Professional Education

  • Doctor of Philosophy, Massachusetts Institute of Technology, Microbiology (2020)
  • Master of Science, Swiss Federal Institute of Technology (EPFL), Life Sciences and technologies (2012)
  • Bachelor of Science, Swiss Federal Institute of Technology (EPFL), Life Sciences and technologies (2010)

Stanford Advisors

All Publications

  • Engineered skin bacteria induce antitumor T cell responses against melanoma. Science (New York, N.Y.) Chen, Y. E., Bousbaine, D., Veinbachs, A., Atabakhsh, K., Dimas, A., Yu, V. K., Zhao, A., Enright, N. J., Nagashima, K., Belkaid, Y., Fischbach, M. A. 2023; 380 (6641): 203-210


    Certain bacterial colonists induce a highly specific T cell response. A hallmark of this encounter is that adaptive immunity develops preemptively, in the absence of an infection. However, the functional properties of colonist-induced T cells are not well defined, limiting our ability to understand anticommensal immunity and harness it therapeutically. We addressed both challenges by engineering the skin bacterium Staphylococcus epidermidis to express tumor antigens anchored to secreted or cell-surface proteins. Upon colonization, engineered S. epidermidis elicits tumor-specific T cells that circulate, infiltrate local and metastatic lesions, and exert cytotoxic activity. Thus, the immune response to a skin colonist can promote cellular immunity at a distal site and can be redirected against a target of therapeutic interest by expressing a target-derived antigen in a commensal.

    View details for DOI 10.1126/science.abp9563

    View details for PubMedID 37053311

  • A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes. Science (New York, N.Y.) Bousbaine, D., Fisch, L. I., London, M., Bhagchandani, P., Rezende de Castro, T. B., Mimee, M., Olesen, S., Reis, B. S., VanInsberghe, D., Bortolatto, J., Poyet, M., Cheloha, R. W., Sidney, J., Ling, J., Gupta, A., Lu, T. K., Sette, A., Alm, E. J., Moon, J. J., Victora, G. D., Mucida, D., Ploegh, H. L., Bilate, A. M. 2022; 377 (6606): 660-666


    The microbiome contributes to the development and maturation of the immune system. In response to commensal bacteria, intestinal CD4+ T lymphocytes differentiate into functional subtypes with regulatory or effector functions. The development of small intestine intraepithelial lymphocytes that coexpress CD4 and CD8αα homodimers (CD4IELs) depends on the microbiota. However, the identity of the microbial antigens recognized by CD4+ T cells that can differentiate into CD4IELs remains unknown. We identified β-hexosaminidase, a conserved enzyme across commensals of the Bacteroidetes phylum, as a driver of CD4IEL differentiation. In a mouse model of colitis, β-hexosaminidase-specific lymphocytes protected against intestinal inflammation. Thus, T cells of a single specificity can recognize a variety of abundant commensals and elicit a regulatory immune response at the intestinal mucosa.

    View details for DOI 10.1126/science.abg5645

    View details for PubMedID 35926021

  • Noninvasive Immuno-PET Imaging of CD8+ T Cell Behavior in Influenza A Virus-Infected Mice. Frontiers in immunology Rothlauf, P. W., Li, Z., Pishesha, N., Xie, Y. J., Woodham, A. W., Bousbaine, D., Kolifrath, S. C., Verschoor, V. L., Ploegh, H. L. 2021; 12: 777739


    Immuno-positron emission tomography (immuno-PET) is a noninvasive imaging method that enables tracking of immune cells in living animals. We used a nanobody that recognizes mouse CD8α and labeled it with 89Zr to image mouse CD8+ T cells in the course of an infection with influenza A virus (IAV). The CD8+ signal showed a strong increase in the mediastinal lymph node (MLN) and thymus as early as 4 days post-infection (dpi), and as early as 6 dpi in the lungs. Over the course of the infection, CD8+ T cells were at first distributed diffusely throughout the lungs and then accumulated more selectively in specific regions of the lungs. These distributions correlated with morbidity as mice reached the peak of weight loss over this interval. CD8+ T cells obtained from control or IAV-infected mice showed a difference in their distribution and migration when comparing their fate upon labeling ex vivo with 89Zr-labeled anti-CD8α nanobody and transfer into infected versus control animals. CD8+ T cells from infected mice, upon transfer, appear to be trained to persist in the lungs, even of uninfected mice. Immuno-PET imaging thus allows noninvasive, dynamic monitoring of the immune response to infectious agents in living animals.

