John Kappler's research while affiliated with National Jewish Health and other places

Publications (457)

Article
The SARS-CoV-2 Delta and Lambda variants had been named variants of concern (VOC) and variants of interest (VOI), respectively, by the World Health Organization (WHO). Both variants have two mutations in the spike receptor binding domain (RBD) region, with L452R and T478K mutations in the Delta variant, and L452Q and F490S mutations in the Lambda v...
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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has lasted more than 2 years with over 260 million infections and 5 million deaths worldwide as of November 2021. To combat the virus, monoclonal antibodies blocking the virus binding to human receptor, the angiotensin converting enzyme 2 (ACE2), have been approved to treat t...
Article
Throughout evolution, proinsulin has exhibited significant sequence variation in both C-peptide and insulin moieties. As the proinsulin coding sequence evolves, the gene product continues to be under selection pressure both for ultimate insulin bioactivity and for the ability of proinsulin to be folded for export through the secretory pathway of pa...
Preprint
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The newly emerging variants of SARS-CoV-2 from India (Delta variant) and South America (Lambda variant) have led to a higher infection rate of either vaccinated or unvaccinated people. We found that sera from Pfizer-BioNTech vaccine remain high reactivity toward the receptor binding domain (RBD) of Delta variant while it drops dramatically toward t...
Article
Background The thymus is a glandular organ that is essential for the formation of the adaptive immune system by educating developing T cells. The thymus is most active during childhood and involutes around the time of adolescence resulting in a severe reduction or absence of naïve T cell output. The ability to generate a patient derived human thymu...
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Significance Tumor vaccines using modified self-antigens that structurally enhance T cell receptor–peptide–major histocompatibility complex interactions greatly improve a T cell protective response against the tumor’s unmodified self-antigen. X-ray crystal structures of these interactions explain how the native and modified peptides can interact wi...
Preprint
Full-text available
Throughout evolution, proinsulin has exhibited significant sequence variation in both C-peptide and insulin moieties. As the proinsulin coding sequence evolves, the gene product continues to be under selection pressure both for ultimate insulin bioactivity and for the ability of proinsulin to be folded for export through the secretory pathway of pa...
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Full-text available
The newly emerging variants of SARS-CoV-2 from South Africa (B.1.351/501Y.V2) and Brazil (P.1/501Y.V3) have led to a higher infection rate and reinfection of COVID-19 patients. We found that the mutations K417N, E484K, and N501Y within the receptor-binding domains (RBDs) of the virus could confer ~2-fold higher binding affinity to the human recepto...
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The T cell antigens driving autoimmune Type 1 Diabetes (T1D) have been pursued for more than three decades. When diabetogenic CD4 T cell clones and their relevant MHCII antigen presenting alleles were first identified in rodents and humans, the path to discovering the peptide epitopes within pancreatic beta cell proteins seemed straightforward. How...
Article
Cytotoxic T cells targeting cancer neoantigens harboring driver mutations can lead to durable tumor regression in an HLAI-dependent manner. However, it is difficult to extend the population of patients who are eligible for neoantigen-based immunotherapy, as immunogenic neoantigen-HLA pairs are rarely shared across different patients. Thus, a way to...
Article
Discovering dominant epitopes for T cells, particularly CD4+ T cells, in human immune-mediated diseases remains a significant challenge. Here, we used bronchoalveolar lavage (BAL) cells from HLA-DP2-expressing patients with chronic beryllium disease (CBD), a debilitating granulomatous lung disorder characterized by accumulations of beryllium (Be)-s...
Preprint
We generated several versions of the receptor binding domain (RBD) of the Spike protein with mutations existing within newly emerging variants from South Africa and Brazil. We found that the mutant RBD with K417N, E484K, and N501Y exchanges has higher binding affinity to the human receptor compared to the wildtype RBD. This mutated version of RBD a...
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Genetic mutations lead to the production of mutated proteins from which peptides are presented to T cells as cancer neoantigens. Evidence suggests that T cells that target neoantigens are the main mediators of effective cancer immunotherapies. Although algorithms have been used to predict neoantigens, only a minority are immunogenic. The factors th...
