Francine E. Garrett-Bakelman

Assistant Professor, Biochemistry and Molecular Genetics

Primary Location

LAB :PO Box 800733, 1340 JPA Pinn Hall Rm 6054A
UVA Cancer Ctr Clinic: PO Box 800334
Charlottesville, Virginia 22908

Primary Phone Number

434.924.9220

Fax Number

434.924.5069

[email protected] (For patients: if you are in need of assistance, please call clinical practice)

Bio & Overview

Acute Myeloid Leukemia (AML) is the most common acute leukemia in adults. AML prognosis and overall survival decline in patients older that 60 years of age and in patients who develop disease relapse after initial treatments. Our main research goal is to understand molecular and epigenetic mechanisms responsible for AML disease phenotypes. Through this aim, in the long-term, findings will help identify novel therapeutic targets in AML. We investigate these questions through the study of samples from AML patients and functional validations in in vitro and in vivo models. Epigenetic (DNA methylation, gene expression, and chromatin assays), molecular and cellular biology techniques are implemented to study how aberrant expression of specific genes contributes to abnormal cellular phenotypes and leukemogenesis. Previous studies have determined that AML progression (from disease diagnosis to relapse) is characterized by significant epigenetic plasticity and differentially expressed genes. Studies are being pursued to identify genes affected by the epigenetic changes observed and how their function contributes to the malignant phenotype. Complete List of Published Work in MyBibliography: https://www.ncbi.nlm.nih.gov/sites/myncbi/francine.garrett-bakelman.1/bibliography/43682539/public/?sort=date&direction=ascending

Academic Information

Department: Biochemistry and Molecular Genetics

Academic Title: Assistant Professor

Primary Education

BS, Biochemistry and Cell Biology, California State University, Fullerton, 1996
Clinical Fellowship, Hematology and Medical Oncology, Weill Cornell Medical Collegenull
MD/PhD, Medicine and Cell Biology, Albert Einstein College of Medicine, 2005
Postdoc, Postdoctoral training in epigenomics & hematological malignancies experimentation, Weill Cornell Medical Collegenull

Other Appointments

Assistant Professor, Medicine- Hematology and Oncology

Other Affiliations

Assistant Professor, BIMS

Research Interests

Acute Myeloid Leukemia: molecular and cellular biology events which mediate aberrant epigenetic and transcriptional mechanisms during disease establishment and progression

Research Disciplines

Bioinformatics and Genomics
Cancer Biology
Epigenetics
Molecular Biology
Translational Science

Research Opportunities

Bioinformatics & Genomics
Cancer Biology
Cell Biology
Epigenetics
Molecular Biology

PhD Programs

Biochemistry & Molecular Genetics
Pharmacology

Selected Publications

2024

Wu, F., Du, H., Overbey, E., Kim, J., Makhijani, P., Martin, N., . . . Winer, D. A. (2024). Single-cell analysis identifies conserved features of immune dysfunction in simulated microgravity and spaceflight. NATURE COMMUNICATIONS, 15(1). doi:10.1038/s41467-023-42013-y

Paudel, B. B., Tan, S. -F., Fox, T. E., Ung, J., Golla, U., Shaw, J. J. P., . . . Loughran, T. P. (2024). Acute myeloid leukemia stratifies as 2 clinically relevantsphingolipidomic subtypes. BLOOD ADVANCES, 8(5), 1137-1142. doi:10.1182/bloodadvances.2023010535

2023

Hu, X., Logan, J. G., Kwon, Y., Lima, J. A. C., Jacobs, D. R., Duprez, D., . . . Manichaikul, A. (2023). Multi-ancestry epigenome-wide analyses identify methylated sites associated with aortic augmentation index in TOPMed MESA. SCIENTIFIC REPORTS, 13(1). doi:10.1038/s41598-023-44806-z

Manichaikul, A., Hu, X., Logan, J., Kwon, Y., Lima, J., Jacobs, D., . . . Garrett-Bakelman, F. (2023). Multi-ancestry epigenome-wide analyses identify methylated sites associated with aortic augmentation index in TOPMed MESA.. Res Sq. doi:10.21203/rs.3.rs-3125948/v1

Rapaport, F., Seier, K., Neelamraju, Y., Hassane, D., Baslan, T., Gildea, D. T., . . . Garrett-Bakelman, F. E. (2023). Integrative analysis identifies an older female-linked AML patient group with better risk in ECOG-ACRIN Cancer Research Group's clinical trial E3999 (vol 12, 137,2022). BLOOD CANCER JOURNAL, 13(1). doi:10.1038/s41408-023-00862-2

