Joel L. Pomerantz, Ph.D.

Research Overview

My laboratory is interested in the molecular mechanisms by which cells interpret signals from their environment that instruct them to proliferate, differentiate, or die by apoptosis. This process is of fundamental importance in the development and function of the immune system. The dysregulation of signal transduction underlies many diseases of the immune system including immunodeficiencies, autoimmunity, and cancers derived from immune cells. A particular focus of the lab is the regulation of NF-κB, a pleiotropic transcription factor that is required for normal innate and adaptive immunity and which is inappropriately activated in several types of human cancer. We have been studying how NF-κB is activated in B and T lymphocytes in response to antigen recognition by the T cell receptor (TCR) and B cell receptor (BCR) complexes. Recently we have characterized the molecular mechanisms by which a multi-domain adapter protein, CARD11, functions in TCR signaling to NF-κB. In response to antigen receptor engagement, CARD11 undergoes a transition from an inactive to an active protein scaffold, and recruits a cadre of signaling cofactors into a complex in a signal-responsive manner. Current research is aimed at understanding how the multiple domains of CARD11 function together to translate activating upstream signals from the antigen receptor into the coordinated signaling activity of associated cofactors. CARD11 has also been directly implicated in the dysregulated signaling to NF-κB that is a signature feature of a subtype of Diffuse Large B cell Lymphoma (DLBCL). This subtype of DLBCL requires constitutive NF-κB activation for oncogenic proliferation, and the knockdown of CARD11 in this lymphoma leads to apoptosis. Interestingly, several oncogenic mutations in CARD11 have been identified in human DLBCL. We are currently studying how the oncogenic CARD11 mutations result in hyperactive signaling to NF-κB. We are hopeful that a mechanistic understanding of these mutants might translate into the development of novel cancer therapeutics. In addition to the antigen receptor signaling pathway, we are also studying the regulation of NF-κB in other arms of the innate and adaptive immune system through the isolation and characterization of novel regulators of NF-κB activity. We have developed several novel expression-cloning approaches for identifying novel signaling molecules that either activate or inhibit NF-κB. Several novel signaling regulators are under current study. Other current projects include the study of novel regulators of the NFAT transcription factor, a key player in T cell activation and tolerance. It is our hope that the study of these signaling molecules will expand our understanding of how inflammatory and immune responses are controlled and they are dysregulated in human disease.

Cellular Stress and Cell Signaling | Genetics, Genomics and Gene Regulation | Immunology and Infectious Diseases

 

Lab Website

Pomerantz Lab – Lab Website

 

Selected Publications

Tamara O’Connor, Ph.D.

Background

Dr. Tamara O’Connor is an Assistant Professor of Biological Chemistry at the Johns Hopkins University School of Medicine and Director of Admission for the Graduate Program in Biological Chemistry. Dr. O’Connor’s research focuses on the molecular basis of infectious disease with a particular emphasis on the network of molecular interactions acting at the host-pathogen interface and pathogen evolution in natural reservoirs.

Dr. O’Connor received her Ph.D. in Biochemistry from McMaster University, Canada where she studied multicellular differentiation of the bacterium Streptomyces coelicolor with Dr. Justin Nodwell. She completed her postdoctoral training dissecting virulence mechanisms of the respiratory pathogen Legionella pneumophila with Dr. Ralph Isberg at Tufts University School of Medicine. She joined the Johns Hopkins faculty in 2013.

Dr. O’Connor is a member of the American Society for Microbiology and the American Society for Biochemistry and Molecular Biology. Dr. O’Connor received an Innovation Award from the Johns Hopkins University School of Medicine Discovery Fund, a Discovery Award from the Johns Hopkins University School of Medicine Fisher Center and was a Natalie V. Zucker Scholars Fellow and recipient of an Ontario Graduate Scholarship and a Bank of Montreal Graduate Scholarship in Science and Technology.

Centers and Institutes

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Research Interests

Microbial pathogenesis, pathogen evolution, antibiotics

Research Summary

The O’Connor lab studies bacterial pathogenesis focusing on defining the mechanisms by which bacterial pathogen establish infection, how they exploit host cell machinery to accomplish this, and how individual virulence proteins and their component pathways coordinately contribute to disease. In parallel, the O’Connor lab investigates how virulence strategies arise in environmental reservoirs as a consequence of bacterial interactions with protozoa and the role of these natural hosts in driving bacterial transmission and disease in humans. Using genetics, biochemistry, molecular and cellular biology, and functional genomics, the O’Connor lab examines the repertoires of virulence proteins required for growth in a broad assortment of hosts, how the network of molecular interactions differs between hosts, and the mechanisms by which bacterial pathogens cope with this variation.