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Activation of T cells specific for insulin B chain amino acids 9 to 23 (B:9–23) is essential for the initiation of type 1 diabetes (T1D) in non-obese diabetic mice. We previously reported that peptide/MHC complexes containing optimized B:9–23 mimotopes can activate most insulin-reactive pathogenic T cells. A monoclonal antibody (mAb287) targeting t...
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The identification of the peptide epitopes presented by major histocompatibility complex class II (MHCII) molecules that drive the CD4 T cell component of autoimmune diseases has presented a formidable challenge over several decades. In type 1 diabetes (T1D), recent insight into this problem has come from the realization that several of the importa...
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Memory T cells respond rapidly in part because they are less reliant on heightened levels of costimulatory molecules. This enables rapid control of secondary infecting pathogens but presents challenges to efforts to control or silence memory CD4 T cells, for example in antigen specific tolerance strategies for autoimmunity. We have examined the tra...
Article
Significance RNA polymerase II (Pol II) is stalled at the transcription starting site for a large number of genes in higher eukaryotes. We previously found that JMJD5/7 proteins act as both endopeptidases and exopeptidases to cleave arginine methylated histone tails including those of H2A, H3, and H4, thus generating relatively “tailless nucleosome...
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Rationale: A subpopulation of B cells (ABCs) is increased in mice and humans with infections or autoimmune diseases. Since depletion of these cells might be valuable in patients with certain lung diseases, the goal was to find out if ABC-like cells were at elevated levels in such patients. Objectives: To measure ABC-like cell percentages in pati...
Preprint
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Memory T cells respond rapidly in part because they are less reliant on heightened levels of costimulatory molecules. This presents challenges to silencing memory T cells in tolerance strategies for autoimmunity or allergy. We find that memory CD4 T cells generated by infection or immunisation survive secondary activation with antigen delivered wit...
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More than 30% of genes in higher eukaryotes are regulated by promoter-proximal pausing of RNA polymerase II (Pol II). Phosphorylation of Pol II CTD by positive transcription elongation factor b (P-TEFb) is a necessary precursor event that enables productive transcription elongation. The exact mechanism on how the sequestered P TEFb is released from...
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Significance Central to adaptive immunity is the interaction between the αβ T cell antigen receptor (TCR) and peptides presented by the major histocompatibility complex (MHC) molecules. It is fundamental to understand any potential generalities regarding a TCR-pMHC recognition event. Two theories have been proposed to explain how TCR recognition of...
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Lipocalins represent the most important protein family of the mammalian respiratory allergens. Four of the seven named dog allergens are lipocalins: Can f 1, Can f 2, Can f 4, and Can f 6. We present the structure of Can f 6 along with data on the biophysical and biological activity of this protein in comparison with other animal lipocalins. The Ca...
Preprint
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More than 30% of genes in higher eukaryotes are regulated by promoter-proximal pausing of RNA polymerase II (Pol II). Phosphorylation of Pol II-CTD by positive transcription elongation factor (P-TEFb) is a necessary precursor event that enables productive transcription elongation. The exact mechanism on how the sequestered P-TEFb is released from t...
Preprint
Full-text available
Cancer mutations lead to the production of mutated proteins from which can be processed and presented to CD8+ T cells as neoantigens. Despite the promise of immunotherapy targeting neoantigens, which mutant peptides are likely to induce immune responses remain elusive. Here, we determined two sets of MHCI bound neoantigen structures and performed b...
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In type 1 diabetes (T1D), proinsulin is a major autoantigen and the insulin B:9-23 peptide contains epitopes for CD4 ⁺ T cells in both mice and humans. This peptide requires carboxyl-terminal mutations for uniform binding in the proper position within the mouse IA g7 or human DQ8 major histocompatibility complex (MHC) class II (MHCII) peptide groov...
Preprint
Full-text available
Lipocalins represent the most important protein family of the mammalian respiratory allergens. Four of the seven named dog allergens are lipocalins: Can f 1, Can f 2, Can f 4, and Can f 6. We present the structure of Can f 6 along with data on the biophysical and biological activity of this protein in comparison with other animal lipocalins. The Ca...
Article
Immortalized T cells such as T cell hybridomas, transfectomas, and transductants are useful tools to study tri-molecular complexes consisting of peptide, MHC, and T cell receptor (TCR) molecules. These cells have been utilized for antigen discovery studies for decades due to simplicity and rapidness of growing cells. However, responsiveness to anti...
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We have reported that JMJD5 and JMJD7 (JMJD5/7) are responsible for the clipping of arginine methylated histone tails to generate "tailless nucleosomes", which could release the pausing RNA polymerase II (Pol II) into productive transcription elongation. JMJD5/7 function as endopeptidases that cleave histone tails specifically adjacent to methylate...
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Significance: By employing proteomic analyses of eluted peptides from breast cancer cells, the current study has built an initial HLA-I-typed antigen collection for breast cancer research. It was also determined that immunogenic epitopes can be identified using established cell lines and that shared immunogenic peptides can be found in different c...
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Significance Insulin is a target of CD4 T cells in type 1 diabetes in mice and humans. Why the major epitope in the insulin B chain is presented poorly to the diabetogenic CD4 T cells by the disease-associated major histocompatibility class II (MHCII) alleles has been highly debated. Here we present high-resolution mouse and human MHCII structures...
Data
After transduction with the DObWT chain, T cells from mice expressing DOb48A react with cells bearing the MHC allele that selected them. CD4 T cells were isolated from individual DOb48A mice and transduced with retorviruses expressing DObWT or DOb48A as described in the Methods section. The cells were vultured with spoleen cells from mice expressin...
Data
In normal mice, a significant number of TCRα sequences appear on naïve CD4 T cells regardless of the selecting MHCII allele. Naïve CD4 T cells were isolated from the lymph nodes of normal mice of the indicated strains and their TCRα sequences identified as described in the Materials and methods section. Shown are the %s of unique sequences and the...
Data
Data from individual mice show that both CD4 and CD8 T cells appear in mice expressing a single TCRb chain regardless of the MHC allele expressed. The numbers of thymus and lymph node cells were counted and analyzed for their expression of CD4 and CD8 and T cell receptor.
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Mature T cells bearing αβ T cell receptors react with foreign antigens bound to alleles of major histocompatibility complex proteins (MHC) that they were exposed to during their development in the thymus, a phenomenon known as positive selection. The structural basis for positive selection has long been debated. Here, using mice expressing one of t...
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Significance Enzymes responsible for the clipping of histone tails and removal of arginine-methylated histone tails still remain elusive. The underlying mechanism of high histone turnover rate in nonproliferated cells is still a mystery. How RNA polymerase II overcomes nucleosome barriers during transcription is unknown. This article described the...
Preprint
Full-text available
Mature T cells bearing αβ T cell receptors react with foreign antigens bound to alleles of major histocompatibility complex proteins (MHC) that they were exposed to during their development in the thymus, a phenomenon known as positive selection. The structural basis for positive selection has long been debated. Here, using mice expressing one of t...
Article
Herpesviruses establish lifelong infections, normally characterized by prolonged periods of latency with intermittent episodes of viral reactivation. Feline herpesvirus-1 (FHV-1) infects domestic cats, and epidemiological studies indicate that many or most domestic cats are exposed to FHV-1, but the strength and longevity of the antibody response t...
Article
B cells contribute to multiple aspects of autoimmune disorders and may play a role in triggering disease. Thus, targeting B cells may be a promising strategy for treating autoimmune disorders. Better understanding of the B cell subsets that are responsible for the development of autoimmunity will be critical for developing efficient therapies. Here...
Article
Type 1 diabetes results from chronic autoimmune destruction of insulin-producing beta cells within pancreatic islets. While insulin is a critical self-antigen in animal models of autoimmune diabetes, due to extremely limited access to pancreas samples, little is known about human antigenic targets for islet-infiltrating T-cells. Here we show that p...
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Knowledge of the processes that underlie IgG subclass switching could inform strategies designed to counteract infections and autoimmunity. Here we show that TLR7 ligands induce subsets of memory CD4 and CD8 T cells to secrete interferon γ (IFNγ) in the absence of antigen receptor stimulation. In turn, TLR ligation and IFNγ cause B cells to express...
Data
T cell specific deletion of MyD88 in MyD88flox/flox x LCK-cre mice. Splenocytes from MyD88flox/flox x LCK-cre (red line), MyD88flox/flox x LCK-wt (blue line) or MyD88KO (gray solid histogram) were stained for surface markers and intracellularly stained for MyD88. MyD88 expression on T cells or B cells is shown. (PDF)
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Research on the specificities, functions, and maturation of T cells would be greatly aided by a collection of monoclonal antibodies which distinguishes different types of TCR. With this end in mind hamsters were immunized and tested for production of pan-reactive anti-mouse αβ TCR antibodies. In this report we describe the properties and uses of a...
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CD8⁺ T cell recognition of virus-infected cells is characteristically restricted by major histocompatibility complex (MHC) class I, although rare examples of MHC class II restriction have been reported in Cd4-deficient mice and a macaque SIV vaccine trial using a recombinant cytomegalovirus vector. Here, we demonstrate the presence of human leukocy...
Data
Document S1. Figures S1–S6, Tables S1 and S2, and Supplemental Experimental Procedures
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Significance The evolutionary hypothesis for T-cell antigen receptor–peptide major histocompatibility complex (TCR–pMHC) interaction posits the existence of germ-line–encoded rules by which the TCR is biased toward recognition of the MHC. Understanding these rules is important for our knowledge of how to manipulate this important interaction at the...
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Aluminum salt (alum) adjuvants have been used for many years as adjuvants for human vaccines because they are safe and effective. Despite its widespread use, the means by which alum acts as an adjuvant remains poorly understood. Recently, it was shown that injected alum is rapidly coated with host chromatin within mice. Experiments suggested that t...
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Significance The essence of the adaptive immune response depends on the specificity of antigen receptors. This report identifies shared alpha–beta T-cell receptor (TCR) pairs from the tissues of HLA-A2 ⁺ patients with breast cancer and control donors. Using an emulsion-based RT-PCR assay, we analyzed TCR sequences from tissues ex vivo. We identifie...
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Chronic beryllium (Be) disease is a granulomatous lung disorder that results from Be exposure in a genetically susceptible host. The disease is characterized by the accumulation of Be-responsive CD4(+) T cells in the lung, and genetic susceptibility is primarily linked to HLA-DPB1 alleles possessing a glutamic acid at position 69 of the b-chain. Re...
Data
Figure S1. TCRA gene conferring Be-specificity for T cell hybridomas LB9-18 and LB10-17. Three Be-specific T cell hybridomas derived from the lungs of BeO-exposed HLA-DP2 Tg mice expressed multiple TCR α-chains paired with a TCR Vβ6-chain (LB9-18/LB10-9 are clonal replicates and LB10-17; see Figure 1B). To ascertain which TCR α/β pair conferred Be-...
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Significance Type 1 diabetes is an autoimmune disease in which the insulin-producing beta cells within the islets of Langerhans of the pancreas are destroyed by T cell-mediated immune attack. The peptide epitopes derived from islet proteins that are targeted by CD4 ⁺ T cells have been difficult to determine. We show in the nonobese diabetic (NOD) m...
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B cell hybridomas are an important source of monoclonal antibodies. In this paper, we developed a high-throughput method to characterize mouse IgG antibodies using surface plasmon resonance technology. This assay rapidly determines their sub-isotypes, whether they bind native antigen and their approximate affinities for the antigen using only 50 μl...
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Full-text available
Chronic beryllium disease (CBD) is a granulomatous lung disorder that is associated with the accumulation of beryllium (Be)-specific CD4(+) T cells into the lung. Genetic susceptibility is linked to HLA-DPB1 alleles that possess a glutamic acid at position 69 (βGlu69), and HLA-DPB1*02:01 is the most prevalent βGlu69-containing allele. Using HLA-DP2...