Jaisri Lingappa's Lab

Former Postdoctoral Fellows

Brook C. Barajas

Brook Barajas

Brook Barajas was born and raised in Seattle, WA. She majored in Microbiology at the University of California at Santa Barbara (UCSB), where she graduated with Highest Honors in 2007 and was the Student Commencement Speaker. As an undergraduate, she was frequently on the Dean’s list and received numerous honors for her academic scholarship, including an award for “Outstanding Critical Thinking and Analysis in the Laboratory”. As a research scientist in the Lingappa laboratory from 2007 – 2009, Brook worked closely with Beth Thielen, who was an MD PhD student at the time. In 2009, she left Seattle to join the Cancer Biology Ph.D. program at Stanford University, where she was awarded a Stanford Graduate Fellowship in 2009 and an NSF Graduate Research Fellowship in 2011. Brook’s Ph.D. studies were in the laboratory of Dr. Paul Khavari, in the Dept. of Dermatology at Stanford University. As a Ph.D. student, she led a project involving the dynamic profiling of chromatin marks and chromosome conformation in differentiating primary epidermal keratinocytes, and became proficient in the generation and bioinformatics analysis of CHIP-seq and other large-scale datasets.  Brook returned to the Lingappa laboraotory for postdoctoral research  from 2016 – 2018, and then joined Juno Therapeutics.

Research:

As a postdoctoral researcher, Brook introduced the proximity ligation assay (PLA) to the Lingappa lab.  Brook utilized this imaging technique to demonstrate that assembling HIV-1 Gag colocalizes with the host enzymes ABCE1 and DDX6 in HIV-expressing cells.  These imaging studies are an excellent validation of our many biochemical studies showing that Gag assembles in association with host ribonucleoprotein complexes, termed RNA granules, that contain ABCE1 and DDX6, two host proteins that facilitate HIV-1 Gag assembly.  In a paper published in PLoS Pathogens in 2018,  Brook and other Lingappa Lab members demonstrated that much of the HIV-1 genomic RNA in the cytoplasm is in small RNA granules containing ABCE1 and DDX6.  Because HIV-1 Gag must encapsidate the viral genome as it assembles into immature capsids, the finding that these RNA granules contain substantial HIV-1 genomic RNA offers yet another rationale for why HIV-1 Gag has evolved to target to these RNA granules during assembly.

Publications:

  1. Rubin, AJ, Barajas, BC, Furlan-Magaril, M, Lopez-Pajares, V, Mumbach, MR, Howard, I, Kim, DS, Boxer, LD, Cairns, J, Spivakov, M, Wingett, SW, Shi, M, Zhao, Z, Greenleaf, WJ, Kundaje, A, Snyder, M, Chang, HY, Fraser, P, Khavari, PA. Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Nat Genet. 2017;49 (10):1522-1528. doi: 10.1038/ng.3935. PubMed PMID:28805829 PubMed Central PMC5715812.
  2. Lopez-Pajares, V, Qu, K, Zhang, J, Webster, DE, Barajas, BC, Siprashvili, Z, Zarnegar, BJ, Boxer, LD, Rios, EJ, Tao, S, Kretz, M, Khavari, PA. A LncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation. Dev Cell. 2015;32 (6):693-706. doi: 10.1016/j.devcel.2015.01.028. PubMed PMID:25805135 PubMed Central PMC4456036.
  3. Boxer, LD, Barajas, B, Tao, S, Zhang, J, Khavari, PA. ZNF750 interacts with KLF4 and RCOR1, KDM1A, and CTBP1/2 chromatin regulators to repress epidermal progenitor genes and induce differentiation genes. Genes Dev. 2014;28 (18):2013-26. doi: 10.1101/gad.246579.114. PubMed PMID:25228645 PubMed Central PMC4173152.
  4. Webster, DE, Barajas, B, Bussat, RT, Yan, KJ, Neela, PH, Flockhart, RJ, Kovalski, J, Zehnder, A, Khavari, PA. Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition. Genome Res. 2014;24 (5):751-60. doi: 10.1101/gr.166231.113. PubMed PMID:24443471 PubMed Central PMC4009605.
  5. Zarnegar, BJ, Webster, DE, Lopez-Pajares, V, Vander Stoep Hunt, B, Qu, K, Yan, KJ, Berk, DR, Sen, GL, Khavari, PA. Genomic profiling of a human organotypic model of AEC syndrome reveals ZNF750 as an essential downstream target of mutant TP63. Am J Hum Genet. 2012;91 (3):435-43. doi: 10.1016/j.ajhg.2012.07.007. PubMed PMID:22922031 PubMed Central PMC3511987.
  6. Thielen, BK, McNevin, JP, McElrath, MJ, Hunt, BV, Klein, KC, Lingappa, JR. Innate immune signaling induces high levels of TC-specific deaminase activity in primary monocyte-derived cells through expression of APOBEC3A isoforms. J Biol Chem. 2010;285 (36):27753-66. doi: 10.1074/jbc.M110.102822. PubMed PMID:20615867 PubMed Central PMC2934643.
  7. Lubin, AA, Hunt, BV, White, RJ, Plaxco, KW. Effects of probe length, probe geometry, and redox-tag placement on the performance of the electrochemical E-DNA sensor. Anal Chem. 2009;81 (6):2150-8. doi: 10.1021/ac802317k. PubMed PMID:19215066 .