    View details for DOI 10.3389/fimmu.2021.777739

    View details for PubMedID 34804069

    View details for PubMedCentralID PMC8595544

  • Deletion of mFICD AMPylase alters cytokine secretion and affects visual short-term learning in vivo. The Journal of biological chemistry McCaul, N., Porter, C. M., Becker, A., Tang, C. A., Wijne, C., Chatterjee, B., Bousbaine, D., Bilate, A., Hu, C. A., Ploegh, H., Truttmann, M. C. 2021; 297 (3): 100991


    Fic domain-containing AMP transferases (fic AMPylases) are conserved enzymes that catalyze the covalent transfer of AMP to proteins. This posttranslational modification regulates the function of several proteins, including the ER-resident chaperone Grp78/BiP. Here we introduce a mouse FICD (mFICD) AMPylase knockout mouse model to study fic AMPylase function in vertebrates. We find that mFICD deficiency is well tolerated in unstressed mice. We also show that mFICD-deficient mouse embryonic fibroblasts are depleted of AMPylated proteins. mFICD deletion alters protein synthesis and secretion in splenocytes, including that of IgM, an antibody secreted early during infections, and the proinflammatory cytokine IL-1β, without affecting the unfolded protein response. Finally, we demonstrate that visual nonspatial short-term learning is stronger in old mFICD-/- mice than in wild-type controls while other measures of cognition, memory, and learning are unaffected. Together, our results suggest a role for mFICD in adaptive immunity and neuronal plasticity in vivo.

    View details for DOI 10.1016/j.jbc.2021.100991

    View details for PubMedID 34419450

    View details for PubMedCentralID PMC8441161

  • Converting an Anti-Mouse CD4 Monoclonal Antibody into an scFv Positron Emission Tomography Imaging Agent for Longitudinal Monitoring of CD4(+) T Cells JOURNAL OF IMMUNOLOGY Islam, A., Pishesha, N., Harmand, T. J., Heston, H., Woodham, A. W., Cheloha, R. W., Bousbaine, D., Rashidian, M., Ploegh, H. L. 2021; 207 (5): 1468-1477


    Immuno-positron emission tomography (PET), a noninvasive imaging modality, can provide a dynamic approach for longitudinal assessment of cell populations of interest. Transformation of mAbs into single-chain variable fragment (scFv)-based PET imaging agents would allow noninvasive tracking in vivo of a wide range of possible targets. We used sortase-mediated enzymatic labeling in combination with PEGylation to develop an anti-mouse CD4 scFv-based PET imaging agent constructed from an anti-mouse CD4 mAb. This anti-CD4 scFv can monitor the in vivo distribution of CD4+ T cells by immuno-PET. We tracked CD4+ and CD8+ T cells in wild-type mice, in immunodeficient recipients reconstituted with monoclonal populations of OT-II and OT-I T cells, and in a B16 melanoma model. Anti-CD4 and -CD8 immuno-PET showed that the persistence of both CD4+ and CD8+ T cells transferred into immunodeficient mice improved when recipients were immunized with OVA in CFA. In tumor-bearing animals, infiltration of both CD4+ and CD8+ T cells increased as the tumor grew. The approach described in this study should be readily applicable to convert clinically useful Abs into the corresponding scFv PET imaging agents.