O’Connor Lab – Lab website is currently under construction and will be available soon

Selected Publications

  • O’Connor TJ, Boyd D, Dorer M, Isberg RR (2012) Aggravating genetic interactions allow a solution to redundancy in a bacterial pathogen. Science 338:1440-1444
  • Boamah DK, Zhou G, Ensminger AW, O’Connor TJ (2017) From many hosts, one accidental pathogen: the diverse protozoan hosts of Legionella. Front Cell Infect Microbiol. 7:477
  • Ghosh S and O’Connor TJ (2017) Beyond paralogs: the multiple layers of redundancy in bacterial pathogenesis. Front Cell Infect Microbiol. 7:467
  • Park JM, Ghosh S, O’Connor TJ (2020) Combinatorial selection in environmental hosts drives the evolution of a human pathogen. Nat Microbiol. 5:599
  • Boamah D, Gilmore MC, Bourget S, Ghosh A, Hossain MJ, Vogel JP, Cava F, O’Connor TJ, (2023) Peptidoglycan deacetylation controls Type IV secretion and the intracellular survival of the bacterial pathogen Legionella pneumophila. Proc Natl Acad Sci USA. 120:e2119658120.
  • Ghosh S, Bandyopadhyay S, Smith DM, Adak S, Semenkovich CF, Nagy L, Wolfgang MJ, O’Connor TJ. (2023) Legionella usurps host cell lipids for vacuole expansion and bacterial growth. PLoS Pathogens. 20:e1011996.
  • Shin CJ and O’Connor TJ. (2024) Novel induction of broad-spectrum antibiotics by the human pathogen Legionella. mSphere. e0012024.

Honors

  • Fisher Center Discovery Program Award, Johns Hopkins University School of Medicine, 2018
  • Discovery Fund Innovation Award, Johns Hopkins University School of Medicine, 2014
  • Natalie V. Zucker Research Scholars Postdoctoral Fellow, 2009
  • Graduate Research Fellow, Ontario Graduate Scholarship Fund, 2003
  • Graduate Research Fellow, Bank of Montreal Graduate Scholarship in Science and Technology, 2002
  • Graduate Program Affiliations
  • Biological Chemistry (BC) Graduate Program
  • Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program
  • Immunology (IMM) Graduate Program
  • Cellular and Molecular Medicine (CMM) Graduate Program
  • Cross Disciplinary Graduate Program in Biomedical Sciences (XDBio)

Memberships

  • American Society for Microbiology
  • American Society for Biochemistry and Molecular Biology

Professional Activities

  • Department of Biological Chemistry Retreat Committee, Co-Chair, 2017-present
  • Department of Biological Chemistry Seminar Series, Chair, 2015-present
  • Biological Chemistry Graduate Program Admissions Committee, Member, 2013-present
  • Cross Disciplinary Gradate Program in Biomedical Sciences Admissions Committee, Member, 2018-present
  • Immunology Gradate Program Admissions Committee, Member, 2019-2020
  • Graduate Program in Biological Chemistry, Director, 2018 -present
  • Johns Hopkins Bug Super Group, Co-Founder, 2017-present
  • Society for Advancement of Chicanos/Hispanics and Native Americans in Science (SACNAS), Baltimore Chapter, Faculty Advisor, 2017-present
  • Frontiers in Cellular and Infection Microbiology, Associate Editor, 2022-present

Additional Training

  • Postdoctoral Fellowship, Tufts University School of Medicine, Boston, MA

Mollie K. Meffert, M.D., Ph.D.

Background

Dr. Mollie Meffert is an associate professor of biological chemistry and neuroscience at the Johns Hopkins University School of Medicine. Her research focuses on the regulation of neuronal gene expression in health and disease. Dr. Meffert currently serves as the Vice Director of the Department of Biological Chemistry.

Research Description

The Meffert lab investigates mechanisms underlying enduring change in mammalian nervous system function in health and disease. We are interested in how cells in the nervous system make decisions to turn genes on or off, and how those decisions are remembered in processes such as development or plasticity, and in injury or disease. The goal of the Meffert lab is to gain a mechanistic understanding of how selective gene programs are recruited and maintained to alter synaptic, neuronal, and cognitive function. Rather than focusing on single genes, we investigate the upstream processes that allow coordinate regulation of many genes to achieve biological impact. Cell-specific and subcellularly localized posttranscriptional control by RNA-binding proteins and noncoding RNAs is an ongoing focus.

Our laboratory elucidated a post-transcriptional mechanism capable of organizing pro-growth gene programs in which activity-dependent regulation of microRNA (miRNA) production governs the selection of gene targets for protein synthesis. An RNA-binding protein, Lin28, is one activity-responsive factor that promotes pro-growth protein synthesis by downregulating only select miRNAs (e.g. the family of let-7 ‘growth-suppressor’ miRNAs), which repress pro-growth genes. In neurons, pro-growth mRNA targets of the let-7 miRNAs include mRNA for proteins involved in excitatory synaptic function, as well as growth, metabolism, and repair. In recent work, we develop discovery-based sequencing strategies to reveal in vivo small RNA targets through the production of small RNA:target chimeric molecules.

Dr. Meffert’s work has been recognized with awards including the: March of Dimes research scholar, Simons Foundation Autism Research Initiative award, PLU Rho Award, Alfred P. Sloan Research Fellow Award, Hamilton Smith Award for Innovative Science, and The Sontag Foundation Distinguished Scientist and Distinguished Alumni Awards.
Dr. Meffert and her laboratory are the current recipients of the Eric C. Aker Award Endowment through the Braude Foundation.

Expertise

Dr. Meffert received her undergraduate degree (BS) from Stanford University. She earned her MD/PhD in neuroscience from Stanford University School of Medicine and completed a postdoctoral fellowship at California Institute of Technology with Dr. David Baltimore.

Areas of research expertise in Dr. Meffert’s laboratory include molecular neuroscience, RNA biology, and gene expression. Her laboratory uses tools of molecular diagnostics, biochemistry, computational biology, quantitative imaging, and mouse and human genetic models of disease

Lab Members

Xinbei Li (BC graduate student), Bonita Powell (BCMB graduate student), Emily Eiss (BCMB graduate student), Ariella Kornfeld (BCMB graduate student), Sydney Pettit (BCMB graduate student), Preksha Jerajani (research technician), Anselmo Rivera (Hopkins undergraduate)

Selected Publications

  • Xinbei Li, William T. Mills IV, Daniel S. Jin, and Mollie K.Meffert. (2024), Genome-wide and cell-type-selective profiling of in vivo small noncoding RNA:target RNA interactions by chimeric RNA sequencing. Cell Reports Methods, 4, 100836.
  • Megha Subramanian, William T. Mills IV, Manish D Paranjpe, Uche Onuchukwu, Manasi Inamdar, Amanda R. Maytin, Xinbei Li, Joel L. Pomerantz, and Mollie K.Meffert. (2023), Growth suppressor microRNAs mediate synaptic overgrowth and behavioral deficits in Fragile X mental retardation protein deficiency. iScience, 27 (1) 108676.
  • William T. Mills IV, Sreenivas Eadara, Andrew E. Jaffe, and Mollie K. Meffert. (2022), SCRAP: a bioinformatic pipeline for the analysis of small chimeric RNA-seq data. RNA 29 (1); 1-17.
  • Alexandra M Amen, Claudia R. Ruiz, Jay Shi, Megha Subramanian, Daniel Pham, and Mollie K. Meffert, (2017) A rapid induction mechanism for Lin28a in trophic responses. Molecular Cell, 65 (3); 490 – 503.
  • Erica C. Dresselhaus, Matthew C. Boersma, and Mollie K. Meffert, (2018), Targeting of NF-kB to dendritic spines is required for synaptic signaling and spine development. J.Neurosci., 8(17); 4093-4103. PMID 29555853.
  • Laurel M. Oldach, Kirill Gorshkov,William T. Mills, Jin Zhang*, and Mollie Meffert* (2018), A biosensor for MAPK-dependent Lin28 signaling. Molecular Biology of the Cell, 29(10), 1157-1167. PMID29540527.
  • Yu-Wen A. Huang*, Claudia R. Ruiz*, E.C.H. Eyler*, Kathie Lin, and Mollie K. Meffert. “Dual regulation of miRNA biogenesis generates target specificity in neurotrophin-induced protein synthesis.” Cell, 148(5); 933-946. 2012.

Seth Margolis, Ph.D.

Background

Dr. Seth Shatkin Margolis is an Associate Professor in the Department of Biological Chemistry with a Secondary appointment in the Sol Snyder Department of Neuroscience at the Johns Hopkins University School of Medicine. Dr. Margolis and his research team are focused on studying the protein homeostasis machinery (protein translation and protein degradation) that control neuronal function in development and disease.
In 2017, Dr. Margolis and his team discovered a novel neuronal specific proteasome complex and a unique class of extracellular signaling peptides that it produces.

Dr. Margolis received his undergraduate degree in biochemistry from the University of Rochester and earned his Ph.D. from Duke University. He completed postdoctoral training in neurobiology at Harvard Medical School. Dr. Margolis joined the Johns Hopkins faculty in 2011.

Centers and Institutes

Basic Biomedical Sciences, Institute for

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Additional Academic Titles

Associate Professor of Neuroscience

Research Interests

Formation and Function of the Neuronal Membrane Proteasome, Neuronal Survival and Neurodegeneration, Proteostasis

Lab Website

Margolis Lab – Lab Website

Projects in The Margolis Laboratory:

Proteasomes are essential for proper neuronal function. Since 2011 we have been focused on studying protein degradation in the nervous system. In 2017, we published on our new discovery of a neuronal specific proteasome complex and its link to neuronal function. Based on extensive original findings in the Margolislaboratory, our central hypothesis is that neuronal activity promotes the degradation of newly synthesized proteins through a membrane associated 20S proteasome complex in order to rapidly generate biologically meaningful peptides that may be critical for normal nervous system function. Nothing is known about this new form of rapid neuronal communication and further understanding is critical in providing vital insight into activity-dependent neuronal functions mediated by protein degradation. In addition, relevant tools are needed to control neuronal subtype specific NMP peptide-receptor signaling to bring this pathway closer to modern day neuroscience approaches. Given the critical importance of protein degradation to human health, the long-range objective of our research is to understand the regulation and function of this degradation program and to apply this knowledge to the detection and eventual treatment of cognitive disorders. Among other projects we aim to accomplish the following:

  • To identify and study specific NMP peptide-receptor interactions relevant to neuronal signaling
  • To identify and study molecular components required for NMP complex assembly
  • To investigate the NMP as a regulator of neuronal function and physiology ex vivo and in vivo

Research Summary

Dr. Margolis has a broad background and expertise in using biochemical, proteomic, molecular cellular, mouse genetic, and behavior approaches to dissect protein homeostasis signaling mechanisms in neuronal biology. Over the years Dr. Margolisand his team has focused the laboratories efforts toward the ubiquitin proteasome pathways and actin cytoskeleton control of early developmental excitatory synapse formation in healthy and diseased brain states. They have spent considerable effort investigating the functions of an ubiquitin ligase, UBE3A in neural development and its role in the human cognitive disorder Angelman syndrome. Specifically, they have been identifying the substrates of UBE3A that are targeted for proteasome-mediated degradation. UBE3A itself and at least one of these substrates is relevant to Alzheimer’s disease. They have since aimed part of our efforts to advancing an understanding of protein degradation mechanisms relevant to Alzheimer’s disease (AD) etiology.

In the course of their studies, Dr. Margolis and his team made an unexpected discovery which was built logically on the laboratories long standing interests. In short, they discovered a novel neuronal specific membrane associated proteasome complex that through extracellular proteasome-derived peptides modulates neuronal signaling. This system is contributes to activity dependent neuronal signaling and is disrupted in disease. The robustness, uniqueness, and reproducibility have kept them moving forward in order to generate significant future advances in tools and information to comprehend the role of this signaling in the nervous system both in health and disease. In the long term, Dr. Margolis envisions the lab following these pathways to address the following questions:

  • What are the substrates of this proteasome complex and the sequences of the signaling peptides?
  • How do these NMP derived peptides mediate their signaling capacity and specificity?
  • What is the full make up of the neuronal membrane proteasome (NMP) complex and how is it regulated?
  • What is the importance of this pathway to neuronal physiology and animal behavior in health and disease?

They hope to leverage their findings in order to better define this emerging field and provide the tools and information important for their research and the field of cellular and molecular neuroscience as a whole.

Selected Publications

  • Ramachandran KV, Margolis SS. A mammalian nervous-system-specific plasma membrane proteasome complex that modulates neuronal function. Nat Struct Mol Biol. (2017) Apr;24(4):419-430. doi: 10.1038/nsmb.3389.
  • Ramachandran KV, Fu JM, Schaffer TB, Na CH, Delannoy M, Margolis SS. Activity-Dependent Degradation of the Nascentome by the Neuronal Membrane Proteasome. Mol Cell. (2018) Jul 5;71(1):169-177.e6. doi: 10.1016/j.molcel.2018.06.013.
  • Schaffer TB, Smith JE, Cook EK, Phan T, Margolis SS. PKCε Inhibits Neuronal Dendritic Spine Development through Dual Phosphorylation of Ephexin5. Cell Rep. (2018) Nov 27;25(9):2470-2483.e8. doi: 10.1016/j.celrep.2018.11.005.
  • Sell GL, Schaffer TB, Margolis SS. Reducing expression of synapse-restricting protein Ephexin5 ameliorates Alzheimer’s-like impairment in mice. J Clin Invest. (2017) May 1;127(5):1646-1650. doi: 10.1172/JCI85504.

Graduate Program Affiliations

  • Graduate Program in Biochemistry, Cell, and Molecular Biology
  • Graduate Program in Neuroscience
  • Graduate Program in Biological Chemistry

Professional Activities

  • Basic Science Institute Summer Internship Program (BSI-SIP), Co-Director and Admissions Committee
  • BCMB Graduate Admissions Committee, 2019, Member,
  • BCMB Graduate Program Retreat,, Co-Director,, 1/1/13
  • Faculty Senate, Representative for Department of Biological Chemistry
  • XDBio Graduate Program, Advisory Board

Additional Training

Postdoctoral Training, Harvard Medical School, Boston, MA, 2011, Neurobiology