Biology subjects

Taylor, J. J.

Publications and source records attributed to Taylor, J. J..

13 recordsLinked to original sources

bioRxiv2025

IgA antibodies against oxidation-specific epitopes are generated by double negative B cells and are associated with impaired lung function in fibrotic interstitial lung diseases.

BackgroundFibrotic interstitial lung diseases (fILD) are characterized by progressive scarring of the lung and high mortality. Oxidation-specific epitopes (OSEs) form on oxidized lipids and proteins, are abundant in lungs of patients with fILD and perpetuate lung injury and fibrosis in animal models. OSE-targeting antibodies bind to OSEs and modulate their downstream effects. The objective of this study was to determine the association of OSE-targeting antibodies with lung function and other clinical outcomes, and to characterize OSE-specific B cell phenotypes in fILD. MethodsTo determine the association of OSE-targeting antibodies and clinical outcomes in fILD, we measured plasma levels of OSE-specific antibodies against the malondialdehyde modified LDL mimotope P1 and anti-ApoB100 immune complex (anti-ApoB100 IC) in patients with fILD and age-matched controls. We then performed B cell phenotyping of patients with idiopathic pulmonary fibrosis (IPF) and healthy controls utilizing mass cytometry time of flight (CyTOF). To investigate effects of pro-fibrotic mediators on anti-OSE IgA antibody production, we measured B cell responses to OSEs in vitro. ResultsCohort of 109 patients with fILD (Hypersensitivity Pneumonitis, Idiopathic Pulmonary Fibrosis, Nonspecific Interstitial Pneumonia, Connective Tissue Disease-Associated Interstitial Lung Disease) and 55 healthy donors, and a second cohort of 20 patients with IPF and 9 healthy donors were included in the study. OSE-specific antibody levels anti-P1 and anti-ApoB100 IC IgA and IgG were significantly elevated in participants with fILD compared to healthy donors (p<0.0001). Higher anti-OSE IgA was associated with worse baseline lung function, including forced vital capacity (FVC) (p<0.001) and diffusing capacity for carbon monoxide (DLCO) (p<0.01). IgA+CD27-CD21-CD11c+ double negative type 2 (DN2) B cells correlated with anti-OSE IgA levels (p<0.05) and were enriched in OSE-specific cells. DN2 B cell precursors, CXCR5-CD11c+ naive B cells and IgA+CD27-CD21-CD11c- DN3 B cells, were significantly expanded in IPF compared to healthy donors. Both DN2 and DN3 B cells correlated with plasmablast pools in IPF patients and showed high baseline levels of IL-21 receptor, which was reduced in more differentiated cells. TGF-{beta} combined with OSEs, but not OSEs alone, induced OSE-specific IgA production in vitro. ConclusionsCirculating anti-OSE IgA antibodies are elevated in patients with fibrotic ILDs regardless of underlying pathology and negatively correlate with lung function. These antibodies correlated with the DN2 B cell subset which was enriched in OSE-specific cells. Phenotypic analysis of B cell subsets showed expression of markers consistent with DN to plasmablast differentiation. Finally, TGF-{beta} promoted OSE-IgA production in vitro. These findings show a novel link between oxidative tissue damage, anti-OSE antibodies and DN2 B cells in fILD which may provide opportunities for new targeted therapies.

immunology↗

bioRxiv2025

Antibody Responses to Melanoma Helper Peptide Vaccines May Enhance Antigen Opsonization Through Formation of Immune Complexes and are Modulated by Vaccine Adjuvants

