Jennifer E. Beane-Ebel, PhD
Associate Professor, Medicine
Biography
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.
Other Positions
- Member, BU-BMC Cancer Center, Boston University
- Member, Genome Science Institute, Boston University
Websites
Education
- Boston University, PhD
- Dartmouth College, BE/BEng
- Dartmouth College, BA
Publications
- Published on 2/17/2025
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. PMID: 39983471.
Read at: PubMed - Published on 2/5/2025
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. PMID: 39975222.
Read at: PubMed - Published on 9/4/2024
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. PMID: 38587959.
Read at: PubMed - Published on 9/1/2024
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.
Read at: PubMed - Published on 6/10/2024
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. PMID: 38915565.
Read at: PubMed - Published on 6/4/2024
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. PMID: 38993668.
Read at: PubMed - Published on 5/22/2024
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; CBM230456. PMID: 39058440.
Read at: PubMed - Published on 5/14/2024
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. PMID: 38464291.
Read at: PubMed - Published on 4/6/2024
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. PMID: 38588853.
Read at: PubMed - Published on 10/2/2023
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. PMID: 37477508.
Read at: PubMed
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