTO, Wachman EM, Taglauer ES, Beane JE, Kefella Y, Koo JS, Saia K, Jones HE, Zhang H. Placental transcriptome analysis in opioid-exposed versus non-opioid exposed pregnancies. Placenta. 2025 Mar 25; 162:27-34.View Related Profiles. PMID: 39983471
     
  2. Ning B, Chiu DJ, Pfefferkorn RM, Kefella Y, Kane E, Reyes-Ortiz V, Liu G, Zhang S, Liu H, Sultan L, Green E, Constant M, Spira AE, Campbell JD, Reid ME, Varelas X, Burks EJ, Lenburg ME, Mazzilli SA, Beane JE. Epithelial miR-149-5p up-regulation is associated with immune evasion in progressive bronchial premalignant lesions. bioRxiv. 2025 Feb 05.View Related Profiles. PMID: 39975222; PMCID: PMC11838605; DOI: 10.1101/2025.02.03.636307;
     
  3. Zheng Y, Conrad RD, Green EJ, Burks EJ, Betke M, Beane JE, Kolachalama VB. Graph Attention-Based Fusion of Pathology Images and Gene Expression for Prediction of Cancer Survival. IEEE Trans Med Imaging. 2024 Sep; 43(9):3085-3097.View Related Profiles. PMID: 38587959; PMCID: PMC11374469; DOI: 10.1109/TMI.2024.3386108;
     
  4. Moghaddam SJ, Savai R, Salehi-Rad R, Sengupta S, Kammer MN, Massion P, Beane JE, Ostrin EJ, Priolo C, Tennis MA, Stabile LP, Bauer AK, Sears CR, Szabo E, Rivera MP, Powell CA, Kadara H, Jenkins BJ, Dubinett SM, Houghton AM, Kim CF, Keith RL. Premalignant Progression in the Lung: Knowledge Gaps and Novel Opportunities for Interception of Non-Small Cell Lung Cancer. An Official American Thoracic Society Research Statement. Am J Respir Crit Care Med. 2024 Sep 01; 210(5):548-571. PMID: 39115548; PMCID: PMC11389570; DOI: 10.1164/rccm.202406-1168ST;
     
  5. Steiner D, Sultan L, Sullivan T, Liu H, Zhang S, LeClerc A, Alekseyev YO, Liu G, Mazzilli SA, Zhang J, Rieger-Christ K, Burks EJ, Beane J, Lenburg ME. Identification of a gene expression signature of vascular invasion and recurrence in stage I lung adenocarcinoma via bulk and spatial transcriptomics. bioRxiv. 2024 Jun 10.View Related Profiles. PMID: 38915565; PMCID: PMC11195124; DOI: 10.1101/2024.06.07.597993;
     
  6. Ysasi AB, Engler AE, Bawa PS, Wang F, Conrad RD, Yeung AK, Rock JR, Beane-Ebel J, Mazzilli SA, Franklin RA, Mizgerd JP, Murphy GJ. A specialized population of monocyte-derived tracheal macrophages promote airway epithelial regeneration through a CCR2-dependent mechanism. iScience. 2024 Jul 19; 27(7):110169.View Related Profiles. PMID: 38993668; PMCID: PMC11238131; DOI: 10.1016/j.isci.2024.110169;
     
  7. Steiner D, Park JA, Singh S, Potter A, Scalera J, Beane J, Suzuki K, Lenburg ME, Burks EJ. A computed tomography-based score indicative of lung cancer aggression (SILA) predicts lung adenocarcinomas with low malignant potential or vascular invasion. Cancer Biomark. 2024 May 22.View Related Profiles. PMID: 39058440; DOI: 10.3233/CBM-230456;
     
  8. Cai L, Gao Y, DeBerardinis RJ, Acquaah-Mensah G, Aidinis V, Beane JE, Biswal S, Chen T, Concepcion-Crisol CP, Grüner BM, Jia D, Jones R, Kurie JM, Lee MG, Lindahl P, Lissanu Y, Lorz Lopez MC, Martinelli R, Mazur PK, Mazzilli SA, Mii S, Moll H, Moorehead R, Morrisey EE, Ng SR, Oser MG, Pandiri AR, Powell CA, Ramadori G, Santos Lafuente M, Snyder E, Sotillo R, Su KY, Taki T, Taparra K, Xia Y, van Veen E, Winslow MM, Xiao G, Rudin CM, Oliver TG, Xie Y, Minna JD. A Lung Cancer Mouse Model Database. bioRxiv. 2024 May 14.View Related Profiles. PMID: 38464291; PMCID: PMC10925271; DOI: 10.1101/2024.02.28.582577;
     
  9. Gindra RH, Zheng Y, Green EJ, Reid ME, Mazzilli SA, Merrick DT, Burks EJ, Kolachalama VB, Beane JE. Graph Perceiver Network for Lung Tumor and Bronchial Premalignant Lesion Stratification from Histopathology. Am J Pathol. 2024 Jul; 194(7):1285-1293.View Related Profiles. PMID: 38588853; PMCID: PMC11220922; DOI: 10.1016/j.ajpath.2024.03.009;
     
  10. Yanagawa J, Tran LM, Salehi-Rad R, Lim RJ, Dumitras C, Fung E, Wallace WD, Prosper AE, Fishbein G, Shea C, Hong R, Kahangi B, Deng JJ, Gower AC, Liu B, Campbell JD, Mazzilli SA, Beane JE, Kadara H, Lenburg ME, Spira AE, Aberle DR, Krysan K, Dubinett SM. Single-Cell Characterization of Pulmonary Nodules Implicates Suppression of Immunosurveillance across Early Stages of Lung Adenocarcinoma. Cancer Res. 2023 Oct 02; 83(19):3305-3319.View Related Profiles. PMID: 37477508; PMCID: PMC10544016; DOI: 10.1158/0008-5472.CAN-23-0128;
     
Showing 10 of 54 results. Show More

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

Bar chart showing 54 publications over 19 distinct years, with a maximum of 7 publications in 2024

YearPublications
20011
20045
20052
20061
20073
20081
20092
20111
20121
20141
20151
20164
20172
20196
20216
20224
20234
20247
20252


BU researcher awarded $4.6 million U2C grant to develop innovative lung cancer biomarkers

News Medical 10/17/2022

Researchers develop novel AI algorithm for digital pathology analysis

Longevity Technology 5/26/2022

What If We Could Stop Lung Cancer Before It Starts?

BU Today 4/23/2019
In addition to these self-described keywords below, a list of MeSH based concepts is available here.

Lung cancer
Computational Biology
Genomics
Lung Disease
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