BackgroundVaccines targeting melanoma antigens can elicit CD8+ T cell responses, but a growing body of work suggests CD4+ T cells also play a role in tumor control. Induction of CD4+ cells may also support B cells in producing tumor antigen-specific antibodies (Abs). We investigated Abs induced by vaccination with a cocktail of six class II MHC-restricted melanoma peptides (6MHP) and the effect of adjuvant type on Ab isotypes. We hypothesized that the vaccines would induce Abs that respond to different epitopes on individual peptides and that IgG subclass distribution varies with different vaccine adjuvants. MethodsSera from patients who received a 6MHP vaccine were evaluated with enzyme-linked immunosorbent assays to map epitopes for polyclonal Ab responses to synthetic melanoma peptides (n=8). IgG subclasses of Ab responses to 6MHP were assessed in patients who received one of 4 adjuvants (Incomplete Freunds Adjuvant (IFA) alone, IFA + polyICLC, IFA + systemic mCy, or IFA + polyICLC + systemic mCy) to characterize IgG subclass distribution (n=2-14). Comparisons were evaluated using a Mann-Whitney rank sum test. ResultsEpitope mapping revealed that at least 50% of patients exhibiting Ab responses to melanoma peptides had responses to two or more epitopes on the same peptide, suggesting polyclonal antibody responses. Serum evaluation for IgG isotypes showed predominant induction of IgG1 and IgG3. Mean total IgG was highest when IFA and polyICLC were used in combination. Patients who received TLR3 agonist polyICLC had significantly higher concentrations of total IgG, IgG1, and IgG3 compared to patients who did not receive polyICLC. ConclusionsThese findings suggest that vaccine-induced Abs may respond to multiple epitopes within the same peptide, which may support creation of large antigen-Ab complexes, with promise to facilitate antigen uptake and presentation. Abs were predominantly IgG1 and IgG3, which are optimal for binding complement and supporting Ab-dependent cellular cytotoxicity. The findings also show that adding polyICLC to IFA can significantly enhance Ab responses. Collectively, this work underscores the immunologic potential of peptide-induced Abs and the importance of adjuvant selection in cancer vaccine design.

cancer biology↗

bioRxiv2025

A searchable database of publications using fluorescent probes and flow cytometry to study antigen-specific B cells

The study of antigen-specific B cells has resulted in important advances in all fields of immunology, the development of experimentally and/or clinically useful antibodies, and as a starting point for rationally designed vaccine antigens. A key innovation allowing for widespread study of antigen-specific B cells was the development of fluorescent antigen probes for use with flow cytometry. Initially these studies were mostly focused upon B cells specific for a variety of model antigens, but over the past decade focus has shifted towards the study of B cells specific for antigens from pathogens such as SARS-CoV-2, HIV, and Influenza virus. Importantly however, these types of approaches have been used for hundreds of different antigens and could be used for thousands more. Unfortunately, studies of B cells specific for an antigen of interest are not easily searchable on current publication databases since these assays are often a small portion of a larger publication. To overcome this, we built a searchable database of studies analyzing antigen-specific B cells by flow cytometry using fluorescent antigen probes that is located at www.immunology.virginia.edu/Taylor/Bcell/Database.php. Using this database, we assessed the number of publications per year revealing rapid growth in the use of this approach in recent years. While much of this rapid growth was focused upon the assessment of B cells specific for SARS-CoV-2, HIV-1, or Influenza virus, studies assessing B cells specific for hundreds of different antigens derived from numerous microbes, animals, plants, or other sources can be found in the database. Combined, the antigen-specific B cell database was built to facilitate identification of studies assessing these cells and for analysis of the field as a whole. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=18 SRC="FIGDIR/small/680531v1_ufig1.gif" ALT="Figure 1"> View larger version (6K): org.highwire.dtl.DTLVardef@f07f5forg.highwire.dtl.DTLVardef@13a3b95org.highwire.dtl.DTLVardef@1dcd79org.highwire.dtl.DTLVardef@9cddaa_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Human immune response to primary cryptosporidiosis parallels murine infection models

