Babushok Laboratory

The long-term goal of the Babushok Laboratory to improve the outcomes of patients with bone marrow failure disorders through bench-to-bedside research aimed at elucidating mechanisms of hematopoietic failure and transforming this knowledge into rational therapies. In our previous studies, we have established an analytical platform that sensitively and reliably identifies somatic changes in hematopoietic cells of patients with bone marrow failure using comparative whole exome sequencing (WES), single nucleotide polymorphism array (SNP-A) analysis, and deep targeted sequencing of the Major Histocompatibility Complex (MHC) region, and have used this pipeline to define the landscape of clonal hematopoiesis in acquired aplastic anemia (AA) and other bone marrow failure disorders. Our results led to novel insights into clonal evolution in patients with AA, and specifically, in the role of Human Leukocyte Antigen (HLA) Class I autoimmunity in the pathogenesis of AA. Based on our studies as well as studies of others, we hypothesize that bone marrow aplasia in AA is caused by autoreactive T cells that are directed against one or a small number of shared autoantigens presented by HLA class I alleles, and that this cytotoxic T cell attack, as well as its associated proinflammatory marrow environment, create a selective pressure that causes outgrowth of cells bearing adaptive somatic mutations. These mutations, in turn, affect the patients’ long-term outcomes, and some of them predispose to the development of MDS.

Our current studies aim to answer the following questions:

  • What causes the emergence of clonal hematopoiesis in premalignant conditions, such as aging, inherited bone marrow failure syndromes, and immune-mediated bone marrow failure
  • How can we use our knowledge of mechanisms of clonal selection to shift the balance in favor of healthy hematopoiesis?
  • What is the pathogenic mechanism of acquired immune-mediated bone marrow failure (e.g. AA)?
  • How can we transform the improved understanding of the immune pathogenesis of AA into novel prevention strategies, improved diagnostic tests, and rational therapies?

How do the mechanism of autoimmunity and immune evasion in AA inform our understanding of related phenomena, including immune surveillance and immune evasion in cancer and mechanisms of resistance to immunotherapies?

Location: Abramson Research Center, ARC 303

People

Daria Babushok, MD, PhD

Photo of Daria Babushok, MD, PhD
Principal Investigator

Dr Daria Babushok is a physician-scientist and an Assistant Professor of Medicine in the Division of Hematology-Oncology at the University of Pennsylvania. Dr Babushok laboratory conducts basic and translational research focusing on the immune pathogenesis of acquired aplastic anemia and the development of clonal hematopoiesis in acquired aplastic anemia and other bone marrow failure disorders.

Natasha Stanley

Natasha Stanley
Research Technician

Natasha received her Bachelor of Science degree in Biology from Haverford College in 2015. Natasha's previous research involved tracking chloroplast inheritance in Chlamydomonas with fluorescent protein tools and studying the effects of psychiatric drug therapies on glucocorticoid receptor translocation in human olfactory epithelial cells. Natasha's studies mechanisms of clonal evolution in acquired aplastic anemia.

Caitlin Ritz

Photo of Caitlin Ritz
Research Technician

Caitlin Ritz received her Bachelors of Arts and Sciences in Biochemistry from the University of Colorado and completed a Post-Baccalaureate Specialized Studies Program at the University of Pennsylvania. She

Kathy Guo

Kathy Guo
Research Technician
Kathy Guo graduated from the University of Pennsylvania in 2017. After graduation, she was a research specialist in the Abramson Family Cancer Research Institute researching neuroblastoma. Kathy later joined the Comprehensive Bone Marrow Failure Center and continued under Dr. Babushok in the Department of Hematology at Penn, studying Aplastic Anemia. Kathy will be pursuing a degree in dentistry at Temple University next fall.

Research

The long-term goal of the Babushok Laboratory to improve the outcomes of patients with bone marrow failure disorders through bench-to-bedside research aimed at elucidating mechanisms of hematopoietic failure and transforming this knowledge into rational therapies.

