المؤلفون: Schramm, Chaim A., Moon, Damee, Peyton, Lowrey, Lima, Noemia S., Wake, Christian, Boswell, Kristin L., Henry, Amy R., Laboune, Farida, Ambrozak, David, Darko, Samuel W., Teng, I-Ting, Foulds, Kathryn E., Carfi, Andrea, Edwards, Darin K., Kwong, Peter D., Koup, Richard A., Seder, Robert A., Douek, Daniel C.

المصدر: Nature Communications ; volume 14, issue 1 ; ISSN 2041-1723

مصطلحات موضوعية: General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary

الوصف: As SARS-CoV-2 variants continue evolving, testing updated vaccines in non-human primates remains important for guiding human clinical practice. To date, such studies have focused on antibody titers and antigen-specific B and T cell frequencies. Here, we extend our understanding by integrating innate and adaptive immune responses to mRNA-1273 vaccination in rhesus macaques. We sorted innate immune cells from a pre-vaccine time point, as well as innate immune cells and antigen-specific peripheral B and T cells two weeks after each of two vaccine doses and used single-cell sequencing to assess the transcriptomes and adaptive immune receptors of each cell. We show that a subset of S-specific T cells expresses cytokines critical for activating innate responses, with a concomitant increase in CCR5-expressing intermediate monocytes and a shift of natural killer cells to a more cytotoxic phenotype. The second vaccine dose, administered 4 weeks after the first, elicits an increase in circulating germinal center-like B cells 2 weeks later, which are more clonally expanded and enriched for epitopes in the receptor binding domain. Both doses stimulate inflammatory response genes associated with elevated antibody production. Overall, we provide a comprehensive picture of bidirectional signaling between innate and adaptive components of the immune system and suggest potential mechanisms for the enhanced response to secondary exposure.

الإتاحة: https://doi.org/10.1038/s41467-023-43420-xTest
https://www.nature.com/articles/s41467-023-43420-x.pdfTest
https://www.nature.com/articles/s41467-023-43420-xTest

المؤلفون: Handy, Nicholas B, Xu, Yiting, Moon, Damee, Sowizral, Jacob J, Moon, Eric, Ho, Mengfei, Wilson, Brenda A

المصدر: mBio ; ISSN:2150-7511

مصطلحات موضوعية: Escherichia coli, G proteins, bacterial toxin, enzyme reaction, mammalian signaling, protein structure-function, substrate specificity, toxin evolution

الوصف: The cytotoxic necrotizing factor (CNF) family of AB-type bacterial protein toxins catalyze two types of modification on their Rho GTPase substrates: deamidation and transglutamination. It has been established that E. coli CNF1 and its close homolog proteins catalyze primarily deamidation and Bordetella dermonecrotic toxin (DNT) catalyzes primarily transglutamination. The rapidly expanding microbial genome sequencing data have revealed that there are at least 13 full-length variants of CNF1 homologs. CNFx from E. coli strain GN02091 is the most distant from all other members of the CNF family with 50%-55% sequence identity at the protein level and 0.45-0.52 nucleotide substitutions per site at the DNA level. CNFx modifies RhoA, Rac1, and Cdc42, and like CNF1, activates downstream SRE-dependent mitogenic signaling pathways in human HEK293T cells, but at a 1,000-fold higher EC50 value. Unlike other previously characterized CNF toxins, CNFx modifies Rho proteins primarily through transglutamination, as evidenced by gel-shift assay and confirmed by MALDI mass spectral analysis, when coexpressed with Rho-protein substrates in E. coli BL21 cells or through direct treatment of HEK293T cells. A comparison of CNF1 and CNFx sequences identified two critical active-site residues corresponding to positions 832 and 862 in CNF1. Reciprocal site-specific mutations at these residues in each toxin revealed hierarchical rules that define the preference for deamidase versus a transglutaminase activity in CNFs. An additional unique Cys residue at the C-terminus of CNFx was also discovered to be critical for retarding cargo delivery.IMPORTANCECytotoxic necrotizing factor (CNF) toxins not only play important virulence roles in pathogenic E. coli and other bacterial pathogens, but CNF-like genes have also been found in an expanding number of genomes from clinical isolates. Harnessing the power of evolutionary relationships among the CNF toxins enabled the deciphering of the hierarchical active-site determinants that define whether they modify their Rho GTPase substrates through deamidation or transglutamination. With our finding that a distant CNF variant (CNFx) unlike other known CNFs predominantly transglutaminates its Rho GTPase substrates, the paradigm of "CNFs deamidate and DNTs transglutaminate" could finally be attributed to two critical amino acid residues within the active site other than the previously identified catalytic Cys-His dyad residues. The significance of our approach and research findings is that they can be applied to deciphering enzyme reaction determinants and substrate specificities for other bacterial proteins in the development of precision therapeutic strategies.