Paudel, B. B., Tan, S. -F., Fox, T. E., Ung, J., Shaw, J., Dunton, W., . . . Loughran, T. P. (2023). Acute myeloid leukemia stratifies as two clinically relevant sphingolipidomic subtypes.. bioRxiv. doi:10.1101/2023.04.13.536805

Neelamraju, Y., Gjini, E., Chhangawala, S., Fan, H., He, S., Jing, C. -B., . . . Garrett-Bakelman, F. E. (2023). Depletion of tet2 results in age-dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome.. Frontiers in hematology, 2, 1235170. doi:10.3389/frhem.2023.1235170

2022

Ganzel, C., Sun, Z., Baslan, T., Zhang, Y., Gonen, M., Abdel-Wahab, O. I., . . . Paietta, E. (2022). Measurable residual disease by flow cytometry in acute myeloid leukemia is prognostic, independent of genomic profiling. LEUKEMIA RESEARCH, 123. doi:10.1016/j.leukres.2022.106971

Rapaport, F., Seier, K., Neelamraju, Y., Hassane, D., Baslan, T., Gildea, D. T., . . . Garrett-Bakelman, F. E. (2022). Integrative analysis identifies an older female-linked AML patient group with better risk in ECOG-ACRIN Cancer Research Group's clinical trial E3999. BLOOD CANCER JOURNAL, 12(9). doi:10.1038/s41408-022-00736-z

Ung, J., Tan, S. -F., Fox, T. E., Shaw, J. J. P., Vass, L. R., Costa-Pinheiro, P., . . . Loughran, T. P. (2022). Harnessing the power of sphingolipids: Prospects for acute myeloid leukemia. BLOOD REVIEWS, 55. doi:10.1016/j.blre.2022.100950

Barreyro, L., Sampson, A. M., Ishikawa, C., Hueneman, K. M., Choi, K., Pujato, M. A., . . . Starczynowski, D. T. (2022). Blocking UBE2N abrogates oncogenic immune signaling in acute myeloid leukemia. SCIENCE TRANSLATIONAL MEDICINE, 14(635). doi:10.1126/scitranslmed.abb7695

Prajapati, S. C., Dunham, N., Fan, H., & Garrett-Bakelman, F. E. (2022). Validation of CRISPR targeting for proliferation and cytarabine resistance control genes in the acute myeloid leukemia cell line MOLM-13. BIOTECHNIQUES, 72(3). doi:10.2144/btn-2021-0089

2021

Batra, R. N., Lifshitz, A., Vidakovic, A. T., Chin, S. -F., Sati-Batra, A., Sammut, S. -J., . . . Caldas, C. (2021). DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation. NATURE COMMUNICATIONS, 12(1). doi:10.1038/s41467-021-25661-w

Olson, T. L., Cheon, H., Xing, J. C., Olson, K. C., Paila, U., Hamele, C. E., . . . Loughran, T. P. J. (2021). Frequent somatic TET2 mutations in chronic NK-LGL leukemia with distinct patterns of cytopenias. BLOOD, 138(8), 662-673. doi:10.1182/blood.2020005831

Rapaport, F., Neelamraju, Y., Baslan, T., Hassane, D., Gruszczynska, A., Robert de Massy, M., . . . Garrett-Bakelman, F. E. (2021). Genomic and evolutionary portraits of disease relapse in acute myeloid leukemia. LEUKEMIA, 35(9), 2688-2692. doi:10.1038/s41375-021-01153-0

Duy, C., Li, M., Teater, M., Meydan, C., Garrett-Bakelman, F. E., Lee, T. C., . . . Melnick, A. M. (2021). Chemotherapy Induces Senescence-Like Resilient Cells Capable of Initiating AML Recurrence. CANCER DISCOVERY, 11(6), 1542-1561. doi:10.1158/2159-8290.CD-20-1375

Sevilla, A., Papatsenko, D., Mazloom, A. R., Xu, H., Vasileva, A., Unwin, R. D., . . . Lemischka, I. R. (2021). An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions. FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY, 9. doi:10.3389/fcell.2021.630067

2020

Bezdan, D., Grigorev, K., Meydan, C., Vatter, F. A. P., Cioffi, M., Rao, V., . . . Mason, C. E. (2020). Cell-free DNA (cfDNA) and Exosome Profiling from a Year-Long Human Spaceflight Reveals Circulating Biomarkers. ISCIENCE, 23(12). doi:10.1016/j.isci.2020.101844

Gertz, M. L., Chin, C. R., Tomoiaga, D., MacKay, M., Chang, C., Butler, D., . . . Mason, C. E. (2020). Multi-omic, Single-Cell, and Biochemical Profiles of Astronauts Guide Pharmacological Strategies for Returning to Gravity. CELL REPORTS, 33(10). doi:10.1016/j.celrep.2020.108429