    View details for DOI 10.4049/jimmunol.2100274

    View details for Web of Science ID 000731217400011

    View details for PubMedID 34408009

    View details for PubMedCentralID PMC8387391

  • Antigen discovery tools for adaptive immune receptor repertoire research Current Opinion in Systems Biology Bousbaine, D., Ploegh, H. L. 2020
  • Recognition of Class II MHC Peptide Ligands That Contain beta-Amino Acids JOURNAL OF IMMUNOLOGY Cheloha, R. W., Woodham, A. W., Bousbaine, D., Wang, T., Liu, S., Sidney, J., Sette, A., Gellman, S. H., Ploegh, H. L. 2019; 203 (6): 1619–28


    Proteins are composed of α-amino acid residues. This consistency in backbone structure likely serves an important role in the display of an enormous diversity of peptides by class II MHC (MHC-II) products, which make contacts with main chain atoms of their peptide cargo. Peptides that contain residues with an extra carbon in the backbone (derived from β-amino acids) have biological properties that differ starkly from those of their conventional counterparts. How changes in the structure of the peptide backbone affect the loading of peptides onto MHC-II or recognition of the resulting complexes by TCRs has not been widely explored. We prepared a library of analogues of MHC-II-binding peptides derived from OVA, in which at least one α-amino acid residue was replaced with a homologous β-amino acid residue. The latter contain an extra methylene unit in the peptide backbone but retain the original side chain. We show that several of these α/β-peptides retain the ability to bind tightly to MHC-II, activate TCR signaling, and induce responses from T cells in mice. One α/β-peptide exhibited enhanced stability in the presence of an endosomal protease relative to the index peptide. Conjugation of this backbone-modified peptide to a camelid single-domain Ab fragment specific for MHC-II enhanced its biological activity. Our results suggest that backbone modification offers a method to modulate MHC binding and selectivity, T cell stimulatory capacity, and susceptibility to processing by proteases such as those found within endosomes where Ag processing occurs.

    View details for DOI 10.4049/jimmunol.1900536

    View details for Web of Science ID 000484842100021

    View details for PubMedID 31391235

    View details for PubMedCentralID PMC6736755

  • Internalization of Influenza Virus and Cell Surface Proteins Monitored by Site-Specific Conjugation of Protease-Sensitive Probes ACS CHEMICAL BIOLOGY Cheloha, R. W., Li, Z., Bousbaine, D., Woodham, A. W., Perrin, P., Volaric, J., Ploegh, H. L. 2019; 14 (8): 1836–44


    Commonly used methods to monitor internalization of cell surface structures involve application of fluorescently or otherwise labeled antibodies against the target of interest. Genetic modification of the protein of interest, for example through creation of fusions with fluorescent or enzymatically active protein domains, is another approach to follow trafficking behavior. The former approach requires indirect methods, such as multiple rounds of cell staining, to distinguish between a target that remains surface-disposed and an internalized and/or recycled species. The latter approach necessitates the creation of fusions whose behavior may not accurately reflect that of their unmodified counterparts. Here, we report a method for the characterization of protein internalization in real time through sortase-mediated, site-specific labeling of single-domain antibodies or viral proteins with a newly developed, cathepsin-sensitive quenched-fluorophore probe. Quenched probes of this type have been used to measure enzyme activity in complex environments and for different cell types, but not as a sensor of protein movement into living cells. This approach allows a quantitative assessment of the movement of proteins into protease-containing endosomes in real time in living cells. We demonstrate considerable variation in the rate of endosomal delivery for different cell surface receptors. We were also able to characterize the kinetics of influenza virus delivery to cathepsin-positive compartments, showing highly coordinated arrival in endosomal compartments. This approach should be useful for identifying proteins expressed on cells of interest for targeted endosomal delivery of payloads, such as antibody-drug conjugates or antigens that require processing.