العلاقة: https://doi.org/10.1128/mbio.01221-24Test; https://pubmed.ncbi.nlm.nih.gov/38920360Test

الإتاحة: https://doi.org/10.1128/mbio.01221-24Test
https://pubmed.ncbi.nlm.nih.gov/38920360Test

المؤلفون: Lima, Noemia S., Musayev, Maryam, Johnston, Timothy S., Wagner, Danielle A., Henry, Amy R., Wang, Lingshu, Yang, Eun Sung, Zhang, Yi, Birungi, Kevina, Black, Walker P., O’Dell, Sijy, Schmidt, Stephen D., Moon, Damee, Lorang, Cynthia G., Zhao, Bingchun, Chen, Man, Boswell, Kristin L., Roberts-Torres, Jesmine, Davis, Rachel L., Peyton, Lowrey, Narpala, Sandeep R., O’Connell, Sarah, Serebryannyy, Leonid, Wang, Jennifer, Schrager, Alexander, Talana, Chloe Adrienna, Shimberg, Geoffrey, Leung, Kwanyee, Shi, Wei, Khashab, Rawan, Biber, Asaf, Zilberman, Tal, Rhein, Joshua, Vetter, Sara, Ahmed, Afeefa, Novik, Laura, Widge, Alicia, Gordon, Ingelise, Guech, Mercy, Teng, I-Ting, Phung, Emily, Ruckwardt, Tracy J., Pegu, Amarendra, Misasi, John, Doria-Rose, Nicole A., Gaudinski, Martin, Koup, Richard A., Kwong, Peter D., McDermott, Adrian B., Amit, Sharon

المساهمون: NIH Intramural funding

المصدر: Nature Communications ; volume 13, issue 1 ; ISSN 2041-1723

مصطلحات موضوعية: General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary

الوصف: An important consequence of infection with a SARS-CoV-2 variant is protective humoral immunity against other variants. However, the basis for such cross-protection at the molecular level is incompletely understood. Here, we characterized the repertoire and epitope specificity of antibodies elicited by infection with the Beta, Gamma and WA1 ancestral variants and assessed their cross-reactivity to these and the more recent Delta and Omicron variants. We developed a method to obtain immunoglobulin sequences with concurrent rapid production and functional assessment of monoclonal antibodies from hundreds of single B cells sorted by flow cytometry. Infection with any variant elicited similar cross-binding antibody responses exhibiting a conserved hierarchy of epitope immunodominance. Furthermore, convergent V gene usage and similar public B cell clones were elicited regardless of infecting variant. These convergent responses despite antigenic variation may account for the continued efficacy of vaccines based on a single ancestral variant.

الإتاحة: https://doi.org/10.1038/s41467-022-35456-2Test
https://www.nature.com/articles/s41467-022-35456-2.pdfTest
https://www.nature.com/articles/s41467-022-35456-2Test

المؤلفون: Lima, Noemia S., Moon, Damee, Darko, Samuel, De La Barrera, Rafael A., Lin, Leyi, Koren, Michael A., Jarman, Richard G., Eckels, Kenneth H., Thomas, Stephen J., Michael, Nelson L., Modjarrad, Kayvon, Douek, Daniel C., Trautmann, Lydie