Trinchant, N. M., MacKay, M. J., Chin, C., Afshinnekoo, E., Foox, J., Meydan, C., . . . Mason, C. E. (2020). Clonal Hematopoiesis Before, During, and After Human Spaceflight. CELL REPORTS, 33(10). doi:10.1016/j.celrep.2020.108458

Luxton, J. J., McKenna, M. J., Taylor, L. E., George, K. A., Zwart, S. R., Crucian, B. E., . . . Bailey, S. M. (2020). Temporal Telomere and DNA Damage Responses in the Space Radiation Environment. CELL REPORTS, 33(10). doi:10.1016/j.celrep.2020.108435

Malkani, S., Chin, C. R., Cekanaviciute, E., Mortreux, M., Okinula, H., Tarbier, M., . . . Beheshti, A. (2020). Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development. CELL REPORTS, 33(10). doi:10.1016/j.celrep.2020.108448

Lawson, J. T., Smith, J. P., Bekiranov, S., Garrett-Bakelman, F. E., & Sheffield, N. C. (2020). COCOA: coordinate covariation analysis of epigenetic heterogeneity. GENOME BIOLOGY, 21(1). doi:10.1186/s13059-020-02139-4

Abshiru, N. A., Sikora, J. W., Camarillo, J. M., Morris, J. A., Compton, P. D., Lee, T., . . . Kelleher, N. L. (2020). Targeted detection and quantitation of histone modifications from 1,000 cells. PLOS ONE, 15(10). doi:10.1371/journal.pone.0240829

2019

Martin, G. H., Roy, N., Chakraborty, S., Desrichard, A., Chung, S. S., Woolthuis, C. M., . . . Park, C. Y. (2019). CD97 is a critical regulator of acute myeloid leukemia stem cell function. JOURNAL OF EXPERIMENTAL MEDICINE, 216(10), 2362-2377. doi:10.1084/jem.20190598

Duy, C., Teater, M., Garrett-Bakelman, F. E., Lee, T. C., Meydan, C., Glass, J. L., . . . Melnick, A. M. (2019). Rational Targeting of Cooperating Layers of the Epigenome Yields Enhanced Therapeutic Efficacy against AML. CANCER DISCOVERY, 9(7), 872-889. doi:10.1158/2159-8290.CD-19-0106

Garrett-Bakelman, F. E., Darshi, M., Green, S. J., Gur, R. C., Lin, L., Macias, B. R., . . . Turek, F. W. (2019). The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. SCIENCE, 364(6436), 144-+. doi:10.1126/science.aau8650

2017

Kunimoto, H., Meydan, C., Nazir, A., Whitfield, J., Shank, K., Rapaport, F., . . . Shih, A. H. (2018). Cooperative Epigenetic Remodeling by TET2 Loss and NRAS Mutation Drives Myeloid Transformation and MEK Inhibitor Sensitivity. CANCER CELL, 33(1), 44-+. doi:10.1016/j.ccell.2017.11.012

Vu, L. P., Pickering, B. F., Cheng, Y., Zaccara, S., Diu, N., Minuesa, G., . . . Kharas, M. G. (2017). The N⁶-methyladenosine (m⁶A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells. NATURE MEDICINE, 23(11), 1369-+. doi:10.1038/nm.4416

Glass, J. L., Hassane, D., Wouters, B. J., Kunimoto, H., Avellino, R., Garrett-Bakelman, F. E., . . . Figueroa, M. E. (2017). Epigenetic Identity in AML Depends on Disruption of Nonpromoter Regulatory Elements and Is Affected by Antagonistic Effects of Mutations in Epigenetic Modifiers. CANCER DISCOVERY, 7(8), 868-883. doi:10.1158/2159-8290.CD-16-1032

Kunimoto, H., McKenney, A. S., Meydan, C., Shank, K., Nazir, A., Rapaport, F., . . . Levine, R. L. (2017). Aid is a key regulator of myeloid/erythroid differentiation and DNA methylation in hematopoietic stem/progenitor cells.. Blood, 129(13), 1779-1790. doi:10.1182/blood-2016-06-721977

Shih, A. H., Meydan, C., Shank, K., Garrett-Bakelman, F. E., Ward, P. S., Intlekofer, A. M., . . . Levine, R. L. (2017). Combination Targeted Therapy to Disrupt Aberrant Oncogenic Signaling and Reverse Epigenetic Dysfunction in IDH2- and TET2-Mutant Acute Myeloid Leukemia. CANCER DISCOVERY, 7(5), 494-505. doi:10.1158/2159-8290.CD-16-1049