Cryptosporidium is a protozoan parasite that causes cryptosporidiosis, an enteric infection associated with diarrhea, malnutrition, and impaired childhood development in low- and middle-income countries. Both humoral and cell-mediated immune responses have been implicated in protection, but the durability and quality of human immune responses in immunocompetent adults remain poorly defined. We investigated the development of immunity in two healthy US adults following primary cryptosporidiosis acquired during travel to Bangladesh. Longitudinal plasma samples were analyzed for antibody responses to Cryptosporidium antigens Cp17 and Cp23 and for circulating cytokine profiles. Circulating antibody peaked at three weeks post-infection but declined rapidly thereafter, approaching baseline within 16 weeks. In contrast, antibody avidity increased steadily over time, consistent with ongoing affinity maturation in germinal centers. While affinity maturation occurred, the composition memory B cells specific to Cryptosporidium antigens was skewed toward IgM+ cells across timepoints suggesting extrafollicular responses dominated and germinal center-derived, class-switched memory was limited. Cytokine profiling revealed an acute Th1-skewed response, with elevations in CXCL9, CXCL10, IL-27, IFN{gamma}, IL-12, and IL-18 during early infection. These signatures mirrored protective pathways identified in murine models, underscoring the importance of type I immunity in parasite clearance. Together, these findings highlight that while antibody responses to Cryptosporidium are short-lived, avidity maturation persists, and Th1-driven cytokine responses dominate during acute infection. This work provides rare longitudinal data on immune responses in naive adults following natural cryptosporidiosis and offers insight into mechanisms that may inform vaccine development and strategies to mitigate recurrent infection in vulnerable populations.

immunology↗

bioRxiv2025

B cells specific for polyomavirus-derived oncoprotein are predictive of Merkel cell carcinoma progression

Merkel cell carcinomas typically arise from clonal integration of the Merkel cell polyomavirus. Immunogenic viral oncoproteins then lead to tumorigenesis. Oncoprotein-specific T cells are essential for anti-MCC immunity, but it is unclear whether B cells promote tumor control. Here, we analyzed the frequency and phenotype of viral oncoprotein-specific and total B cells in 47 blood samples and 19 unmatched tumors from MCC patients-- of which 8 out 19 progressed. The phenotype of blood B cells did not correlate with MCC patient outcomes. In contrast, all 11 patients with robust oncoprotein-specific antibody-secreting and/or germinal center B cells in tumors experienced long-term MCC control. In vitro, B cells engineered to be specific for viral oncoproteins increased the sensitivity of oncoprotein-specific CD4+ T cells by over 50-fold. Together, our findings suggest that cancer-specific B cells promote anti-tumor immunity via increased T cell responses and that cancer-specific B cell augmentation could be therapeutically relevant. Statement of SignificanceThe link between cancer-specific B cells in anti-tumor immunity and clinical outcomes remains poorly defined. Here, we show that tumor-associated B cells specific for a viral oncoprotein expressed in MCC patient tumors predict disease control with remarkable accuracy, establishing their potential as active participants in tumor immunity.

immunology↗

bioRxiv2025

In vivo production of an anti-HIV antibody from primate hematopoietic cells by non-viral knock-in

Non-viral gene editing offers a practical alternative to viral delivery for durable biologics production. Clinical trials have shown that adeno-associated virus encoding broadly neutralizing antibodies can protect against HIV, but result in limited, short-lived responses. The development of non-viral gene editing approaches in hematopoietic stem and progenitor cells holds promise for long-term antibody production. In this study, we evaluated CRISPR/Cas9 and CRISPR/Cas12a for gene knock-in at the immunoglobulin heavy chain locus in non-human primate hematopoietic stem and progenitor cells. Delivering the nuclease as a protein alongside a custom DNA template, we optimized editing with Cas12a and demonstrated higher knock-in efficiency and fewer non-specific edits than Cas9. Transplantation of edited non-human primate hematopoietic stem and progenitor cells into MISTRG mice led to engraftment, B cell differentiation, and transgene expression of a reporter transgene or anti-HIV antibody after HIV immunization with detectable anti-HIV antibody titers in peripheral blood circulation. These findings demonstrate the feasibility of using non-viral gene editing in HSPC as a potential strategy for sustained biologics production in the treatment of chronic diseases such as HIV. Future work will assess the efficacy of this model in a non-human primate model of HIV infection.

immunology↗

bioRxiv2024

Merkel cell carcinoma-derived macrophage migration inhibitory factor (MIF) may promote persistence of Chronic Lymphocytic Leukemia

