@article{gookin_holmes_clarke_stauffer_meredith_vandewege_torres-machado_friedenberg_seiler_mathews_et al._2024, title={Acquired dysfunction of CFTR underlies cystic fibrosis-like disease of the canine gallbladder}, volume={327}, ISSN={["1522-1547"]}, DOI={10.1152/ajpgi.00145.2024}, abstractNote={Mucocele formation in dogs is a unique and enigmatic muco-obstructive disease of the gallbladder caused by the amassment of abnormal mucus that bears striking pathological similarity to cystic fibrosis. We investigated the role of cystic fibrosis transmembrane conductance regulatory protein (CFTR) in the pathogenesis of this disease. The location and frequency of disease-associated variants in the coding region of CFTR were compared using whole genome sequence data from 2,642 dogs representing breeds at low-risk, high-risk, or with confirmed disease. Expression, localization, and ion transport activity of CFTR were quantified in control and mucocele gallbladders by NanoString, Western blotting, immunofluorescence imaging, and studies in Ussing chambers. Our results establish a significant loss of CFTR-dependent anion secretion by mucocele gallbladder mucosa. A significantly lower quantity of CFTR protein was demonstrated relative to E-cadherin in mucocele compared with control gallbladder mucosa. Immunofluorescence identified CFTR along the apical membrane of epithelial cells in control gallbladders but not in mucocele gallbladder epithelium. Decreases in mRNA copy number for}, number={4}, journal={AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY}, author={Gookin, Jody L. and Holmes, Jenny and Clarke, Lane L. and Stauffer, Stephen H. and Meredith, Bryanna and Vandewege, Michael W. and Torres-Machado, Nicole and Friedenberg, Steven G. and Seiler, Gabriela S. and Mathews, Kyle G. and et al.}, year={2024}, month={Oct}, pages={G513–G530} }
 @article{john_criollo_gaghan_armwood_holmes_thachil_crespo_kulkarni_2024, title={Immunization of turkeys with <i>Clostridium septicum</i> alpha toxin-based recombinant subunit proteins can confer protection against experimental Clostridial dermatitis}, volume={19}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0302555}, DOI={10.1371/journal.pone.0302555}, abstractNote={Clostridial dermatitis (CD), caused by Clostridium septicum , is an emerging disease of increasing economic importance in turkeys. Currently, there are no effective vaccines for CD control. Here, two non-toxic domains of C . septicum alpha toxin, namely ntATX-D1 and ntATX-D2, were identified, cloned, and expressed in Escherichia coli as recombinant subunit proteins to investigate their use as potential vaccine candidates. Experimental groups consisted of a Negative control (NCx) that did not receive C . septicum challenge, while the adjuvant-only Positive control (PCx), ntATX-D1 immunization (D1) and ntATX-D2 immunization (D2) groups received C . septicum challenge. Turkeys were immunized subcutaneously with 100 μg of protein at 7, 8 and 9 weeks of age along with an oil-in-water nano-emulsion adjuvant, followed by C . septicum challenge at 11 weeks of age. Results showed that while 46.2% of birds in the PCx group died post-challenge, the rate of mortality in D1- or D2-immunization groups was 13.3%. The gross and histopathological lesions in the skin, muscle and spleen showed that the disease severity was highest in PCx group, while the D2-immunized birds had significantly lower lesion scores when compared to PCx. Gene expression analysis revealed that PCx birds had significantly higher expression of pro-inflammatory cytokine genes in the skin, muscle and spleen than the NCx group, while the D2 group had significantly lower expression of these genes compared to PCx. Peripheral blood cellular analysis showed increased frequencies of activated CD4+ and/or CD8+ cells in the D1 and D2-immunized groups. Additionally, the immunized turkeys developed antigen-specific serum IgY antibodies. Collectively, these findings indicate that ntATX proteins, specifically the ntATX-D2 can be a promising vaccine candidate for protecting turkeys against CD and that the protection mechanisms may include downregulation of C . septicum -induced inflammation and increased CD4+ and CD8+ cellular activation.}, number={4}, journal={PLOS ONE}, author={John, Feba Ann and Criollo, Valeria and Gaghan, Carissa and Armwood, Abigail and Holmes, Jennifer and Thachil, Anil J. and Crespo, Rocio and Kulkarni, Raveendra R.}, editor={Chang, Yung-FuEditor}, year={2024}, month={Apr} }
