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.
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.
| Michael W. Craige Post-Doctoral Fellow |
Mohamed Ahmed Post-Doctoral Scientist |
| Sukanya Panja 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 |
Grant Funding
Title: Mechanism-Centric Predictive Modeling for Prostate Cancer
Source of Support: DOD Prostate Cancer Data Science Award
Major Goals:
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
Title: Generalizable biomedical informatics strategies for predictive modeling of treatment response
Supporting Agency: NIH NLM
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
Title: Systems analysis of drug resistance in prostate cancer
Supporting Agency: American Cancer Society
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
Title: Generalizable systems biology paradigm for predictive modeling of treatment response
Supporting Agency: Rutgers School of Health Professions
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
Title: Scalable generalizable framework for predicting treatment response in prostate cancer
Supporting Agency: New Jersey Commission on Cancer Research (NJCCR)
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
Title: Computational systems biology approaches to discover therapeutic strategies for patients with castration resistant prostate cancer
Supporting Agency: Rutgers School of Health Professions
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
Professional Achievements
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!!
July 2018
My Ph.D. student Nusrat Epsi was selected to receive Katrina Kehlet Graduate Award from NJ HIMSS. Congratulations, Nusrat!
May 2018
My Ph.D. student Sukanya Panja received the Gallo Award for Scientific Excellence in Cancer Research at The 2018 Annual Retreat on Cancer Research in New Jersey. Congratulations, Sukanya!
April 2018
Our lab received a Summer Student Intern Project grant, awarded by Rutgers SHP. Thank you, SHP!!
April 2018
I have been honored to receive an Excellence in Research Award from Rutgers SHP, sponsored by New Jersey Health Foundation. Thank you very much for this honor!!
May 2017
My Ph.D. student, Nusrat Epsi, has been awarded a Grace Hopper Celebration (GHC) Student Scholarship grant to attend a GHC of Women in Computing conference. Congratulations, Nusrat!
May 2017
Our lab received a Summer Student Intern Program grant, sponsored by the New Jersey Health Foundation and awarded by Rutgers SHP. My PhD student Nusrat Epsi was selected to execute this project. Congratulations, Nusrat!
April 2017
My Ph.D. student, Laura Harris, has been awarded a Center for Teaching Excellence faculty grant from Davenport to publish two of her PhD papers. Congratulations, Laura!
April 2016
Our lab has been awarded a Dean’s Intramural Pilot grant from the Rutgers School of Health Professions!
Selected Publications
- 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.† (2024).
Mechanism-centric regulatory network identifies NME2 and MYC programs as markers of Enzalutamide resistance in CRPC.
Nature Communications, 15(1):352. PMID: 38191557.v - 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.† (2023).
Tissue-specific biological aging predicts progression in prostate cancer and acute myeloid leukemia.
Frontiers in Oncology, 6:13:1222168. PMID: 37746266. - Bohannan, Z., Coffman, F., and Mitrofanova, A.† (2022).
Random survival forest model identifies novel biomarkers of event-free survival in high-risk pediatric acute lymphoblastic leukemia. Computational and Structural Biotechnology Journal, 20: 583-597. PMID: 35116134.
† Senior Corresponding author. - Yu, Ch., Mitrofanova, A.† (2021).
Mechanism-centric approaches for biomarker detection and precision therapeutics in cancer. Frontiers in Genetics, 12: 687813. PMID: 34408770.
† Senior Corresponding author. - Rahem, S.M., Epsi, N.J., Coffman, F.D., Mitrofanova, A.† (2020).
Genome-wide analysis of therapeutic response uncovers molecular pathways governing tamoxifen resistance in ER+ breast cancer. EBioMedicine (published by THE LANCET), 61:103047, PMID: 33099086.
† Senior Corresponding author. - 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 †(2020). A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance. Nature Cancer, 1(11):1082-1096, PMID: 34085047.
† Co-Senior Co-Corresponding authors. - Epsi, N., Panja, S., Pine, Sh. and Mitrofanova, A.† (2019).
pathCHEMO, a generalizable computational framework uncovers molecular pathways of chemoresistance in lung adenocarcinoma. Nature Communications Biology, 2:334, PMID: 31508508.
† Senior Corresponding author.
Please reach out to Dr. Mitrofanova at antonina.mitrofanova@rutgers.edu to learn more about her research or get involved.
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