While concurrent diagnoses of Merkel cell carcinoma (MCC) and other cancers, like Chronic lymphocytic leukemia (CLL), are rare, patients with MCC have a 30-fold higher incidence of CLL. While these increases have been attributed to the ability of CLL to suppress immune responses allowing for the emergence of MCC, here we found evidence that MCC could support the persistence of CLL. Using single cell sequencing approaches and computational analyses of MCC and CLL from a patient where both cancers were present in the same lymph node, we found that production of macrophage migration inhibitory factor (MIF) by MCC could promote the persistence of CLL through stimulation of CD74 and CXCR4. These results may explain why blood cell counts rapidly normalized after treatment for MCC and were maintained at normal levels despite the absence of treatment for CLL. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/611517v2_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@188968forg.highwire.dtl.DTLVardef@54c084org.highwire.dtl.DTLVardef@2b3a14org.highwire.dtl.DTLVardef@1f20eba_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

Type I interferon dynamics determines memory B cell epigenetic identity in chronic viral infection

Memory B cells are key providers of long-lived immunity against infectious disease, yet in chronic viral infection they do not produce effective protection. How chronic viral infection disrupts memory B cell development, and whether such changes are reversible, remains unknown. Here, we uncover type-I interferon (IFN-I) dynamics as a key determinant in shaping chronic memory B cell development. Through single-cell (sc)ATAC-sequencing and scRNA-sequencing, we identified a unique memory subset enriched for IFN-stimulated genes (ISGs) during chronic lymphocytic choriomeningitis virus infection. Blockade of IFNAR-1 early in infection transformed the chromatin landscape of chronic memory B cells, decreasing accessibility at ISG-inducing transcription factor binding motifs and inducing a phenotypic change in the dominating memory B cell subset. However, timing was critical, with memory B cells resistant to intervention after 4 weeks post-infection. Together, our research identifies a key mechanism to instruct memory B cell identity during viral infection. One Sentence Summary: IFN dynamics in chronic versus acute viral infection determines memory B cell development.

immunology↗

bioRxiv2022

Validation of antigen tetramers for the detection of antigen-specific B cells

The study of antigen-specific lymphocytes has been a key advancement in immunology the past few decades. The development of multimerized probes containing antigens, peptide:MHC complexes, or other ligands was one innovation allowing the direct study antigen-specific lymphocytes by flow cytometry. While these types of studies are now common and performed by thousands of laboratories, quality control and assessment of probe quality is often minimal. In fact, many of these types of probes are made in-house and protocols vary between labs. While peptide:MHC multimers can often be obtained from commercial sources or core facilities, few such services exist for antigen multimers. To ensure high quality and consistency with ligand probes, we have developed an easy and robust multiplexed approach using commercially available beads able to bind antibodies specific for the ligand of interest. Using this assay, we have sensitively assessed the performance of peptide:MHC and antigen tetramers and find considerable batch-to-batch variability in performance and stability over time. This assay can also reveal common production errors such as miscalculation of antigen concentration. Unexpectedly, probes including the fluorochrome allophycocyanin exhibited more rapid performance decline compared to probes including the fluorochrome R-phycoerythrin when both were stored at 4{degrees}C. This performance decline was reduced for most, but not all, batches when antigen tetramers were instead stored at -20{degrees}C in 50% glycerol. This work could set the stage for the development of standardized assays for all commonly used ligand probes to limit lab-to-lab technical variation, and experimental failure due to probe underperformance.