 @article{adams_collins_williams_holmes_hess_atkins_scheidemantle_liu_lodge_johnson_et al._2024, title={Myeloid cell MHC I expression drives CD8<SUP>+</SUP> T cell activation in nonalcoholic steatohepatitis}, volume={14}, ISSN={["1664-3224"]}, url={https://doi.org/10.3389/fimmu.2023.1302006}, DOI={10.3389/fimmu.2023.1302006}, abstractNote={Background & aimsActivated CD8+ T cells are elevated in Nonalcoholic steatohepatitis (NASH) and are important for driving fibrosis and inflammation. Despite this, mechanisms of CD8+ T cell activation in NASH are largely limited. Specific CD8+ T cell subsets may become activated through metabolic signals or cytokines. However, studies in NASH have not evaluated the impact of antigen presentation or the involvement of specific antigens. Therefore, we determined if activated CD8+ T cells are dependent on MHC class I expression in NASH to regulate fibrosis and inflammation.MethodsWe used H2Kb and H2Db deficient (MHC I KO), Kb transgenic mice, and myeloid cell Kb deficient mice (LysM Kb KO) to investigate how MHC class I impacts CD8+ T cell function and NASH. Flow cytometry, gene expression, and histology were used to examine hepatic inflammation and fibrosis. The hepatic class I immunopeptidome was evaluated by mass spectrometry.ResultsIn NASH, MHC class I isoform H2Kb was upregulated in myeloid cells. MHC I KO demonstrated protective effects against NASH-induced inflammation and fibrosis. Kb mice exhibited increased fibrosis in the absence of H2Db while LysM Kb KO mice showed protection against fibrosis but not inflammation. H2Kb restricted peptides identified a unique NASH peptide Ncf2 capable of CD8+ T cell activation in vitro. The Ncf2 peptide was not detected during fibrosis resolution.ConclusionThese results suggest that activated hepatic CD8+ T cells are dependent on myeloid cell MHC class I expression in diet induced NASH to promote inflammation and fibrosis. Additionally, our studies suggest a role of NADPH oxidase in the production of Ncf2 peptide generation.}, journal={FRONTIERS IN IMMUNOLOGY}, author={Adams, Victoria R. and Collins, Leonard B. and Williams, Taufika Islam and Holmes, Jennifer and Hess, Paul and Atkins, Hannah M. and Scheidemantle, Grace and Liu, Xiaojing and Lodge, Mareca and Johnson, Aaron J. and et al.}, editor={Williams, Taufika Islam and Collins, Leonard B. and Kennedy, ArionEditors}, year={2024}, month={Jan} }
 @article{herrmann_mamo_holmes_mohammed_murphy_bizikova_2022, title={Long‐term effects of ciclosporin and oclacitinib on mediators of tolerance, regulatory T‐cells, <scp>IL</scp>‐10 and <scp>TGF</scp>‐β, in dogs with atopic dermatitis}, volume={34}, ISSN={0959-4493 1365-3164}, url={http://dx.doi.org/10.1111/vde.13140}, DOI={10.1111/vde.13140}, abstractNote={AbstractBackgroundAtopic dogs often are managed with allergen‐specific immunotherapy (AIT) and concurrent dosages of ciclosporin (CSA) or oclacitinib to alleviate their clinical signs. Both drugs might affect proper tolerance induction by inhibiting regulatory T‐cell (Treg) induction.Hypothesis/ObjectivesWe evaluated Treg cell numbers and serum interleukin (IL)‐10 and transforming growth factor‐beta (TGF‐β)1 levels in dogs diagnosed with atopic dermatitis (AD) and successfully treated with either CSA or oclacitinib for nine or more months.AnimalsWe included 15 dogs receiving oclacitinib, 14 dogs treated with CSA, 15 healthy dogs, 13 dogs with untreated moderate‐to‐severe AD and 15 atopic dogs controlled with AIT.Materials and MethodsPeripheral blood CD4+CD25+FOXP3+ T‐cell percentages were determined using flow cytometry. Serum concentrations of IL‐10 and TGF‐β1 were measured by enzyme‐linked immunosorbent assay.ResultsThe percentage of Treg cells in the CSA group was significantly lower in comparison with the healthy group (p = 0.0003), the nontreated AD group (p = 0.0056) or the AIT group (p = 0.0186). There was no significant difference in Treg cell percentages between the CSA and oclacitinib groups, nor between the oclacitinib and the healthy, nontreated AD or AIT‐treated dogs. No significant differences were detected in IL‐10 and TGF‐β1 serum concentrations between the five groups.Conclusions and Clinical RelevanceLower Treg cell percentages in the CSA‐treated dogs suggest an impact of this drug on this cell population; however, it does not necessarily mean that it diminishes tolerance. Functionality and cytokine production may be more important than the number of Treg cells. Further studies evaluating the treatment outcome of dogs receiving AIT and concurrent drugs are needed to show clinical relevance.