    View details for DOI 10.1021/acschembio.9b00493

    View details for Web of Science ID 000481979400018

    View details for PubMedID 31348637

  • One-step generation of monoclonal B cell receptor mice capable of isotype switching and somatic hypermutation JOURNAL OF EXPERIMENTAL MEDICINE Jacobsen, J. T., Mesin, L., Markoulaki, S., Schiepers, A., Cavazzoni, C. B., Bousbaine, D., Jaenisch, R., Victora, G. D. 2018; 215 (10): 2686–95


    We developed a method for rapid generation of B cell receptor (BCR) monoclonal mice expressing prerearranged Igh and Igk chains monoallelically from the Igh locus by CRISPR-Cas9 injection into fertilized oocytes. B cells from these mice undergo somatic hypermutation (SHM), class switch recombination (CSR), and affinity-based selection in germinal centers. This method combines the practicality of BCR transgenes with the ability to study Ig SHM, CSR, and affinity maturation.

    View details for DOI 10.1084/jem.20172064

    View details for Web of Science ID 000447673200017

    View details for PubMedID 30181412

    View details for PubMedCentralID PMC6170169

  • One-Pot Dual Labeling of IgG 1 and Preparation of C-to-C Fusion Proteins Through a Combination of Sortase A and Butelase 1 BIOCONJUGATE CHEMISTRY Harmand, T. J., Bousbaine, D., Chan, A., Zhang, X., Liu, D. R., Tam, J. P., Ploegh, H. L. 2018; 29 (10): 3245–49


    Site-specific chemical modification of proteins can assist in the study of their function. Furthermore, these methods are essential to develop biologicals for diagnostic and therapeutic use. Standard protein engineering protocols and recombinant expression enable the production of proteins with short peptide tags recognized by enzymes capable of site-specific modification. We report here the application of two enzymes of orthogonal specificity, sortase A and butelase 1, to prepare non-natural C-to-C fusion proteins. Using these enzymes, we further demonstrate site-selective installation of different chemical moieties at two sites in a full-size antibody molecule.

    View details for DOI 10.1021/acs.bioconjchem.8b00563

    View details for Web of Science ID 000447953500003

    View details for PubMedID 30231608

    View details for PubMedCentralID PMC6429940

  • The studies of ParA and ParB dynamics reveal asymmetry of chromosome segregation in mycobacteria MOLECULAR MICROBIOLOGY Ginda, K., Santi, I., Bousbaine, D., Zakrzewska-Czerwinska, J., Jakimowicz, D., McKinney, J. 2017; 105 (3): 453–68


    Active segregation of bacterial chromosomes usually involves the action of ParB proteins, which bind in proximity of chromosomal origin (oriC) regions forming nucleoprotein complexes - segrosomes. Newly duplicated segrosomes are moved either uni- or bidirectionally by the action of ATPases - ParA proteins. In Mycobacterium smegmatis the oriC region is located in an off-centred position and newly replicated segrosomes are segregated towards cell poles. The elimination of M. smegmatis ParA and/or ParB leads to chromosome segregation defects. Here, we took advantage of microfluidic time-lapse fluorescent microscopy to address the question of ParA and ParB dynamics in M. smegmatis and M. tuberculosis cells. Our results reveal that ParB complexes are segregated in an asymmetrical manner. The rapid movement of segrosomes is dependent on ParA that is transiently associated with the new pole. Remarkably in M. tuberculosis, the movement of the ParB complex is much slower than in M. smegmatis, but segregation as in M. smegmatis lasts approximately 10% of the cell cycle, which suggests a correlation between segregation dynamics and the growth rate. On the basis of our results, we propose a model for the asymmetric action of segregation machinery that reflects unequal division and growth of mycobacterial cells.

    View details for DOI 10.1111/mmi.13712

    View details for Web of Science ID 000405994500010

    View details for PubMedID 28517109

  • Engineered erythrocytes covalently linked to antigenic peptides can protect against autoimmune disease PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Pishesha, N., Bilate, A. M., Wibowo, M. C., Huang, N., Li, Z., Dhesycka, R., Bousbaine, D., Li, H., Patterson, H. C., Dougan, S. K., Maruyama, T., Lodish, H. F., Ploegh, H. L. 2017; 114 (12): 3157-3162


    Current therapies for autoimmune diseases rely on traditional immunosuppressive medications that expose patients to an increased risk of opportunistic infections and other complications. Immunoregulatory interventions that act prophylactically or therapeutically to induce antigen-specific tolerance might overcome these obstacles. Here we use the transpeptidase sortase to covalently attach disease-associated autoantigens to genetically engineered and to unmodified red blood cells as a means of inducing antigen-specific tolerance. This approach blunts the contribution to immunity of major subsets of immune effector cells (B cells, CD4(+) and CD8(+) T cells) in an antigen-specific manner. Transfusion of red blood cells expressing self-antigen epitopes can alleviate and even prevent signs of disease in experimental autoimmune encephalomyelitis, as well as maintain normoglycemia in a mouse model of type 1 diabetes.

