Olivier Elemento, Ph.D.

Professor of Physiology and Biophysics

  • Walter B. Wriston Research Scholar
  • Professor of Computational Genomics in Computational Biomedicine and Associate Director of the Institute for Computational Biomedicine
  • Director of the Englander Institute for Precision Medicine
  • Associate Director of the Institute for Computational Biomedicine

646-962-5726

1305 York Avenue, Room Y-13.13
New York, NY 10021


Techniques

Research Areas


Research Summary:

The Elemento lab combines Big Data analytics with experimentation to develop entirely new ways to help prevent, diagnose, understand, treat and ultimately cure cancer. Our research involves routine use of ultrafast DNA sequencing, proteomics, high-performance computing, mathematical modeling, and artificial intelligence/machine learning.

More specifically, we are working on :

  • Systems biology of regulatory networks in normal and malignant cells, with a strong focus on blood cancers (lymphomas and leukemias). We use ChIP-seq, RNA-seq, computational modeling to investigate how genes are regulated in cancer cells and how gene regulation in cancer cells differs from normal cells.
  • Cancer genomics and precision medicine. Using novel computational algorithms, we seek to identify new cancer mutations and understand why and where cancer mutations occur. We work on determining whether 3D chromatin architecture predicts where mutations are most likely to occur.
  • Epigenomics of cancer. Genes coding for proteins that modify, maintain or read the epigenome (DNA methylation and histone modifications) and are among the most frequently mutated genes in cancer. We use high-throughput experimental approaches and pattern detection techniques to investigate what these genes do and the genomewide epigenomic patterns they mediate.
  • Tumor genome evolution, anticancer drug resistance. Cancer is a fundamentally evolutionary disease. Using high-throughput sequencing, we are investigating how the tumor genome (and epigenome) evolves in time and particularly upon drug treatment.
  • Early cancer detection using machine learning. We use advanced machine learning approaches (artificial intelligence techniques) to detect cancer as early as possible and help guide treatment accordingly. One of our algorithms for thyroid cancer detection, based on Support Vector Machines, was recently licensed by Prolias Technologies.
  • Development of innovative computational approaches for analysis of high-throughput experiments (metabolomics, proteomics, high-throughout sequencing, etc) performed on cancer cells. For example we have developed ChIPseeqer, a broadly used ChIPseq data analysis framework.

 

Recent Publications:

  1. Guillet, S, Lazarov, T, Jordan, N, Boisson, B, Tello, M, Craddock, B et al.. ACK1 and BRK non-receptor tyrosine kinase deficiencies are associated with familial systemic lupus and involved in efferocytosis. medRxiv. 2024; :. doi: 10.1101/2024.02.15.24302255. PubMed PMID:38883731 PubMed Central PMC11177913.
  2. Greenberg, JA, Shah, Y, Ivanov, NA, Marshall, T, Kulm, S, Williams, J et al.. Developing a predictive model for metastatic potential in pancreatic neuroendocrine tumor. J Clin Endocrinol Metab. 2024; :. doi: 10.1210/clinem/dgae380. PubMed PMID:38817124 .
  3. Yaron-Barir, TM, Joughin, BA, Huntsman, EM, Kerelsky, A, Cizin, DM, Cohen, BM et al.. The intrinsic substrate specificity of the human tyrosine kinome. Nature. 2024;629 (8014):1174-1181. doi: 10.1038/s41586-024-07407-y. PubMed PMID:38720073 PubMed Central PMC11136658.
  4. Tasci, E, Shah, Y, Jagasia, S, Zhuge, Y, Shephard, J, Johnson, MO et al.. MGMT ProFWise: Unlocking a New Application for Combined Feature Selection and the Rank-Based Weighting Method to Link MGMT Methylation Status to Serum Protein Expression in Patients with Glioblastoma. Int J Mol Sci. 2024;25 (7):. doi: 10.3390/ijms25074082. PubMed PMID:38612892 PubMed Central PMC11012706.
  5. Shah, Y, Kulm, S, Nauseef, JT, Chen, Z, Elemento, O, Kensler, KH et al.. Benchmarking multi-ancestry prostate cancer polygenic risk scores in a real-world cohort. PLoS Comput Biol. 2024;20 (4):e1011990. doi: 10.1371/journal.pcbi.1011990. PubMed PMID:38598551 PubMed Central PMC11034641.
  6. Elemento, O. How Artificial Intelligence Unravels the Complex Web of Cancer Drug Response. Cancer Res. 2024;84 (11):1745-1746. doi: 10.1158/0008-5472.CAN-24-1123. PubMed PMID:38588311 .
  7. Ohara, K, Rendeiro, AF, Bhinder, B, Eng, KW, Ravichandran, H, Nguyen, D et al.. The evolution of metastatic upper tract urothelial carcinoma through genomic-transcriptomic and single-cell protein markers analysis. Nat Commun. 2024;15 (1):2009. doi: 10.1038/s41467-024-46320-w. PubMed PMID:38499531 PubMed Central PMC10948878.
  8. Manzo, OL, Nour, J, Sasset, L, Marino, A, Rubinelli, L, Palikhe, S et al.. Rewiring Endothelial Sphingolipid Metabolism to Favor S1P Over Ceramide Protects From Coronary Atherosclerosis. Circ Res. 2024;134 (8):990-1005. doi: 10.1161/CIRCRESAHA.123.323826. PubMed PMID:38456287 PubMed Central PMC11009055.
  9. Newman, LA, Chen, Y, Martini, R, Demaria, S, Formenti, S, Elemento, O et al.. Tumor-Associated Lymphocytes and Breast Cancer Survival in Black and White Women. JAMA Surg. 2024;159 (6):712-714. doi: 10.1001/jamasurg.2023.8024. PubMed PMID:38446467 PubMed Central PMC10918575.
  10. Altorki, NK, Bhinder, B, Borczuk, AC, Elemento, O, Mittal, V, McGraw, TE et al.. A signature of enhanced proliferation associated with response and survival to anti-PD-L1 therapy in early-stage non-small cell lung cancer. Cell Rep Med. 2024;5 (3):101438. doi: 10.1016/j.xcrm.2024.101438. PubMed PMID:38401548 PubMed Central PMC10982989.
  11. Bensoussan, Y, Elemento, O, Rameau, A. Voice as an AI Biomarker of Health-Introducing Audiomics. JAMA Otolaryngol Head Neck Surg. 2024;150 (4):283-284. doi: 10.1001/jamaoto.2023.4807. PubMed PMID:38386315 .
  12. Al Assaad, M, Michaud, O, Semaan, A, Sigouros, M, Tranquille, M, Phan, A et al.. Whole-Genome Sequencing Analysis of Male Breast Cancer Unveils Novel Structural Events and Potential Therapeutic Targets. Mod Pathol. 2024;37 (4):100452. doi: 10.1016/j.modpat.2024.100452. PubMed PMID:38369186 .
  13. Noch, EK, Palma, L, Yim, I, Bullen, N, Barnett, D, Walsh, A et al.. Cysteine induces mitochondrial reductive stress in glioblastoma through hydrogen peroxide production. Proc Natl Acad Sci U S A. 2024;121 (8):e2317343121. doi: 10.1073/pnas.2317343121. PubMed PMID:38359293 PubMed Central PMC10895255.
  14. Vicario, R, Fragkogianni, S, Weber, L, Lazarov, T, Hu, Y, Hayashi, SY et al.. A microglia clonal inflammatory disorder in Alzheimer's Disease. bioRxiv. 2024; :. doi: 10.1101/2024.01.25.577216. PubMed PMID:38328106 PubMed Central PMC10849735.
  15. Deng, Z, Loyher, PL, Lazarov, T, Li, L, Shen, Z, Bhinder, B et al.. The nuclear factor ID3 endows macrophages with a potent anti-tumour activity. Nature. 2024;626 (8000):864-873. doi: 10.1038/s41586-023-06950-4. PubMed PMID:38326607 PubMed Central PMC10881399.
  16. Al Assaad, M, Shin, N, Sigouros, M, Manohar, J, Antysheva, Z, Kotlov, N et al.. Deciphering the origin and therapeutic targets of cancer of unknown primary: a case report that illustrates the power of integrative whole-exome and transcriptome sequencing analysis. Front Oncol. 2023;13 :1274163. doi: 10.3389/fonc.2023.1274163. PubMed PMID:38318324 PubMed Central PMC10838960.
  17. Madorsky Rowdo, FP, Xiao, G, Khramtsova, GF, Nguyen, J, Martini, R, Stonaker, B et al.. Patient-derived tumor organoids with p53 mutations, and not wild-type p53, are sensitive to synergistic combination PARP inhibitor treatment. Cancer Lett. 2024;584 :216608. doi: 10.1016/j.canlet.2024.216608. PubMed PMID:38199587 PubMed Central PMC10922546.
  18. Franceschini, GM, Quaini, O, Mizuno, K, Orlando, F, Ciani, Y, Ku, SY et al.. Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation. Cancer Discov. 2024;14 (3):424-445. doi: 10.1158/2159-8290.CD-23-0754. PubMed PMID:38197680 PubMed Central PMC10905672.
  19. Altorki, NK, Walsh, ZH, Melms, JC, Port, JL, Lee, BE, Nasar, A et al.. Author Correction: Neoadjuvant durvalumab plus radiation versus durvalumab alone in stages I-III non-small cell lung cancer: survival outcomes and molecular correlates of a randomized phase II trial. Nat Commun. 2024;15 (1):225. doi: 10.1038/s41467-023-44575-3. PubMed PMID:38172131 PubMed Central PMC10764801.
  20. Duan, X, Zhang, T, Feng, L, de Silva, N, Greenspun, B, Wang, X et al.. A pancreatic cancer organoid platform identifies an inhibitor specific to mutant KRAS. Cell Stem Cell. 2024;31 (1):71-88.e8. doi: 10.1016/j.stem.2023.11.011. PubMed PMID:38151022 PubMed Central PMC11022279.
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