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Joel L. Pomerantz, Ph.D.

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

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

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.

Ryuya Fukunaga, Ph.D.

Description of Research

Fukunaga lab investigates the mechanism and biology of post-transcriptional gene regulation controlled by RNA-binding proteins and small silencing RNAs. Our research projects will answer fundamental biological questions and also potentially lead to therapeutic applications to human disease.
For the RNA-binding proteins projects, we are interested in novel post-transcriptional gene regulation mechanism performed by uncharacterized or poorly characterized RNA-binding proteins. We use Drosophila oogenesis and spermatogenesis as one of the model systems since post-transcriptional gene regulation is particularly important during these processes.

For the small silencing RNA projects, we are particularly interested in the mechanisms by which microRNAs (miRNAs) and small interfering RNAs (siRNAs) are produced by Dicer enzymes and the mechanisms by the Dicer enzymes are regulated by Dicer-partner RNA-binding proteins. Specifically, we aim to understand the molecular mechanism by which the length of small silencing RNAs produced by Dicer is defined and regulated, which is a biologically significant question.

We use a combination of biochemistry, biophysics, Drosophila genetics, cell culture, and next-generation sequencing, in order to understand important biological questions from the atomic to the organismal level.

Lab Members

  • Azali Azlan (postdoc)
  • Yuki Taira (postdoc)

Publications

  • Zhu L, Fukunaga R. RNA-binding protein Maca is crucial for gigantic male fertility factor gene expression, spermatogenesis, and male fertility, in Drosophila. PLoS Genetics. 17, e1009655, (2021)
  • Vakrou S, Liu Y, Zhu L, Greenland GV, Simsek B, Hebl BV, Guan Y, Woldemichael K, Talbot CC, Aon MA, Fukunaga R, Abraham MR. Differences in molecular phenotype in mouse and human hypertrophic cardiomyopathy. Scientific Reports. 11, 13163, (2021)
  • Liu Y, Afzal J, Vakrou S, Greenland GV, Talbot CC Jr, Hebl VB, Guan Y, Karmali R, Tardiff JC, Leinwand LA, Olgin JE, Das S, Fukunaga R, Abraham MR. Differences in microRNA-29 and Pro-fibrotic Gene Expression in Mouse and Human Hypertrophic Cardiomyopathy. Front Cardiovasc Med. 6,170, (2019)
  • Zhu L, Liao ES, Fukunaga R. Drosophila Regnase-1 RNase is required for mRNA and miRNA profile remodelling during larva-to-adult metamorphosis. RNA Biology 16, 1386-1400, (2019)
  • Zhu L, Liao ES, Ai Y, Fukunaga R. RNA methyltransferase BCDIN3D is crucial for female fertility and miRNA and mRNA profiles in Drosophila ovaries. PLoS ONE 14, e0217603, (2019)
  • Liao ES, Kandasamy SK, Zhu L, Fukunaga R. DEAD-box RNA helicase Belle post-transcriptionally promotes gene expression in an ATPase activity-dependent manner. RNA 25, 825-839, (2019)
  • Zhu L, Kandasamy SK, Liao ES, Fukunaga R. LOTUS domain protein MARF1 binds CCR4-NOT deadenylase complex to post-transcriptionally regulate gene expression in oocytes. Nature Communications, 9, 4031, (2018)
  • Liao ES, Ai Y, Fukunaga R. An RNA-binding protein Blanks plays important roles in defining small RNA and mRNA profiles in Drosophila testes. Heliyon, 4, e00706, (2018)
  • Vakrou S, Fukunaga R, Foster DB, Sorensen L, Liu Y, Guan Y, Woldemichael K, Pineda-Reyes R, Liu T, Jill C. Tardiff JC, Leinwand LA, Tocchetti CG, Abraham TP, Brian O’Rourke B, Aon MA, Abraham MR. Allele-specific differences in transcriptome, miRNome, and mitochondrial function in two hypertrophic cardiomyopathy mouse models. JCI insight, 3, e94493, (2018)
  • Fukunaga R. Dicer-2 partner protein Loquacious-PD allows hairpin RNA processing into siRNAs in the presence of inorganic phosphate. Biochemical and Biophysical Research Communications, 498, 1022–1027, (2018)
  • Zhu L, Kandasamy SK, Fukunaga R. Dicer partner protein tunes the length of miRNAs using base-mismatch in the pre-miRNA stem. Nucleic Acids Res., 46, 3726-3741, (2018)
  • Kandasamy SK, Zhu L, Fukunaga R. The C-terminal dsRNA-binding domain of Drosophila Dicer-2 is crucial for efficient and high-fidelity production of siRNA and loading of siRNA to Argonaute2. RNA, 23, 1139-1153, (2017)
  • Kandasamy SK, Fukunaga R. Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production. Proc. Natl. Acad. Sci. U S A. 113, 14031-14036, (2016)
  • Lin X, Steinberg S, Kandasamy S, Afzal J, Mbiyangandu B, Liao ES, Guan Y, Corona-Villalobos C, Matkovich S, Epstein N, Tripodi D, Huo Z, Cutting G, Abraham T, Fukunaga R, Abraham R. Common MiR-590 Variant rs6971711 present only in African Americans reduces miR-590 biogenesis. PLoS ONE. 11, e0156065, (2016)
  • Yanagisawa T, Ishii R, Hikida Y, Fukunaga R, Sengoku T, Sekine SI, Yokoyama S. A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNACys. J. Struct. Funct. Genomics. 16, 25-41, (2015)
  • Fukunaga R, Colpan C, Han BW, Zamore PD. Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain. EMBO Journal, 18, 371-384, (2014)
  • Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD. Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals. Cell, 151, 533-546, (2012)
  • Cenik ES, Fukunaga R, Lu G, Dutcher R, Wang Y, Tanaka Hall TM, Zamore PD. Phosphate and R2D2 Restrict the Substrate Specificity of Dicer-2, an ATP-Driven Ribonuclease. Mol. Cell, 42, 172-814, (2011)
  • Naganuma M, Sekine SI, Fukunaga R, Yokoyama S. Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization. Proc. Natl. Acad. Sci., 106, 8489-8494, (2009)
  • Fukunaga R, Doudna JA. dsRNA with 5¢ overhangs contributes to endogenous and antiviral RNA silencing pathways in plants. EMBO J., 28, 545-555, (2009)
  • Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S. Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N¢-(o-Azidobenzyloxycarbonyl) lysine for site-specific protein modification. Chem. Biol., 15, 1187-1197, (2008)
  • Fukunaga R, Harada Y, Hirao I, Yokoyama S. Phosphoserine aminoacylation of tRNA bearing an unnatural base anticodon. Biochem Biophys Res Commun., 372, 480-485, (2008)
  • Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S. Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase. J. Mol. Biol., 378, 634-652, (2008)
  • Fukunaga R, Yokoyama S. Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus. J. Mol. Biol., 370, 128-141, (2007)
  • Fukunaga R, Yokoyama S. The C-terminal domain of the archaeal leucyl-tRNA synthetase prevents misediting of isoleucyl-tRNAIle. Biochemistry, 46, 4985-4996, (2007)
  • Fukunaga R, Yokoyama S. Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea. Nat. Struct. Mol. Biol., 14, 272-279, (2007)
  • Fukunaga R, Yokoyama S. Crystallization and preliminary X-ray crystallographic study of alanyl-tRNA synthetase from the archaeon Archaeoglobus fulgidus. Acta Crystallogr. F, 63, 224-228, (2007)
  • Fukunaga R, Yokoyama S. Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii. Acta Crystallogr. D, 63, 390-400, (2007)
  • Yanagisawa T, Ishii R, Fukunaga R, Nureki O, Yokoyama S. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of pyrrolysyl-tRNA synthetase from the Methanogenic archaeon Methanosarcina mazei. Acta Crystallogr. F, 62, 1031-1033, (2006)
  • Sasaki H, Sekine S, Sengoku T, Fukunaga R, Hattori M, Utsunomiya Y, Kuroishi C, Kuramitsu S, Shirouzu M, Yokoyama S. Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase. Proc. Natl. Acad. Sci. 103, 14744-14749, (2006)
  • Fukunaga R, Yokoyama S. Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase. J. Mol. Biol. 359, 901-912, (2006)
  • Kuratani M, Ishii R, Bessho Y, Fukunaga R, Sengoku T, Sekine S, Shirouzu M, Yokoyama S. Crystal structure of tRNA adenosine deaminase TadA from Aquifex aeolicus. J. Biol. Chem., 280, 16002-16008, (2005)
  • Tukalo M, Yaremchuk A, Fukunaga R, Yokoyama S, Cusack S. The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation. Nat. Struct. Mol. Biol. 12, 923-930, (2005)
  • Fukunaga R, Yokoyama S. Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator base recognition for 3¢-end relocation toward the editing domain. Nat. Struct. Mol. Biol. 12, 915-922, (2005)
  • Fukunaga R, Yokoyama S. Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain. J. Biol. Chem. 280, 29937-29945, (2005)
  • Fukunaga R, Ishitani R, Nureki O, Yokoyama S. Crystallization of Leucyl-tRNA synthetase complexed with tRNALeu from the archaeon Pyrococcus horikoshii. Acta Crystallogr. F, 61, 30-32, (2005).
  • Fukunaga R, Yokoyama S. Crystal Structure of Leucyl-tRNA Synthetase from the Archaeon Pyrococcus horikoshii Reveals a novel editing domain orientation. J. Mol. Biol. 346, 57-71, (2005).
  • Fukunaga R, Yokoyama S. Crystallization and preliminary X-ray crystallographic study of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii. Acta Crystallogr. D, 60, 1916-1918, (2004)
  • Fukunaga R, Yokoyama S. Crystallization and preliminary X-ray crystallographic study of the editing domain of Thermus thermophilus isoleucyl-tRNA synthetase complexed with pre- and post-transfer editing-substrate analogues. Acta Crystallogr. D, 60, 1900-1902, (2004)
  • Fukunaga R, Fukai S, Ishitani R, Nureki O, Yokoyama S. Crystal Structures of the CP1 Domain from Thermus thermophilus Isoleucyl-tRNA synthetase and Its Complex with L-Valine. J. Biol. Chem. 279, 8396-8402, (2004)