Search PubMed

Motoko Tanaka

Motoko Tanaka grew up in Awaji Island in Japan, which is famous for having the world’s longest suspension bridge, the fourth fastest currents in the world (in the Naruto whirlpools), and a 500-year-old form of traditional puppet theatre.  She did her undergraduate studies at the University of Tokushima, where she majored in Biological science and Technology and worked in the laboratory of Professor Hitoshi Hori.   In 2007, she entered the Kobe University PhD program, where she studied host genetic factors related to the susceptibility to Mycobacterium infection in the infection control laboratory of Dr. Masato Kawabata.  In 2008, she moved to the laboratory of Dr. Yoshihiro Kawaoka, in the Division of Zoonosis, Department of Microbiology and Infectious Diseases, Graduate School of Medicine at Kobe University, where she studied the host adaptation mechanism of influenza virus.  In April 2010, she joined the Lingappa laboratory as a short term visiting graduate student, through the University of Washington School of Medicine and Kobe University Graduate School of Medicine exchange program and the Kobe University Global COE Program Kobe University Global COE Program funded by the Ministry of Education, Culture, Sports, Science, and Technology of Japan.  In September 2011, she obtained her Ph.D. from Kobe University, and returned to the Lingappa lab as a postdoctoral fellow.  Motoko was a postdoctoral fellow in the Lingappa lab from 2012-2017 and joined Keith Jerome’s laboratory at the Fred Hutchinson Research Center in 2018.

Research:

In her project as a visiting student in the Lingappa lab, Motoko worked with Kevin Klein and Jon Reed to study the role of the nucleocapsid domain in HIV capsid assembly using Gag-leucine zipper chimeras. During this time, she demonstrated that well-studied mutations in the highly conserved major homology region of Gag arrest the HIV-1 capsid assembly pathway, resulting in accumulation of assembly intermediates containing Gag as well as host proteins such as ABCE1 and the RNA granule protein DDX6.  Motoko also made major contributions to our 2018 publication in PLoS Pathogens showing that in the cytoplasm, the HIV-1 genome is primarily in host ribonucleoprotein complexes termed RNA granules, and that the capsid protein HIV-1 Gag is directed to these complexes thereby allowing Gag to encapsidate HIV-1 genomic RNA during assembly.  Motoko’s as yet unpublished studies identified ABCE1 binding sites within Gag and other proteins, offering exciting answers to the question of how assembling Gag traffics to RNA granules containing ABCE1.

