Antonina Mitrofanova, Ph.D.
At Rutgers, my laboratory develops and clinically adopts computational algorithms to elucidate genomic, transcriptomic, and epigenomic mechanisms of disease progression and therapeutic response in cancer and other diseases, and identifies optimal treatment strategies for patients based on their molecular profiles and clinical characteristics.
Research Overview
Engineering Smarter Cancer Treatments
Our goal is to build a multi-level panel of markers to predict patients’ risk of treatment resistance and provide personalized advice on their optimal therapeutic course.
Research Team
The people behind the science
Michael W. Craige
Post-Doctoral Fellow
Sukanya Panja
Post-Doctoral Scientist
Mohamed Ahmed
Post-Doctoral Scientist
Mayra Vendramini Tuiche
Ph.D. student
Indrani Datta
Doctoral student
Mehdi Nostrati
Graduate student
Anitha Ramakrishnan
M.S. student
Vamshi Saggurthi
M.S. student
Jay Patil
M.S. student
Funding & Grants
Supported Research Programs
Federal, foundation, and institutional funding advancing predictive modeling of treatment responses
DOD Prostate Cancer Data Science Award
$785,000
Mechanism-Centric Predictive Modeling for Prostate Cancer
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We propose to develop a novel computational paradigm LeNA-TR2PATH that investigates relationships between epigenomic and transcriptomic mechanisms: long-non-coding RNAs (lnRNAs), transcriptional regulatory (TR) programs, and molecular pathways, and evaluates them as effective biomarkers for the risk of metastatic progression and ARSI (androgen-receptor signaling inhibitors) treatment failure.
In particular, we propose to:
- develop and apply LeNA-TR2PATH to elucidate PC metastatic progression; and
- refine and apply LeNA-TR2PATH to elucidate therapeutic response to ARSIs.
Status of Support: Active
Project Number: HT94252410346
Name of PD/PI: Antonina Mitrofanova
Primary Place of Performance: Rutgers, The State University of New Jersey-RBHS-SHP
Total Award Amount (including Indirect Costs): $785,000
Project/Proposal Start and End Date: : 07/2024 – 06/2027
- 7/24 - 6/ 27
American Cancer Society
$792,000
Systems Analysis of Drug Resistance in Prostate Cancer
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Specific Aims:
- Aim 1: Identification of key master regulators of castration-resistant prostate cancer.
- Aim 2: Systems biology approach to predict drug combinations to overcome resistance in CRPC.
Total Award Amount (including Indirect Costs): $792,000.00
Project/Proposal Start and End Date: 07/2021 – 06/2025
- 7/21 - 6/25
Rutgers School of Health Professions
$35,000
Generalizable Systems Biology Paradigm for Predictive Modeling of Treatment Response
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Specific Aims:
- Aim 1: Develop a versatile computational network-based paradigm through modeling response to androgen-targeted therapies in prostate cancer.
- Aim 2: Develop an open-source web-based portal for treatment response modeling
Total Award Amount (including Indirect Costs): $35,000
Project/Proposal Start and End Date: 09/2020 – 08/2024
- 9/20 - 8/24
NIH NLM
$1,300,906
Generalizable Biomedical Informatics Strategies for Predictive Modeling of Treatment Response
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Specific Aims:
- Aim 1. Develop and disseminate PREDICTTR through a web-based open-source portal
- Aim 2. Application of PREDICTTR to treatment response in prostate cancer
- Aim 3. Application of PREDICTTR to elucidate chemo response in acute myeloid leukemia
Total Award Amount (including Indirect Costs): $1,300,906
Project/Proposal Start and End Date: : 09/2020 – 09/2024
- 9/20 - 9/24
New Jersey Commission on Cancer Research (NJCCR)
$250,000
Scalable Generalizable Framework for Predicting Treatment Response in Prostate Cancer
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Specific Aims:
- Aim 1: Develop novel computational method for generating alternative-splicing regulatory network for prostate cancer
- Aim 2: Establish a relationship between alternative splicing and long non-coding RNAs in prostate cancer
Total Award Amount (including Indirect Costs): $250,000
Project/Proposal Start and End Date: 05/2021 – 08/2023
- 5/21 - 8/23
Rutgers School of Health Professions
$785,000
Computational systems biology approaches to discover therapeutic strategies for patients with castration resistant prostate cancer
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Specific Aims:
- Aim 1. Identification of drivers that transcriptionally control signatures of castration-resistance.
- Aim 2. Systems analysis of treatment response in castration-resistant tumors.
- Aim 3. Prediction of optimal drug combinations for human patients with castration-resistance.
Total Award Amount (including Indirect Costs): $35,000
Project/Proposal Start and End Date: 6/15/2016 – 01/01/2018
- 6/15/2016 - 1/1/2018
Publications & Impact
Selected Research Publications
2024
Mechanism-centric regulatory network identifies NME2 and MYC programs as markers of Enzalutamide resistance in CRPC
Panja, S.*, Truica, M.I.*, Yu, Ch.Y., Saggurthi, V., Craige, M.W., Whitehead, K., Tuiche, M.V., Al-Saadi, A., Vyas, R., Ganesan, Sh., Gohel, S., Coffman, F., Parrott, J.S., Jha, Sh., Kim, I., Schaeffer, E., Kothari, V.†, Abdulkadir, S.A.†, Mitrofanova, A.
Nature Communications, 15(1):352. PMID: 38191557.v
2023
Tissue-specific biological aging predicts progression in prostate cancer and acute myeloid leukemia
Ramakrishnan, A.*, Datta, I.*, Panja, S.*, Patel, H., Liu, Y., Craige, M.W., Chu, C., Jean-Marie, G., Oladoja, A-R.,
Kim, I.Y., and Mitrofanova, A.†
Frontiers in Oncology, 6:13:1222168. PMID: 37746266
2022
Random survival forest model identifies novel biomarkers of event-free survival in high-risk pediatric acute lymphoblastic leukemia
Bohannan, Z., Coffman, F., and Mitrofanova, A.†
Computational and Structural Biotechnology Journal, 20: 583-597. PMID: 35116134.
† Senior Corresponding author.
2021
Mechanism-centric approaches for biomarker detection and precision therapeutics in cancer
Yu, Ch., Mitrofanova, A.†
Frontiers in Genetics, 12: 687813. PMID: 34408770. † Senior Corresponding author.
2020
Genome-wide analysis of therapeutic response uncovers molecular pathways governing tamoxifen resistance in ER+ breast cancer
Rahem, S.M., Epsi, N.J., Coffman, F.D., Mitrofanova, A.†
EBioMedicine (published by THE LANCET), 61:103047, PMID: 33099086
2020
A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance
Arriaga, J., Panja, S., Alshalalfa, M., Zhao, J., Zou, M., Giacobbe, A., Madubata4, C.J., Kim, J.Y., Rodriguez, A., Coleman, I., Virk, R.K., Hibshoosh, H., Ertunc, O., Ozbek, B., Fountain, J., Karnes, R.J., Luo, J., Antonarakis, E.S., Nelson, P.S., Feng, F.Y., Rubin, M.A., De Marzo, A.M., Rabadan, R., Sims, P.A., Mitrofanova, A.†, Abate-Shen, C †
Nature Cancer, 1(11):1082-1096, PMID: 34085047.
† Co-Senior Co-Corresponding authors
2019
pathCHEMO, a generalizable computational framework uncovers molecular pathways of chemoresistance in lung adenocarcinoma
Epsi, N., Panja, S., Pine, Sh. and Mitrofanova, A.†
Nature Communications Biology, 2:334, PMID: 31508508.
† Senior Corresponding author
Achievements
Awards & Honors
April 2022
I have been awarded a Presidential Fellowship for Teaching Excellence for teaching and mentoring students at Rutgers.
April 2022
My Ph.D. student Daniel Martingano has been awarded Stanley S. Bergen, Jr. M.D. Medal of Excellence from Rutgers SHP for his contributions to research and clinical practice in community settings. Congratulations, Daniel!
June 2021
Michael Craige will be joining our lab as a PostDoctoral Computing Innovation Fellow (CIFellow) awarded by CRA/CCC/NSF! Congratulations, Michael!
August 2020
Our lab has been awarded a Dean’s Bridge grant from the Rutgers School of Health Professions. Thank you, SHP!
February 2020
My Ph.D. student, Sukanya Panja, has been awarded a New Jersey Commission on Cancer Research (NJCCR) Pre-Doctoral Fellowship from New Jersey Department of Health. Congratulations, Sukanya!
May 2019
My Ph.D. student Nusrat Epsi received the Gallo Award for Outstanding Cancer Research at The 2019 Annual Retreat on Cancer Research in New Jersey. Congratulations, Nusrat!
May 2019
My Ph.D. student Sukanya Panja received a full scholarship to attend a 1-week Epigenomics workshop at Van Andel Institute. Congratulations, Sukanya!
April 2019
Our lab received a Graduate Student Summer Intern grant, awarded by Rutgers SHP (funded New Jersey Health Foundation). Thank you, SHP!!
Get Involved
Join our Research
Interested in advancing precision cancer medicine? Reach out to Dr. Mitrofanova
to learn more about opportunities to get involved.