}, number={2}, journal={Veterinary Dermatology}, publisher={Wiley}, author={Herrmann, Ina and Mamo, Lisa B. and Holmes, Jenny and Mohammed, Javid P. and Murphy, K. Marcia and Bizikova, Petra}, year={2022}, month={Dec}, pages={107–114} }
 @article{nemec_holmes_hess_2021, title={Dog leukocyte antigen-88*034:01 presents nonamer peptides from canine distemper virus hemagglutinin, large polymerase, and matrix proteins}, volume={97}, ISSN={["2059-2310"]}, url={https://doi.org/10.1111/tan.14197}, DOI={10.1111/tan.14197}, abstractNote={Canine spontaneous cancers may offer greater fidelity than rodent models in advancing clinical immunotherapies. Boxers in particular are distinguished as study subjects by their popularity, and high incidence of human‐relevant cancers. Further, the MHC class I allele DLA‐88*034:01, with a known motif, dominates the breed, facilitating discovery of shared CTL responses against mutation‐origin neoepitopes by standard prediction methods. We experimentally confirmed the allomorph's binding motif by developing an MHC surface stabilization assay. The assay validated four DLA‐88*034:01‐presented peptides from canine distemper virus, ubiquitously administered in routine vaccines, for positive controls in future CTL studies. In turn, these viral peptides substantiated motif‐based prediction for DLA‐88*034:01. The study adds new tools for studying neoepitope‐specific CTL in Boxers to foster canine comparative oncology.}, number={5}, journal={HLA}, publisher={Wiley}, author={Nemec, Paige S. and Holmes, Jennifer C. and Hess, Paul R.}, year={2021}, month={May}, pages={428–434} }
 @article{holmes_scholl_dickey_hess_2021, title={High-resolution characterization of the structural features and genetic variation of six feline leukocyte antigen class I loci via single molecule, real-time (SMRT) sequencing}, volume={6}, ISSN={["1432-1211"]}, DOI={10.1007/s00251-021-01221-w}, abstractNote={Of the 12 full-length feline leukocyte antigen class I (FLAI) loci, 3 are presumed to be classical: FLAI-E, FLAI-H, and FLAI-K. As diversity is a class Ia hallmark, multi-allelism is an important surrogate supporting a classical designation, in the absence of direct demonstration of T-cell restriction. Conversely, limited polymorphism at an expressed locus suggests regulation of immune effectors with invariant receptors, and non-classical status. FLAI-A, FLAI-J, FLAI-L, and FLAI-O are putative class Ib genes in cats. For both classes, identifying prevalent variants across outbred populations can illuminate specific genotypes to be prioritized for immune studies, as shared alleles direct shared responses. Since variation is concentrated in exons 2 and 3, which encode the antigen-binding domains, partial-length cloning/sequencing can be used for allele discovery, but is laborious and occasionally ambiguous. Here we develop a targeted approach to FLAI genotyping, using the single-molecule real-time (SMRT) platform, which allows full-length (3.4-kb) reads without assembly. Consensus sequences matched full-length Sanger references. Thirty-one new class Ia genes were found in 17 cats. Alleles segregated strongly by loci, and the origins of formerly difficult-to-assign sequences were resolved. Although not targeted, FLAI-L and FLAI-J, and the pseudogene FLAI-F, were also returned. Eighteen class Ib alleles were identified. Diversity was restricted and outside hypervariable regions. Both class Ib genes were transcriptionally active. Novel alternative splicing of FLAI-L was observed. SMRT sequencing of FLAI amplicons is useful for full-length genotyping at feline class Ia loci. High-throughput sequencing could allow highly accurate allele surveys in large cat cohorts.}, journal={IMMUNOGENETICS}, author={Holmes, Jennifer C. and Scholl, Elizabeth H. and Dickey, Allison N. and Hess, Paul R.}, year={2021}, month={Jun} }