Bio

Honors & Awards


  • School of Medicine Dean's Postdoctoral Fellowship, Stanford University (Jan - Dec 2021)

Professional Education


  • Doctor of Philosophy, Indian Institute of Science (2019)
  • Master of Science, Jawaharlal Nehru University (2013)
  • Bachelor of Science, St. Xavier's College, University of Calcutta (2011)

Stanford Advisors


  • Jin Li, Postdoctoral Faculty Sponsor

Patents


  • Datta R, Najar TA, Varadarajan R.. "United States Patent PCT Publication No. WO/2018/104967 Mapping protein binding sites and conformational epitopes using cysteine labelling and surface display library.", Indian Institute of Science, Jun 14, 2018

Publications

All Publications


  • A facile method of mapping HIV-1 neutralizing epitopes using chemically masked cysteines and deep sequencing PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Datta, R., Chowdhury, R., Manjunath, K., Hanna, L., Varadarajan, R. 2020; 117 (47): 29584?94

    Abstract

    Identification of specific epitopes targeted by neutralizing antibodies is essential to advance epitope-based vaccine design strategies. We report a facile methodology for rapid epitope mapping of neutralizing antibodies (NAbs) against HIV-1 Envelope (Env) at single-residue resolution, using Cys labeling, viral neutralization assays, and deep sequencing. This was achieved by the generation of a library of Cys mutations in Env glycoprotein on the viral surface, covalent labeling of the Cys residues using a Cys-reactive label that masks epitope residues, followed by infection of the labeled mutant virions in mammalian cells in the presence of NAbs. Env gene sequencing from NAb-resistant viruses was used to accurately delineate epitopes for the NAbs VRC01, PGT128, and PGT151. These agreed well with corresponding experimentally determined structural epitopes previously inferred from NAb:Env structures. HIV-1 infection is associated with complex and polyclonal antibody responses, typically composed of multiple antibody specificities. Deconvoluting the epitope specificities in a polyclonal response is a challenging task. We therefore extended our methodology to map multiple specificities of epitopes targeted in polyclonal sera, elicited in immunized animals as well as in an HIV-1-infected elite neutralizer capable of neutralizing tier 3 pseudoviruses with high titers. The method can be readily extended to other viruses for which convenient reverse genetics or lentiviral surface display systems are available.

    View details for DOI 10.1073/pnas.2010256117

    View details for Web of Science ID 000593986600003

    View details for PubMedID 33168755

    View details for PubMedCentralID PMC7703538

  • Probing the Structure of the HIV-1 Envelope Trimer Using Aspartate Scanning Mutagenesis JOURNAL OF VIROLOGY Das, R., Datta, R., Varadarajan, R. 2020; 94 (21)

    Abstract

    HIV-1 envelope (Env) glycoprotein gp160 exists as a trimer of heterodimers on the viral surface. In most structures of the soluble ectodomain of trimeric HIV-1 envelope glycoprotein, the regions from 512 to 517 of the fusion peptide and from 547 to 568 of the N-heptad repeat are disordered. We used aspartate scanning mutagenesis of subtype B strain JRFL Env as an alternate method to probe residue burial in the context of cleaved, cell surface-expressed Env, as buried residues should be intolerant to substitution with Asp. The data are inconsistent with a fully disordered 547 to 568 stretch, as residues 548, 549, 550, 555, 556, 559, 562, and 566 to 569 are all sensitive to Asp substitution. In the fusion peptide region, residues 513 and 515 were also sensitive to Asp substitution, suggesting that the fusion peptide may not be fully exposed in native Env. gp41 is metastable in the context of native trimer. Introduction of Asp at residues that are exposed in the prefusion state but buried in the postfusion state is expected to destabilize the postfusion state and any intermediate states where the residue is buried. We therefore performed soluble CD4 (sCD4)-induced gp120 shedding experiments to identify Asp mutants at residues 551, 554 to 559, 561 to 567, and 569 that could prevent gp120 shedding. We also observed similar mutational effects on shedding for equivalent mutants in the context of clade C Env from isolate 4-2J.41. These substitutions can potentially be used to stabilize native-like trimer derivatives that are used as HIV-1 vaccine immunogens.IMPORTANCE In most crystal structures of the soluble ectodomain of the HIV-1 Env trimer, some residues in the fusion and N-heptad repeat regions are disordered. Whether this is true in the context of native, functional Env on the virion surface is not known. This knowledge may be useful for stabilizing Env in its prefusion conformation and will also help to improve understanding of the viral entry process. Burial of the charged residue Asp in a protein structure is highly destabilizing. We therefore used Asp scanning mutagenesis to probe the burial of apparently disordered residues in native Env and to examine the effect of mutations in these regions on Env stability and conformation as probed by antibody binding to cell surface-expressed Env, CD4-induced shedding of HIV-1 gp120, and viral infectivity studies. Mutations that prevent shedding can potentially be used to stabilize native-like Env constructs for use as vaccine immunogens.