immunology↗

bioRxiv2022

Cross-Protective Antibodies Against Common Endemic Respiratory Viruses

Respiratory syncytial virus (RSV), human metapneumovirus (HMPV), and human parainfluenza virus types one (HPIV1) and three (HPIV3) are a major cause of death, morbidity, and health care costs worldwide, and they can exact a significant toll on immunocompromised patients, the elderly, and those with underlying lung disease. There is an unmet medical need for safe and effective medications for many of the viruses responsible for common respiratory viral infections in vulnerable patient populations. While a protective monoclonal antibody exists for RSV, clinical use is limited to high-risk infant populations. Here, we present the discovery, in vitro characterization, and in vivo efficacy testing of two cross-neutralizing monoclonal antibodies, one targeting both HPIV3 and HPIV1 and the other targeting both RSV and HMPV. The 3x1 antibody is capable of targeting multiple parainfluenza viruses; the MxR antibody shares features with other previously reported monoclonal antibodies that are capable of neutralizing both RSV and HMPV. We obtained structures using cryo-electron microscopy of these antibodies in complex with their antigens to 3.62 [A] resolution for 3x1:HPIV3 and to 2.24 [A] for MxR:RSV, providing a structural basis to corroborate our in vitro characterization of binding and neutralization. Together, a cocktail of 3x1 and MxR could have clinical utility in providing broad protection against four of the respiratory viruses that cause significant morbidity and mortality in at-risk individuals.

microbiology↗

bioRxiv2020

PROTECTIVE ANTIBODIES AGAINST HPIV3 INFECTION

Human parainfluenza virus type III (HPIV3) is a common respiratory pathogen that afflicts children and can be fatal in vulnerable populations, including the immunocompromised. Unfortunately, an effective vaccine or therapeutic is not currently available, resulting in tens of thousands of hospitalizations per year. In an effort to discover a protective antibody against HPIV3, we screened the B cell repertoires from peripheral blood, tonsils, or spleen from healthy children and adults. These analyses yielded five monoclonal antibodies that potently neutralized HPIV3 in vitro. These HPIV3 neutralizing antibodies targeted two non-overlapping epitopes of the HPIV3 F protein, with most targeting the apex. Importantly, prophylactic administration of one of these antibodies, named PI3-E12, resulted in potent protection against HPIV3 infection in cotton rats. Additionally, PI3-E12 could also be used therapeutically to suppress HPIV3 in immunocompromised animals. These results demonstrate the potential clinical utility of PI3-E12 for the prevention or treatment of HPIV3 in both immunocompetent and immunocompromised individuals.

immunology↗

bioRxiv2019

B cells engineered to express pathogen-specific antibodies using CRISPR/Cas9 protect against infection

Effective vaccines inducing lifelong protection against many important infections such as respiratory syncytial virus (RSV), human immunodeficiency virus (HIV), influenza and Epstein-Barr virus (EBV) are not yet available despite decades of research. As an alternative to a protective vaccine we developed a genetic engineering strategy in which CRISPR/Cas9 was utilized to replace endogenously-encoded antibodies with antibodies protective against RSV, HIV, influenza or EBV in primary human or murine B cells. The engineered antibodies were expressed in up to 59% of primary B cells under the control of endogenous regulatory elements, which maintained normal antibody expression and secretion. Importantly, a single transfer of murine B cells engineered to express an antibody protective against RSV resulted in potent and durable protection against RSV infection in immunocompromised hosts. This approach offers the opportunity to achieve sterilizing immunity against pathogens for which traditional vaccination has failed to induce or maintain protective antibody responses.

immunology↗

bioRxiv2019

Antigen-specific humoral immune responses by CRISPR/Cas9-edited B cells

A small number of HIV-1 infected individuals develop broadly neutralizing-antibodies to the virus (bNAbs). These antibodies are protective against infection in animal models. However, they only emerge 1 - 3 years after infection, and show a number of highly unusual features including exceedingly high levels of somatic mutations. It is therefore not surprising that elicitation of protective immunity to HIV-1 has not yet been possible. Here we show that mature, primary mouse and human B cells can be edited in vitro using CRISPR/Cas9 to express mature bNAbs from the endogenous Igh locus. Moreover, edited B cells retain the ability to participate in humoral immune responses. Immunization with cognate antigen in wild type mouse recipients of edited B cells elicits bNAb titers that neutralize HIV-1 at levels associated with protection against infection. This approach enables humoral immune responses that may be difficult to elicit by traditional immunization. One-sentence summaryB cells edited by CRISPR/Cas9 to produce antibodies participate in humoral immune reactions and secrete neutralizing serum titers of anti-HIV bNAbs.

immunology↗