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. Drozdz, MM, Doane, AS, Alkallas, R, Desman, G, Bareja, R, Reilly, M et al.. A nuclear cAMP microdomain suppresses tumor growth by Hippo pathway inactivation. Cell Rep. 2022;40 (13):111412. doi: 10.1016/j.celrep.2022.111412. PubMed PMID:36170819 .
  2. Yu, H, Sfakianos, JP, Wang, L, Hu, Y, Daza, J, Galsky, MD et al.. Tumor Infiltrating Myeloid Cells Confer de novo Resistance to PD-L1 Blockade through EMT-stromal and Tgf-beta Dependent Mechanisms. Mol Cancer Ther. 2022; :. doi: 10.1158/1535-7163.MCT-22-0130. PubMed PMID:36129800 .
  3. Martini, R, Delpe, P, Chu, TR, Arora, K, Lord, B, Verma, A et al.. African Ancestry Associated Gene Expression Profiles in Triple Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome in Women of African Descent. Cancer Discov. 2022; :. doi: 10.1158/2159-8290.CD-22-0138. PubMed PMID:36121736 .
  4. Laurent, P, Yang, C, Rendeiro, AF, Nilsson-Payant, BE, Carrau, L, Chandar, V et al.. Sensing of SARS-CoV-2 by pDCs and their subsequent production of IFN-I contribute to macrophage-induced cytokine storm during COVID-19. Sci Immunol. 2022;7 (75):eadd4906. doi: 10.1126/sciimmunol.add4906. PubMed PMID:36083891 .
  5. Xu, X, Wang, K, Vera, O, Verma, A, Jasani, N, Bok, I et al.. Gain of Chromosome 1q Perturbs a Competitive Endogenous RNA Network to Promote Melanoma Metastasis. Cancer Res. 2022;82 (17):3016-3031. doi: 10.1158/0008-5472.CAN-22-0283. PubMed PMID:36052492 .
  6. He, Y, Kim, IK, Bian, J, Polyzos, A, Di Giammartino, DC, Zhang, YW et al.. A Knock-In Mouse Model of Thymoma With the GTF2I L424H Mutation. J Thorac Oncol. 2022; :. doi: 10.1016/j.jtho.2022.08.008. PubMed PMID:36049655 .
  7. Kulm, S, Kolin, DA, Langhans, MT, Kaidi, AC, Elemento, O, Bostrom, MP et al.. Characterization of Genetic Risk of End-Stage Knee Osteoarthritis Treated with Total Knee Arthroplasty: A Genome-Wide Association Study. J Bone Joint Surg Am. 2022; :. doi: 10.2106/JBJS.22.00364. PubMed PMID:36000784 .
  8. Cappelli, LV, Fiore, D, Phillip, JM, Yoffe, L, Di Giacomo, F, Chiu, W et al.. Endothelial-leukemia interactions remodel drug responses uncovering T-ALL vulnerabilities. Blood. 2022; :. doi: 10.1182/blood.2022015414. PubMed PMID:35981563 .
  9. Jessurun, J, Orr, C, McNulty, SN, Hagen, CE, Alnajar, H, Wilkes, D et al.. GLI1-Rearranged Enteric Tumor: Expanding the Spectrum of Gastrointestinal Neoplasms with GLI1 gene fusions. Am J Surg Pathol. 2022; :. doi: 10.1097/PAS.0000000000001950. PubMed PMID:35968961 .
  10. Podaza, E, Kuo, HH, Nguyen, J, Elemento, O, Martin, ML. Next generation patient derived tumor organoids. Transl Res. 2022; :. doi: 10.1016/j.trsl.2022.08.003. PubMed PMID:35964899 .
  11. Xu, X, Wang, K, Vera, O, Verma, A, Jasani, N, Bok, I et al.. Gain of chromosome 1q perturbs a competitive endogenous RNA network to promote melanoma metastasis. Cancer Res. 2022; :. doi: 10.1158/0008-5472.CAN-22-0283. PubMed PMID:35820070 .
  12. Jacobsen, JOB, Baudis, M, Baynam, GS, Beckmann, JS, Beltran, S, Buske, OJ et al.. The GA4GH Phenopacket schema defines a computable representation of clinical data. Nat Biotechnol. 2022;40 (6):817-820. doi: 10.1038/s41587-022-01357-4. PubMed PMID:35705716 PubMed Central PMC9363006.
  13. Hu, Y, Bloy, N, Elemento, O, Buqué, A. Nicotinamide drives T cell activation in the mammary tumor microenvironment. J Transl Med. 2022;20 (1):251. doi: 10.1186/s12967-022-03454-z. PubMed PMID:35659314 PubMed Central PMC9164530.
  14. Brendel, M, Getseva, V, Assaad, MA, Sigouros, M, Sigaras, A, Kane, T et al.. Weakly-supervised tumor purity prediction from frozen H&E stained slides. EBioMedicine. 2022;80 :104067. doi: 10.1016/j.ebiom.2022.104067. PubMed PMID:35644123 PubMed Central PMC9157012.
  15. Doane, AS, Elemento, O. Alterations in transcriptional networks in cancer: the role of noncoding somatic driver mutations. Curr Opin Genet Dev. 2022;75 :101919. doi: 10.1016/j.gde.2022.101919. PubMed PMID:35609422 .
  16. Schad, SE, Chow, A, Mangarin, L, Pan, H, Zhang, J, Ceglia, N et al.. Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions. J Exp Med. 2022;219 (6):. doi: 10.1084/jem.20212169. PubMed PMID:35604411 PubMed Central PMC9130031.
  17. Linares, JF, Cid-Diaz, T, Duran, A, Osrodek, M, Martinez-Ordoñez, A, Reina-Campos, M et al.. The lactate-NAD+ axis activates cancer-associated fibroblasts by downregulating p62. Cell Rep. 2022;39 (6):110792. doi: 10.1016/j.celrep.2022.110792. PubMed PMID:35545049 PubMed Central PMC9136538.
  18. Jaiswal, A, Verma, A, Dannenfelser, R, Melssen, M, Tirosh, I, Izar, B et al.. An activation to memory differentiation trajectory of tumor-infiltrating lymphocytes informs metastatic melanoma outcomes. Cancer Cell. 2022;40 (5):524-544.e5. doi: 10.1016/j.ccell.2022.04.005. PubMed PMID:35537413 PubMed Central PMC9122099.
  19. Raman, R, Villefranc, JA, Ullmann, TM, Thiesmeyer, J, Anelli, V, Yao, J et al.. Inhibition of FGF receptor blocks adaptive resistance to RET inhibition in CCDC6-RET-rearranged thyroid cancer. J Exp Med. 2022;219 (6):. doi: 10.1084/jem.20210390. PubMed PMID:35510953 PubMed Central PMC9082625.
  20. Alnajar, H, Ravichandran, H, Figueiredo Rendeiro, A, Ohara, K, Al Zoughbi, W, Manohar, J et al.. Tumor-immune microenvironment revealed by Imaging Mass Cytometry in a metastatic sarcomatoid urothelial carcinoma with a prolonged response to pembrolizumab. Cold Spring Harb Mol Case Stud. 2022;8 (3):. doi: 10.1101/mcs.a006151. PubMed PMID:35483877 PubMed Central PMC9059779.
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