Chung, S. S., Eng, W. S., Hu, W., Khalaj, M., Garrett-Bakelman, F. E., Tavakkoli, M., . . . Park, C. Y. (2017). CD99 is a therapeutic target on disease stem cells in myeloid malignancies. SCIENCE TRANSLATIONAL MEDICINE, 9(374). doi:10.1126/scitranslmed.aaj2025

Kunimoto, H., McKenney, A. S., Meydan, C., Shank, K., Nazir, A., Rapaport, F., . . . Levine, R. L. (2017). Aid is a key regulator of myeloid/erythroid differentiation and DNA methylation in hematopoietic stem/progenitor cells. BLOOD, 129(13), 1779-1790. doi:10.1182/blood-2016-06-721977

2016

Guryanova, O. A., Shank, K., Spitzer, B., Luciani, L., Koche, R. P., Garrett-Bakelman, F. E., . . . Levine, R. L. (2016). DNMT3A mutations promote anthracycline resistance in acute myeloid leukemia via impaired nucleosome remodeling. NATURE MEDICINE, 22(12), 1488-+. doi:10.1038/nm.4210

Garrett-Bakelman, F. E., & Melnick, A. M. (2016). Mutant IDH: a targetable driver of leukemic phenotypes linking metabolism, epigenetics and transcriptional regulation. EPIGENOMICS, 8(7), 945-957. doi:10.2217/epi-2016-0008

Li, S., Garrett-Bakelman, F. E., Chung, S. S., Sanders, M. A., Hricik, T., Rapaport, F., . . . Mason, C. E. (2016). Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia. NATURE MEDICINE, 22(7), 792-799. doi:10.1038/nm.4125

2015

Guryanova, O. A., Lieu, Y. K., Garrett-Bakelman, F. E., Spitzer, B., Glass, J. L., Shank, K., . . . Levine, R. L. (2016). Dnmt3a regulates myeloproliferation and liver-specific expansion of hematopoietic stem and progenitor cells. LEUKEMIA, 30(5), 1133-1142. doi:10.1038/leu.2015.358

Garrett-Bakelman, F. E., Sheridan, C. K., Kacmarczyk, T. J., Ishii, J., Betel, D., Alonso, A., . . . Melnick, A. M. (2015). Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution. JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, (96). doi:10.3791/52246

2014

Li, S., Garrett-Bakelman, F., Perl, A. E., Luger, S. M., Zhang, C., To, B. L., . . . Mason, C. E. (2014). Dynamic evolution of clonal epialleles revealed by methclone. GENOME BIOLOGY, 15(9). doi:10.1186/s13059-014-0472-5

2013

Magro, C. M., Wang, X., Garrett-Bakelman, F., Laurence, J., Shapiro, L. S., & DeSancho, M. T. (2013). The effects of Eculizumab on the pathology of malignant atrophic papulosis. ORPHANET JOURNAL OF RARE DISEASES, 8. doi:10.1186/1750-1172-8-185

Hatzi, K., Jiang, Y., Huang, C., Garrett-Bakelman, F., Gearhart, M. D., Giannopoulou, E. G., . . . Melnick, A. (2013). A Hybrid Mechanism of Action for BCL6 in B Cells Defined by Formation of Functionally Distinct Complexes at Enhancers and Promoters. CELL REPORTS, 4(3), 578-588. doi:10.1016/j.celrep.2013.06.016

Garrett-Bakelman, F. E., & Melnick, A. M. (2013). Differentiation therapy for IDH1/2 mutant malignancies. CELL RESEARCH, 23(8), 975-977. doi:10.1038/cr.2013.73

Will, B., Vogler, T. O., Bartholdy, B., Garrett-Bakelman, F., Mayer, J., Barreyro, L., . . . Steidl, U. (2013). Satb1 regulates the self-renewal of hematopoietic stem cells by promoting quiescence and repressing differentiation commitment. NATURE IMMUNOLOGY, 14(5), 437-+. doi:10.1038/ni.2572

Li, S., Garrett-Bakelman, F. E., Akalin, A., Zumbo, P., Levine, R., To, B. L., . . . Mason, C. E. (2013). An optimized algorithm for detecting and annotating regional differential methylation. BMC BIOINFORMATICS, 14. doi:10.1186/1471-2105-14-S5-S10

2012

Akalin, A., Kormaksson, M., Li, S., Garrett-Bakelman, F. E., Figueroa, M. E., Melnick, A., & Mason, C. E. (2012). methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. GENOME BIOLOGY, 13(10). doi:10.1186/gb-2012-13-10-R87

Akalin, A., Garrett-Bakelman, F. E., Kormaksson, M., Busuttil, J., Zhang, L., Khrebtukova, I., . . . Figueroa, M. E. (2012). Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia. PLOS GENETICS, 8(6). doi:10.1371/journal.pgen.1002781