المساهمون: National Institutes of Health, U.S. Department of Defense

المصدر: Frontiers in Immunology ; volume 12 ; ISSN 1664-3224

مصطلحات موضوعية: Immunology, Immunology and Allergy

الوصف: The epidemic spread of Zika virus (ZIKV), associated with devastating neurologic syndromes, has driven the development of multiple ZIKV vaccines candidates. An effective vaccine should induce ZIKV-specific T cell responses, which are shown to improve the establishment of humoral immunity and contribute to viral clearance. Here we investigated how previous immunization against Japanese encephalitis virus (JEV) and yellow fever virus (YFV) influences T cell responses elicited by a Zika purified-inactivated virus (ZPIV) vaccine. We demonstrate that three doses of ZPIV vaccine elicited robust CD4 T cell responses to ZIKV structural proteins, while ZIKV-specific CD4 T cells in pre-immunized individuals with JEV vaccine, but not YFV vaccine, were more durable and directed predominantly toward conserved epitopes, which elicited Th1 and Th2 cytokine production. In addition, T cell receptor repertoire analysis revealed preferential expansion of cross-reactive clonotypes between JEV and ZIKV, suggesting that pre-existing immunity against JEV may prime the establishment of stronger CD4 T cell responses to ZPIV vaccination. These CD4 T cell responses correlated with titers of ZIKV-neutralizing antibodies in the JEV pre-vaccinated group, but not in flavivirus-naïve or YFV pre-vaccinated individuals, suggesting a stronger contribution of CD4 T cells in the generation of neutralizing antibodies in the context of JEV-ZIKV cross-reactivity.

الإتاحة: https://doi.org/10.3389/fimmu.2021.640190Test

المؤلفون: Ho, Mengfei, Moon, Damee, Pires-Alves, Melissa, Thornton, Patrick D., McFarlin, Barbara L., Wilson, Brenda A.

المصدر: Computational and Structural Biotechnology Journal ; volume 19, page 5126-5139 ; ISSN 2001-0370

مصطلحات موضوعية: Computer Science Applications, Genetics, Biochemistry, Structural Biology, Biophysics, Biotechnology

الإتاحة: https://doi.org/10.1016/j.csbj.2021.08.050Test
https://api.elsevier.com/content/article/PII:S2001037021003810?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S2001037021003810?httpAccept=text/plainTest

المؤلفون: Nganou-Makamdop, Krystelle, Talla, Aarthi, Sharma, Ashish Arunkumar, Darko, Sam, Ransier, Amy, Laboune, Farida, Chipman, Jeffrey G., Beilman, Gregory J., Hoskuldsson, Torfi, Fourati, Slim, Schmidt, Thomas E., Arumugam, Sahaana, Lima, Noemia S., Moon, Damee, Callisto, Samuel, Schoephoerster, Jordan, Tomalka, Jeffery, Mugyenyi, Peter, Ssali, Francis, Muloma, Proscovia, Ssengendo, Patrick, Leda, Ana R., Cheu, Ryan K., Flynn, Jacob K., Morou, Antigoni, Brunet-Ratnasingham, Elsa, Rodriguez, Benigno, Lederman, Michael M., Kaufmann, Daniel E., Klatt, Nichole R., Kityo, Cissy, Brenchley, Jason M., Schacker, Timothy W., Sekaly, Rafick P., Douek, Daniel C.

المصدر: Cell ; volume 184, issue 15, page 3899-3914.e16 ; ISSN 0092-8674

مصطلحات موضوعية: General Biochemistry, Genetics and Molecular Biology

الإتاحة: https://doi.org/10.1016/j.cell.2021.05.023Test
https://api.elsevier.com/content/article/PII:S009286742100653X?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S009286742100653X?httpAccept=text/plainTest

المؤلفون: Zeng, Xiancheng, Chi, Xuelin, Ho, Brian T., Moon, Damee, Lambert, Christine, Hall, Richard J., Baybayan, Primo, Wang, Shihua, Wilson, Brenda A., Ho, Mengfei

المساهمون: Segata, Nicola, Pacific Biosiences, Inc., UofI | University of Illinois at Urbana-Champaign, Fujian Agriculture and Forestry University

المصدر: mSystems ; volume 4, issue 1 ; ISSN 2379-5077

الوصف: E. coli strain Sanji is the first sequenced and analyzed genome of the recently emerged pathogenic XDR strains with sequence type ST167 and novel in silico serotype O89b:H9. Comparison of the genomes of Sanji with other ST167 strains revealed distinct sets of different plasmids, mobile IS elements, and antibiotic resistance genes in each genome, indicating that there exist multiple paths toward achieving XDR. The emergence of these pathogenic ST167 E. coli strains with diverse XDR capabilities highlights the difficulty of preventing or mitigating the development of XDR properties in bacteria and points to the importance of better understanding of the shared underlying virulence mechanisms and physiology of pathogenic bacteria.

الإتاحة: https://doi.org/10.1128/msystems.00242-18Test