    View details for DOI 10.1073/pnas.1701746114

    View details for Web of Science ID 000396893600066

    View details for PubMedID 28270614

  • Tissue-specific emergence of regulatory and intraepithelial T cells from a clonal T cell precursor SCIENCE IMMUNOLOGY Bilate, A. M., Bousbaine, D., Mesin, L., Agudelo, M., Leube, J., Kratzert, A., Dougan, S. K., Victora, G. D., Ploegh, H. L. 2016; 1 (2): eaaf7471


    Peripheral Foxp3+ regulatory T cells (pTregs) maintain immune homeostasis by controlling potentially harmful effector T cell responses toward dietary and microbial antigens. Although the identity of the T cell receptor (TCR) can impose commitment and functional specialization of T cells, less is known about how TCR identity governs pTreg development from conventional CD4+ T cells. To investigate the extent to which TCR identity dictates pTreg fate, we used somatic cell nuclear transfer to generate a transnuclear (TN) mouse carrying a monoclonal TCR from a pTreg (pTreg TN mice). We found that the pTreg TCR did not inevitably predispose T cells to become pTreg but instead allowed for differentiation of noninflammatory CD4+CD8αα+ intraepithelial lymphocytes (CD4IELs) in the small intestine. Only when we limited the number of T cell precursors that carried the TN pTreg TCR did we observe substantial pTreg development in the mesenteric lymph nodes and small intestine lamina propria of mixed bone marrow chimeras. Small clonal sizes and therefore decreased intraclonal competition were required for pTreg development. Despite bearing the same TCR, small intestine CD4IEL developed independently of precursor frequency. Both pTreg and CD4IEL development strictly depended on the resident microbiota. A single clonal CD4+ T cell precursor can thus give rise to two functionally distinct and anatomically segregated T cell subsets in a microbiota-dependent manner. Therefore, plasticity of the CD4 T cell compartment depends not only on the microbiota but also on specialized environmental cues provided by different tissues.

    View details for DOI 10.1126/sciimmunol.aaf7471

    View details for Web of Science ID 000434298000003

    View details for PubMedID 28783695

    View details for PubMedCentralID PMC6296461

  • Single-cell dynamics of the chromosome replication and cell division cycles in mycobacteria NATURE COMMUNICATIONS Santi, I., Dhar, N., Bousbaine, D., Wakamoto, Y., McKinney, J. D. 2013; 4: 2470


    During the bacterial cell cycle, chromosome replication and cell division must be coordinated with overall cell growth in order to maintain the correct ploidy and cell size. The spatial and temporal coordination of these processes in mycobacteria is not understood. Here we use microfluidics and time-lapse fluorescence microscopy to measure the dynamics of cell growth, division and chromosome replication in single cells of Mycobacterium smegmatis. We find that single-cell growth is size-dependent (large cells grow faster than small cells), which implicates a size-control mechanism in cell-size homoeostasis. Asymmetric division of mother cells gives rise to unequally sized sibling cells that grow at different velocities but show no differential sensitivity to antibiotics. Individual cells are restricted to one round of chromosome replication per cell division cycle, although replication usually initiates in the mother cell before cytokinesis and terminates in the daughter cells after cytokinesis. These studies reveal important differences between cell cycle organization in mycobacteria compared with better-studied model organisms.

    View details for DOI 10.1038/ncomms3470

    View details for Web of Science ID 000325533900017

    View details for PubMedID 24036848