Publications:

  1. Barajas, BC, Tanaka, M, Robinson, BA, Phuong, DJ, Chutiraka, K, Reed, JC, Lingappa, JR. Identifying the assembly intermediate in which Gag first associates with unspliced HIV-1 RNA suggests a novel model for HIV-1 RNA packaging. PLoS Pathog. 2018;14 (4):e1006977. doi: 10.1371/journal.ppat.1006977. PubMed PMID:29664940 PubMed Central PMC5940231.
  2. Tanaka, M, Robinson, BA, Chutiraka, K, Geary, CD, Reed, JC, Lingappa, JR. Mutations of Conserved Residues in the Major Homology Region Arrest Assembling HIV-1 Gag as a Membrane-Targeted Intermediate Containing Genomic RNA and Cellular Proteins. J Virol. 2016;90 (4):1944-63. doi: 10.1128/JVI.02698-15. PubMed PMID:26656702 PubMed Central PMC4734008.
  3. Lingappa, JR, Reed, JC, Tanaka, M, Chutiraka, K, Robinson, BA. How HIV-1 Gag assembles in cells: Putting together pieces of the puzzle. Virus Res. 2014;193 :89-107. doi: 10.1016/j.virusres.2014.07.001. PubMed PMID:25066606 PubMed Central PMC4351045.
  4. Manríquez, ME, Makino, A, Tanaka, M, Abe, Y, Yoshida, H, Morioka, I, Arakawa, S, Takeshima, Y, Iwata, K, Takasaki, J, Manabe, T, Nakaya, T, Nakamura, S, Iglesias, AL, Rossales, RM, Mirabal, EP, Ito, T, Kitazawa, T, Oka, T, Yamashita, M, Kudo, K, Shinya, K. Emergence of HA mutants during influenza virus pneumonia. Int J Clin Exp Pathol. 2012;5 (8):787-95. . PubMed PMID:23071861 PubMed Central PMC3466977.
  5. Shinya, K, Ito, M, Makino, A, Tanaka, M, Miyake, K, Eisfeld, AJ, Kawaoka, Y. The TLR4-TRIF pathway protects against H5N1 influenza virus infection. J Virol. 2012;86 (1):19-24. doi: 10.1128/JVI.06168-11. PubMed PMID:22031950 PubMed Central PMC3255869.
  6. Klein, KC, Reed, JC, Tanaka, M, Nguyen, VT, Giri, S, Lingappa, JR. HIV Gag-leucine zipper chimeras form ABCE1-containing intermediates and RNase-resistant immature capsids similar to those formed by wild-type HIV-1 Gag. J Virol. 2011;85 (14):7419-35. doi: 10.1128/JVI.00288-11. PubMed PMID:21543480 PubMed Central PMC3126549.
  7. Shinya, K, Okamura, T, Sueta, S, Kasai, N, Tanaka, M, Ginting, TE, Makino, A, Eisfeld, AJ, Kawaoka, Y. Toll-like receptor pre-stimulation protects mice against lethal infection with highly pathogenic influenza viruses. Virol J. 2011;8 :97. doi: 10.1186/1743-422X-8-97. PubMed PMID:21375734 PubMed Central PMC3061943.
  8. Tanaka, M, Tsumura, K, Ito, H, Ito, T, Ono, E, Makino, A, Kawaoka, Y, Shinya, K. Characteristics of influenza virus genome mutations. Kobe J Med Sci. 2012;57 (3):E116-27. . PubMed PMID:22971946 .
  9. Hatta, M, Ratnawati,, Tanaka, M, Ito, J, Shirakawa, T, Kawabata, M. NRAMP1/SLC11A1 gene polymorphisms and host susceptibility to Mycobacterium tuberculosis and M. leprae in South Sulawesi, Indonesia. Southeast Asian J Trop Med Public Health. 2010;41 (2):386-94. . PubMed PMID:20578522 .
  10. Nakae, T, Uto, Y, Tanaka, M, Shibata, H, Nakata, E, Tominaga, M, Maezawa, H, Hashimoto, T, Kirk, KL, Nagasawa, H, Hori, H. Design, synthesis, and radiosensitizing activities of sugar-hybrid hypoxic cell radiosensitizers. Bioorg Med Chem. 2008;16 (2):675-82. doi: 10.1016/j.bmc.2007.10.035. PubMed PMID:18029186 .

Search PubMed

Bridget Robinson

Bridget RobinsonBridget Robinson attended South Dakota State University, where she received her B.S. in Microbiology.  She subsequently received her M.S. within the department of Molecular Microbiology, Immunology, and Pathology under the direction of Dr. Joseph Smith at Colorado Statue University.  Her work characterized the binding properties of a variant family of cytoadhesive proteins encoded within Plasmodium falciparum.  She was also employed at the University of Colorado Health Sciences Center as a research associate in the laboratories of Dr. Ken Tyler and Dr. Roberta DeBiasi, where she studied apoptotic signaling in a Reovirus model of viral myocarditis.  Bridget received her PhD from Oregon Health & Science University in 2011, within the laboratory of Dr. Scott Wong.  She characterized immune evasion properties of the viral interferon regulatory factors encoded within Rhesus Rhadinovirus, a non-human primate model used to study Kaposi’s Sarcoma-associated Herpesvirus pathogenesis.  Bridget was in the Lingappa Lab from 2012-2015, after which she returned to Portland, OR where she joined Tim Nice’s laboratory in 2016.

Research:

During her time as a postdoctoral fellow in the Lingappa lab , Bridget had three projects.  She published a first-author manuscript on her first project while in her second year in the Lingappa lab – a very impressive time from start to completion.  In this project, Bridget used biochemical and imaging approaches to generate a detailed temporospatial map of the assembly pathway that correlated steps in the HIV-1 capsid assembly with structural features of the completed immature capsid.  In her second project, Bridget showed that HIV-1 packaging is initiated in RNA granules which go on to become assembly intermediates once they are co-opted by HIV-1 Gag.  These studies set the stage for our 2018 PLOS Pathogens paper.  Bridget also contributed to a project that addresses whether some HIV variants selected during infection in vivo progress through the assembly pathway more rapidly, possibly leading to higher viral loads.

 

Publications:

  1. Barajas, BC, Tanaka, M, Robinson, BA, Phuong, DJ, Chutiraka, K, Reed, JC, Lingappa, JR. Identifying the assembly intermediate in which Gag first associates with unspliced HIV-1 RNA suggests a novel model for HIV-1 RNA packaging. PLoS Pathog. 2018;14 (4):e1006977. doi: 10.1371/journal.ppat.1006977. PubMed PMID:29664940 PubMed Central PMC5940231.
  2. Tanaka, M, Robinson, BA, Chutiraka, K, Geary, CD, Reed, JC, Lingappa, JR. Mutations of Conserved Residues in the Major Homology Region Arrest Assembling HIV-1 Gag as a Membrane-Targeted Intermediate Containing Genomic RNA and Cellular Proteins. J Virol. 2016;90 (4):1944-63. doi: 10.1128/JVI.02698-15. PubMed PMID:26656702 PubMed Central PMC4734008.
  3. Lingappa, JR, Reed, JC, Tanaka, M, Chutiraka, K, Robinson, BA. How HIV-1 Gag assembles in cells: Putting together pieces of the puzzle. Virus Res. 2014;193 :89-107. doi: 10.1016/j.virusres.2014.07.001. PubMed PMID:25066606 PubMed Central PMC4351045.
  4. Robinson, BA, Reed, JC, Geary, CD, Swain, JV, Lingappa, JR. A temporospatial map that defines specific steps at which critical surfaces in the Gag MA and CA domains act during immature HIV-1 capsid assembly in cells. J Virol. 2014;88 (10):5718-41. doi: 10.1128/JVI.03609-13. PubMed PMID:24623418 PubMed Central PMC4019110.
  5. Robinson, BA, O'Connor, MA, Li, H, Engelmann, F, Poland, B, Grant, R, DeFilippis, V, Estep, RD, Axthelm, MK, Messaoudi, I, Wong, SW. Viral interferon regulatory factors are critical for delay of the host immune response against rhesus macaque rhadinovirus infection. J Virol. 2012;86 (5):2769-79. doi: 10.1128/JVI.05657-11. PubMed PMID:22171275 PubMed Central PMC3302252.
  6. Robinson, BA, Estep, RD, Messaoudi, I, Rogers, KS, Wong, SW. Viral interferon regulatory factors decrease the induction of type I and type II interferon during rhesus macaque rhadinovirus infection. J Virol. 2012;86 (4):2197-211. doi: 10.1128/JVI.05047-11. PubMed PMID:22156526 PubMed Central PMC3302421.
  7. Estep, RD, Messaoudi, I, O'Connor, MA, Li, H, Sprague, J, Barron, A, Engelmann, F, Yen, B, Powers, MF, Jones, JM, Robinson, BA, Orzechowska, BU, Manoharan, M, Legasse, A, Planer, S, Wilk, J, Axthelm, MK, Wong, SW. Deletion of the monkeypox virus inhibitor of complement enzymes locus impacts the adaptive immune response to monkeypox virus in a nonhuman primate model of infection. J Virol. 2011;85 (18):9527-42. doi: 10.1128/JVI.00199-11. PubMed PMID:21752919 PubMed Central PMC3165757.
  8. DeBiasi, RL, Robinson, BA, Leser, JS, Brown, RD, Long, CS, Clarke, P. Critical role for death-receptor mediated apoptotic signaling in viral myocarditis. J Card Fail. 2010;16 (11):901-10. doi: 10.1016/j.cardfail.2010.05.030. PubMed PMID:21055654 PubMed Central PMC2994069.
  9. Messaoudi, I, Estep, R, Robinson, B, Wong, SW. Nonhuman primate models of human immunology. Antioxid Redox Signal. 2011;14 (2):261-73. doi: 10.1089/ars.2010.3241. PubMed PMID:20524846 PubMed Central PMC3014769.
  10. Miyamoto, SD, Brown, RD, Robinson, BA, Tyler, KL, Long, CS, Debiasi, RL. Cardiac cell-specific apoptotic and cytokine responses to reovirus infection: determinants of myocarditic phenotype. J Card Fail. 2009;15 (6):529-39. doi: 10.1016/j.cardfail.2009.01.004. PubMed PMID:19643365 PubMed Central PMC2772824.
  11. DeFilippis, VR, Robinson, B, Keck, TM, Hansen, SG, Nelson, JA, Früh, KJ. Interferon regulatory factor 3 is necessary for induction of antiviral genes during human cytomegalovirus infection. J Virol. 2006;80 (2):1032-7. doi: 10.1128/JVI.80.2.1032-1037.2006. PubMed PMID:16379004 PubMed Central PMC1346858.
  12. Clarke, P, Debiasi, RL, Meintzer, SM, Robinson, BA, Tyler, KL. Inhibition of NF-kappa B activity and cFLIP expression contribute to viral-induced apoptosis. Apoptosis. 2005;10 (3):513-24. doi: 10.1007/s10495-005-1881-4. PubMed PMID:15909114 PubMed Central PMC2394667.
  13. Hoyt, CC, Richardson-Burns, SM, Goody, RJ, Robinson, BA, Debiasi, RL, Tyler, KL. Nonstructural protein sigma1s is a determinant of reovirus virulence and influences the kinetics and severity of apoptosis induction in the heart and central nervous system. J Virol. 2005;79 (5):2743-53. doi: 10.1128/JVI.79.5.2743-2753.2005. PubMed PMID:15708993 PubMed Central PMC548430.
  14. DeBiasi, RL, Robinson, BA, Sherry, B, Bouchard, R, Brown, RD, Rizeq, M, Long, C, Tyler, KL. Caspase inhibition protects against reovirus-induced myocardial injury in vitro and in vivo. J Virol. 2004;78 (20):11040-50. doi: 10.1128/JVI.78.20.11040-11050.2004. PubMed PMID:15452224 PubMed Central PMC521817.
  15. Gratepanche, S, Gamain, B, Smith, JD, Robinson, BA, Saul, A, Miller, LH. Induction of crossreactive antibodies against the Plasmodium falciparum variant protein. Proc Natl Acad Sci U S A. 2003;100 (22):13007-12. doi: 10.1073/pnas.2235588100. PubMed PMID:14569009 PubMed Central PMC240735.
  16. Robinson, BA, Welch, TL, Smith, JD. Widespread functional specialization of Plasmodium falciparum erythrocyte membrane protein 1 family members to bind CD36 analysed across a parasite genome. Mol Microbiol. 2003;47 (5):1265-78. doi: 10.1046/j.1365-2958.2003.03378.x. PubMed PMID:12603733 .
  17. Rowland, RR, Robinson, B, Stefanick, J, Kim, TS, Guanghua, L, Lawson, SR, Benfield, DA. Inhibition of porcine reproductive and respiratory syndrome virus by interferon-gamma and recovery of virus replication with 2-aminopurine. Arch Virol. 2001;146 (3):539-55. doi: 10.1007/s007050170161. PubMed PMID:11338389 PubMed Central PMC7087212.

Search PubMed

Jonathan C. Reed

See Graduate Students

Brenna Kelley-Clarke

Brenna Kelley-ClarkePrior to her postdoctoral work in the Lingappa lab, Brenna earned her PhD from Harvard University in the laboratory of Dr. Kenneth Kaye, where her work focused on the latency-associated nuclear antigen (LANA) of Kaposi’s sarcoma-associated herpesvirus (KSHV). In the Lingappa lab, Brenna identified an early intermediate in the assembly pathway for Venezuelan equine encephalitis virus (VEEV) and studied novel drugs that inhibit this pathway. While a postdoc, Brenna was funded by an NIH F32 postdoctoral fellowship.  She also played cello in the Puget Sound Symphony Orchestra.

Brenna left the Lingappa lab and joined Immune Design Corporation, a Seattle biotech, in 2010.  She is currently Director of Applied Virology at Celgene in Seattle.

Publications:

  1. Role of Kaposi's sarcoma-associated herpesvirus C-terminal LANA chromosome binding in episome persistence. Kelley-Clarke B, De Leon-Vazquez E, Slain K, Barbera AJ, Kaye KM.J Virol. 2009 May;83(9):4326-37.
  2. Determination of Kaposi's sarcoma-associated herpesvirus C-terminal latency-associated nuclear antigen residues mediating chromosome association and DNA binding.Kelley-Clarke B, Ballestas ME, Srinivasan V, Barbera AJ, Komatsu T, Harris TA, Kazanjian M, Kaye KM.J Virol. 2007 Apr;81(8):4348-56.
  3. Kaposi's sarcoma herpesvirus C-terminal LANA concentrates at pericentromeric and peri-telomeric regions of a subset of mitotic chromosomes.Kelley-Clarke B, Ballestas ME, Komatsu T, Kaye KM.
    Virology. 2007 Jan 20;357(2):149-57.
  4. Kaposi's sarcoma-associated herpesvirus LANA hitches a ride on the chromosome.Barbera AJ, Chodaparambil JV, Kelley-Clarke B, Luger K, Kaye KM.Cell Cycle. 2006 May;5(10):1048-52.
  5. The nucleosomal surface as a docking station for Kaposi's sarcoma herpesvirus LANA. Barbera AJ, Chodaparambil JV, Kelley-Clarke B, Joukov V, Walter JC, Luger K, Kaye KM.Science. 2006 Feb 10;311(5762):856-61.
  6. Evaluation of the conformational switch model for alfalfa mosaic virus RNA replication.Petrillo JE, Rocheleau G, Kelley-Clarke B, Gehrke L. J Virol. 2005 May;79(9):5743-51.
  7. On the role of the starved codon and the takeoff site in ribosome bypassing in Escherichia coli. Gallant J, Bonthuis P, Lindsley D, Cabellon J, Gill G, Heaton K, Kelley-Clarke B, MacDonald L, Mercer S, Vu H, Worsley A.J Mol Biol. 2004 Sep 17;342(3):713-24.
  8. KSHV LANA1 binds DNA as an oligomer and residues N-terminal to the oligomerization domain are essential for DNA binding, replication, and episome persistence.Komatsu T, Ballestas ME, Barbera AJ, Kelley-Clarke B, Kaye KM. Virology. 2004 Feb 20;319(2):225-36.