Publication Highlights

Ganetsky A, Han JH, Hughes ME, Babushok DV, Frey NV, Gill SI, Hexner EO, Loren AW, Luger SM, Mangan JK, Martin ME, Smith J, Freyer CW, Gilmar C, Schuster M, Stadtmauer EA, Porter DL. . . Oral vancomycin prophylaxis is highly effective in preventing Clostridium difficile infection in allogeneic hematopoietic cell transplant recipients. Clin Infect Dis.. 2018 Sep 26. doi: 10.1093/cid/ciy822. [Epub ahead of print] PMID: 30256954.

Babushok DV, Bessler M, Olson TS. Genetic predisposition to myelodysplastic syndrome and acute myeloid leukemia in children and young adults. Leuk Lymphoma. 2016;57(3):520-36. doi: 10.3109/10428194.2015.1115041. Epub 2015 Dec 23. PMID: 26693794.

Ganetsky A, Frey NV, Hexner EO, Loren AW, Gill SI, Luger SM, Mangan JK, Martin ME, Babushok DV, Drobyski WR, Smith J, Timlin C, Freyer CW, Stadtmauer EA, Porter DL. Tocilizumab for the treatment of severe steroid-refractory acute graft-versus-host disease of the lower gastrointestinal tract. Bone Marrow Transplant. 2018 May 24. doi: 10.1038/s41409-018-0236-z. [Epub ahead of print] PMID: 29795429 .

Babushok DV, Nelson EJ, Morrissette JJD, Joshi S, Palmer MB, Frank D, Cambor CL, Hexner EO. Myelofibrosis patients can develop extramedullary complications including renal amyloidosis and sclerosing hematopoietic tumor while otherwise meeting traditional measures of ruxolitinib response. Leuk Lymphoma. 2018 Sep 19:1-4. doi: 10.1080/10428194.2018.1509319. [Epub ahead of print] No abstract available. PMID: 30227762 .

Babushok DV. A brief, but comprehensive, guide to clonal evolution in aplastic anemia. Hematology Am Soc Hematol Educ Program. 2018 Nov 30;2018(1):457-466. doi: 10.1182/asheducation-2018.1.457. Review. PMID: 30504346.

Betensky M, Babushok D, Roth JJ, Mason, PJ, Biegel JA, Busse TM, Li Y, Lind C, Papazoglou A, Monos D, Podsakoff G, Bessler M, and Olson TS. Clonal evolution and clinical significance of copy number neutral loss of heterozygosity of chromosome arm 6p in acquired aplastic anemia.. Cancer Genet. 2016 Jan-Feb;209(1-2):1-10. doi: 10.1016/j.cancergen.2015.10.002. Epub 2015 Oct 30. PMID: 26702937 .

Babushok DV, Stanley NL, Morrissette JJD, Lieberman DB, Olson TS, Chou ST, Hexner EO. Germline duplication of ATG2B and GSKIP genes is not required for the familial myeloid malignancy syndrome associated with the duplication of chromosome 14q32. Leukemia. 2018 Dec;32(12):2720-2723. doi: 10.1038/s41375-018-0231-9. Epub 2018 Aug 7. No abstract available. PMID: 30087419 .

Articles

Postdoctoral Fellow Opening

Tuesday, February 5, 2019 Full Article: view

The Babushok laboratory seeks an enthusiastic and dedicated Ph.D. or M.D./Ph.D. scientist to join our laboratory as a Post-Doctoral Fellow at the Perelman School of Medicine University of Pennsylvania. The Babushok laboratory performs cutting-edge translational research at the interface of hematology, immunology and molecular genetics to interrogate the mechanisms of acquired and inherited bone marrow failure and the link between bone marrow failure and leukemia. We recently identified a critical connection between the development of clonal hematopoiesis in immune-mediated bone marrow failure called aplastic anemia and somatic loss of specific HLA class I alleles, shedding light on the mechanism of the autoimmune attack in this disease. Research opportunities are available investigating various facets of the immune mechanism of aplastic anemia. The studies will utilize a variety of cutting-edge proteomics and immunogenetic approaches, including mass spectrometry-based proteomic analyses of immune epitopes, next-generation sequencing analyses of HLA and TCR genes, use of genetic engineering technologies to create cell lines bearing designer TCR and HLA alleles, CRISPR-based cell culture models, cytotoxicity assays, RNA interference and pharmacologic inhibition of involved pathways using in vitro and murine models.