    View details for DOI 10.1128/JVI.01426-20

    View details for Web of Science ID 000579834200007

    View details for PubMedID 32817217

    View details for PubMedCentralID PMC7565623

  • Glycosylation of the core of the HIV-1 envelope subunit protein gp120 is not required for native trimer formation or viral infectivity JOURNAL OF BIOLOGICAL CHEMISTRY Rathore, U., Saha, P., Kesavardhana, S., Kumar, A., Datta, R., Devanarayanan, S., Das, R., Mascola, J. R., Varadarajan, R. 2017; 292 (24): 10197?219

    Abstract

    The gp120 subunit of the HIV-1 envelope (Env) protein is heavily glycosylated at ?25 glycosylation sites, of which ?7-8 are located in the V1/V2 and V3 variable loops and the others in the remaining core gp120 region. Glycans partially shield Env from recognition by the host immune system and also are believed to be indispensable for proper folding of gp120 and for viral infectivity. Previous attempts to alter glycosylation sites in Env typically involved mutating the glycosylated asparagine residues to structurally similar glutamines or alanines. Here, we confirmed that such mutations at multiple glycosylation sites greatly diminish viral infectivity and result in significantly reduced binding to both neutralizing and non-neutralizing antibodies. Therefore, using an alternative approach, we combined evolutionary information with structure-guided design and yeast surface display to produce properly cleaved HIV-1 Env variants that lack all 15 core gp120 glycans, yet retain conformational integrity and multiple-cycle viral infectivity and bind to several broadly neutralizing antibodies (bNAbs), including trimer-specific antibodies and a germline-reverted version of the bNAb VRC01. Our observations demonstrate that core gp120 glycans are not essential for folding, and hence their likely primary role is enabling immune evasion. We also show that our glycan removal approach is not strain restricted. Glycan-deficient Env derivatives can be used as priming immunogens because they should engage and activate a more divergent set of germlines than fully glycosylated Env. In conclusion, these results clarify the role of core gp120 glycosylation and illustrate a general method for designing glycan-free folded protein derivatives.

    View details for DOI 10.1074/jbc.M117.788919

    View details for Web of Science ID 000403580600029

    View details for PubMedID 28446609

    View details for PubMedCentralID PMC5473224

  • Structure-based Design of Cyclically Permuted HIV-1 gp120 Trimers That Elicit Neutralizing Antibodies JOURNAL OF BIOLOGICAL CHEMISTRY Kesavardhana, S., Das, R., Citron, M., Datta, R., Ecto, L., Srilatha, N., DiStefano, D., Swoyer, R., Joyce, J. G., Dutta, S., LaBranche, C. C., Montefiori, D. C., Flynn, J. A., Varadarajan, R. 2017; 292 (1): 278?91

    Abstract

    A major goal for HIV-1 vaccine development is an ability to elicit strong and durable broadly neutralizing antibody (bNAb) responses. The trimeric envelope glycoprotein (Env) spikes on HIV-1 are known to contain multiple epitopes that are susceptible to bNAbs isolated from infected individuals. Nonetheless, all trimeric and monomeric Env immunogens designed to date have failed to elicit such antibodies. We report the structure-guided design of HIV-1 cyclically permuted gp120 that forms homogeneous, stable trimers, and displays enhanced binding to multiple bNAbs, including VRC01, VRC03, VRC-PG04, PGT128, and the quaternary epitope-specific bNAbs PGT145 and PGDM1400. Constructs that were cyclically permuted in the V1 loop region and contained an N-terminal trimerization domain to stabilize V1V2-mediated quaternary interactions, showed the highest homogeneity and the best antigenic characteristics. In guinea pigs, a DNA prime-protein boost regimen with these new gp120 trimer immunogens elicited potent neutralizing antibody responses against highly sensitive Tier 1A isolates and weaker neutralizing antibody responses with an average titer of about 115 against a panel of heterologous Tier 2 isolates. A modest fraction of the Tier 2 virus neutralizing activity appeared to target the CD4 binding site on gp120. These results suggest that cyclically permuted HIV-1 gp120 trimers represent a viable platform in which further modifications may be made to eventually achieve protective bNAb responses.

    View details for DOI 10.1074/jbc.M116.725614

    View details for Web of Science ID 000391578000024

    View details for PubMedID 27879316

    View details for PubMedCentralID PMC5217686

  • Molecular identification of a common bacterial pathogen reducing shelf life of Agaricus bisporus and its prevention J. Mycopathol. Res. Datta, R., Ghosh, A., Sengupta, D., Ghosh, M., Mal, A., Dey, S., Mitra, A. 2011: 49, 301

Footer Links:

Stanford Medicine Resources: