About

Welcome to the homepage of the DeKosky research laboratory! We use new approaches in molecular biotechnology to better understand human health and immune interactions.

Research topics

• Biology
• Computational biology
• Immunology
• Medicine
• Chemistry
• Virology
• Pharmacology
• Biochemistry
• Molecular biology

Selected publications

• Duration of Initial Viremia Modulates Functional Properties of HIV-specific T Cell Receptors

  Research Square · 2026-02-18

  preprintOpen access
  PublisherOA PDFDOI

• Duration of Initial Viremia Modulates Functional Properties of HIV-specific T Cell Receptors

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-02

  articleOpen access

  Abstract Virus-specific CD8 + T cells are crucial in controlling chronic human viral infections such as HIV-1, but the effect of persistent antigen exposure on T cell repertoire formation is not well understood. In this study, we examined epitope-specific CD8 + T cell repertoires in people living with HIV-1, where duration of viremia following hyperacute infection was modulated by the time of initiation of continuous suppressive antiretroviral therapy (ART). After ART-induced undetectable viremia in persons expressing the same HLA class I allele, we analyzed the impact of early (n=6) versus delayed (n=6) ART initiation on the clonotypic composition, clonotypic cross-reactivity, functional avidity and memory differentiation profile of the HIV-specific T cell repertoire restricted by HLA-B*58:01. Using a panel of barcoded tetramers, we mapped T cell receptor (TCR) clonotypes specific for three dominant epitopes and their variants. Both groups exhibited polyclonal TCR repertoires with evidence of cross-reactivity, which was significantly enriched in donors with prolonged antigen exposure. Within this cohort, broadly cross-reactive clonotypes capable of recognizing all autologous variants were identified, but these were rare (<1%). Early ART initiation preserved repertoires characterized by higher-avidity TCRs and a relative enrichment of transitional memory CD8 + T cell subsets. These functional differences were not associated with differences in TRBV gene sharing, indicating that ART timing shapes repertoire quality and memory differentiation without altering TRBV gene bias. These findings demonstrate how antigen suppression dynamics differentially shape the breadth, functional sensitivity, and memory composition of the HIV-specific TCR repertoire, with implications for T cell-directed immunotherapies and HIV cure strategies. One Sentence Summary The duration of viral antigen exposure during early HIV infection shapes the functional quality, breadth, and memory composition of virus-specific CD8⁺ T cell receptor repertoires.

  PublisherDOI

• The adaptive immune receptors in a big data world

  ImmunoHorizons · 2026-04-01 · 1 citations

  articleOpen access1st authorCorresponding

  Antibodies and T cell receptors are the molecular basis of immune memory, and have become the foundation for generations of clinically successful biologics. Decades of research have established diverse systems to observe, identify, discover, and optimize the adaptive immune receptors, both from natural and synthetic sources. Recent advances in high-throughput display, next-generation sequencing analysis, and machine learning data mining are accelerating our capabilities to characterize immune receptor repertoires, including based on functional properties. This commentary discusses common principles in modern immune receptor studies, with an eye toward the near-term horizon in large functional dataset collection and analysis.

  PublisherDOI

• High-Throughput Antibody Neutralization Screening in Massively Parallel Droplet Arrays

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-04 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Neutralizing antibodies provide rapid immune defense against infectious diseases, but are difficult to discover at scale because neutralization assays require live reporter cells and soluble monoclonal antibodies. Here we report Droplet Reporter Cell Testing for Neutralization (DrReCT-Neutralization) to screen antibody gene libraries for their ability to neutralize viral infections. We established the necessary engineered cell lines and validated the DrReCT screening platform using synthetic oligoclonal libraries, followed by an example discovery campaign that demonstrated scalable functional antibody data collection against viral diseases.

  PublisherOA PDFDOI

• Potent Monoclonal Antibodies Against Circulating Yellow Fever Virus Strains from Donors Immunized with the 17D Vaccine

  American Journal of Tropical Medicine and Hygiene · 2025-11-20

  articleOpen accessSenior author

  Yellow fever (YF) causes approximately 50,000 deaths annually worldwide and is transmitted by infection with the yellow fever virus (YFV), which is endemic in Sub-Saharan Africa and tropical South America. The live-attenuated YFV 17D vaccine, developed in 1937, is essential to control YFV transmission, but the finite shelf life and manufacturing constraints of egg-based vaccine production, the rare but severe adverse events, and the lack of effective therapeutic options for YF disease highlight the need for new YFV vaccines and therapies. Potent YFV antibodies that neutralize circulating strains could be promising passive immunizations or treatments and guide nonreplicating YF vaccine development. In this study, we captured and screened natively paired heavy and light chain antibody libraries from two donors immunized with the YFV 17D vaccine. Yeast surface display libraries were generated and stained using YF virus-like particles purified by chromatographic techniques. Three anti-YFV antibodies were identified with potent neutralizing activity against circulating strains from Western Africa and South America, including one potent antibody with a neutralizing half-maximal inhibitory concentration of <5 ng/mL against the 17D vaccine strain. These new YFV antibodies have the potential to serve as YFV outbreak countermeasures for treatment or prevention and guide future vaccine efforts.

  PublisherOA PDFDOI

• Gene syntax defines supercoiling-mediated transcriptional feedback

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-19 · 5 citations

  preprintOpen access

  Gene syntax-the order and arrangement of genes and their regulatory elements-shapes the dynamic coordination of both natural and synthetic gene circuits. Transcription at one locus profoundly impacts the transcription of nearby adjacent genes, but the molecular basis of this effect remains poorly understood. Here, using integrated reporter circuits in human cells, we show that supercoiling-mediated feedback regulates expression of adjacent genes in a syntax-specific manner. Using Region Capture Micro-C, we measure induction-dependent formation of supercoiled plectonemes and syntax-specific chromatin structures in human induced pluripotent stem cells. Using syntax as a design parameter, we built compact gene circuits, tuning the mean, variance, and stoichiometries of expression across diverse delivery methods and cell types. Integrating supercoiling-mediated feedback into models of gene regulation will expand our understanding of native systems and enhance the design of synthetic gene circuits.

  PublisherDOI

• Yeast Display Reveals Plentiful Mutations that Improve Fusion-Peptide Vaccine-Elicited Antibodies Beyond 59% HIV-1-Neutralization Breadth

  Preprints.org · 2025-09-25

  preprintOpen accessSenior author

  Background/Objectives: Vaccine elicitation of antibodies with high HIV-1-neutralization breadth is a long-standing goal. Recently, induction of such antibodies has been achieved at the fusion peptide-site of vulnerability; questions remain, however, as to whether their neutralization breadth and potency were sufficient to prevent HIV-1 infection. Methods: Here, we use yeast display coupled with deep-mutational screening, biochemical and structural analysis to study improvement of the best fusion-peptide-directed, vaccine-elicited antibody, DFPH_a.01, with initial 59% breadth. Results: Yeast display identified both single and double mutations that improved recognition of HIV-1-envelope trimers. We characterized two paratope-distal light chain (LC) mutations, S10R and S59P, which together increased breadth to 63%. Biochemical analysis demonstrated DFPH-a.01_10R59P-LC, and its component mutations, to have increased affinity and stability. Cryo-EM structural analysis revealed elbow-angle influencing by S10RLC and isosteric positioning by S59PLC as explanations for enhanced breadth, affinity, and stability. Conclusions: These results, along with another antibody with enhanced performance (DFPH-a.01_1G10A56K-LC with 64% breadth), suggest possible mutations that improve DFPH_a.01 are plentiful, an important vaccine insight.

  PublisherDOI

• Yeast Display Reveals Plentiful Mutations That Improve Fusion Peptide Vaccine-Elicited Antibodies Beyond 59% HIV-1 Neutralization Breadth

  Vaccines · 2025-10-27

  articleOpen accessSenior authorCorresponding

  Background/Objectives: Vaccine elicitation of antibodies with high HIV-1 neutralization breadth is a long-standing goal. Recently, the induction of such antibodies has been achieved at the fusion peptide site of vulnerability. Questions remain, however, as to how much anti-fusion peptide antibodies can be improved and whether their neutralization breadth and potency are sufficient to prevent HIV-1 infection. Methods: Here, we use yeast display coupled with deep mutational screening and biochemical and structural analyses to study the improvement of the best fusion peptide-directed, vaccine-elicited antibody, DFPH_a.01, with an initial 59% breadth. Results: Yeast display identified both single and double mutations that improved recognition of HIV-1 envelope trimers. We characterized two paratope-distal light chain (LC) mutations, S10R and S59P, which together increased breadth to 63%. Biochemical analysis demonstrated DFPH-a.01_10R59P-LC, and its component mutations, to have increased affinity and stability. Cryo-EM structural analysis revealed elbow-angle influencing by S10R-LC and isosteric positioning by S59P-LC as explanations for enhanced breadth, affinity, and stability. Conclusions: These results, along with another antibody with enhanced performance (DFPH-a.01_1G10A56K-LC with 64% breadth), suggest that mutations improving DFPH_a.01 are plentiful, an important vaccine insight.

  PublisherOA PDFDOI

• Anti-Malaria Antibody Engineering Broadens Recognition Motifs and Reveals New Homotypic Interactions that Enhance Protective Breadth

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-01 · 2 citations

  preprintOpen accessSenior authorCorresponding

  ABSTRACT The monoclonal antibody L9 mediates high-level protection against malaria in children for up to 6 months in Africa. L9 preferentially binds with high affinity to the NVDP minor repeat on the P. falciparum circumsporozoite protein (PfCSP). Here, we sought to improve the affinity of L9 to enhance protection against rare strains with two spatially separated minor repeats or a single minor repeat. Site saturation mutagenesis and yeast display-screening identified a panel of affinity-improved variants. In vivo challenge showed one variant, L9_yd19, to be modestly more potent against a chimeric transgenic Plasmodium encoding PfCSP with two widely spaced minor repeats from a Kenyan parasite strain, with no loss in potency against the benchmark 3D7 strain with its standard complement of minor repeats. L9_yd19 also had high affinity against NANP major repeats and was protective against transgenic Plasmodium with PfCSP containing only NANP major repeats (NANP 12 ). Cryo-EM studies revealed L9_yd19 to recognize PfCSP with two distinct homotypic interfaces, which combined to yield two trimeric layers of antibodies comprising asymmetric trimers that dimerized in a head-to-head fashion. These data reveal a new antibody mechanism that utilizes interfaces involving dual homotypic symmetry elements, a 2-fold and an asymmetric 3-fold, for potentially improved malaria prevention. HIGHLIGHTS L9 is a highly protective antimalarial antibody that preferentially binds the NVDP minor repeat on Plasmodium falciparum circumsporozoite protein (PfCSP) and also binds with low affinity to the NANP major repeat; due to these targeting preferences, it has shown reduced protection against designed transgenic malaria strains with only a single NVDP motif (Fig. 1). Using yeast display, a panel of L9 variants were generated based on higher affinity against the minor NVDP and major NANP motifs to determine if they could improve protection against strains with fewer minor repeat regions or only containing major repeats (Figs 1-4). One L9 variant, L9_yd19 showed enhanced protection against chimeric transgenic CSP variants with a single minor repeat or two minor repeats in which the spacing was separated; L9_yd19 also showed protection against chimeric transgenic CSP variants containing only the NANP major repeat (Figs. 4-5). Cryo-EM analyses revealed L9_yd19 recognition of CSP to comprise two distinct homotypic interfaces: a side-to-side interface within asymmetric antibody trimer and a head-to-head interface between antibody trimers related by 2-fold symmetry that combined to yield a higher-order complex comprising two trimeric layers of antibodies (Figs. 6-7) Structure-function studies reveal a new antibody-based structural mechanism with dual homotypic interfaces mediating protection against varying numbers and spacing of minor repeats and major repeats.

  PublisherOA PDFDOI

• Control of antigen presentation on MHC-I by a bacterial secretion system

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-20

  preprintOpen access

  (Mtb) remains one of the world's leading infectious killers. Although CD8 T cells contribute to immune control of tuberculosis, the pathways through which bacterial antigens access major histocompatibility complex class I (MHC-I) antigen presentation remain incompletely defined. Here, we show that the activity of an Mtb secretion system actively promotes antigen presentation on MHC-I. Using quantitative immunopeptidomics, host and bacterial genetic perturbations, and T cell activation assays, we demonstrate that presentation of Mtb-derived peptides on MHC-I requires the ESX-1 type VII secretion system. Presentation of these peptides proceeds in a manner dependent on the transporter associated with antigen processing (TAP) but independent of host cell mechanisms such as autophagy or MPEG1-mediated pore formation. Chemical induction of phagosomal membrane damage fails to restore antigen presentation in the absence of ESX-1 activity, suggesting that pathogen-encoded secretion, not nonspecific membrane rupture, governs access to MHC-I antigen processing pathways. These findings reveal a secretion system-driven mechanism of antigen presentation, redefining how mycobacteria interface with host MHC-I pathways, potentially informing tuberculosis vaccine design strategies, and highlighting a potential route for synthetic antigen delivery to the cytosol in therapeutics and vaccination.

  PublisherDOI

Recent grants

• Comprehensive molecular and functional analyses of anti-HIV-1 broadly neutralizing antibody repertoires

  NIH · $435k · 2018–2022

• Antibody display libraries for precision screening of antibody immune responses to SARS-CoV-2

  NIH · $2.2M · 2022–2023

• Dissecting the mechanisms of HIV resistance in vivo to broadly neutralizing antibodies

  NIH · $6.5M · 2022–2027

• Probing antigen specificity and response of autoimmune B cells in Neuromyelitis Optica

  NIH · $417k · 2019–2021

Frequent coauthors

• Bharat Madan

  Ragon Institute of MGH, MIT and Harvard

  78 shared

• Peter D. Kwong

  National Institutes of Health

  75 shared

• Ahmed S. Fahad

  Ragon Institute of MGH, MIT and Harvard

  61 shared

• Matheus Oliveira de Souza

  Ragon Institute of MGH, MIT and Harvard

  54 shared

• John R. Mascola

  45 shared

• Lawrence Shapiro

  Columbia University

  43 shared

• Xiaoli Pan

  Northeast Ohio Medical University

  43 shared

• Matías Gutiérrez-González

  39 shared

Labs

• Immune Engineering LabPI

Education

• Ph.D., Immunology

  University of California, San Francisco

  1996

• M.D., Medicine

  University of California, San Francisco

  1990

• B.S., Biology

  University of California, San Diego

  1986

Awards & honors

• AAI ASPIRE Award (2025)
• Amgen Young Investigator Award (2023)
• James S. Huston Antibody Science Talent Award (2022)
• Industrial and Chemical Engineering Research Class of Influe…
• Miller Award for Research Excellence, KU School of Engineeri…