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Wagoner ZW, Yates TB, Hernandez-Davies JE, Sureshchandra S, Joloya EM, Jain A, de Assis R, Kastenschmidt JM, Sorn AM, Mitul MT, Tamburini I, Ahuja G, Zhong Q, Trask D, Seldin M, Davies DH, Wagar LE. Systems immunology analysis of human immune organoids identifies host-specific correlates of protection to different influenza vaccines. Cell Stem Cell 2025; 32:529-546.e6. [PMID: 39986275 PMCID: PMC11974613 DOI: 10.1016/j.stem.2025.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 11/27/2024] [Accepted: 01/27/2025] [Indexed: 02/24/2025]
Abstract
Vaccines are an essential tool to significantly reduce pathogen-related morbidity and mortality. However, our ability to rationally design vaccines and identify correlates of protection remains limited. Here, we employed an immune organoid approach to capture human adaptive immune response diversity to influenza vaccines and systematically identify host and antigen features linked to vaccine response variability. Our investigation identified established and unique immune signatures correlated with neutralizing antibody responses across seven different influenza vaccines and antigens. Unexpectedly, heightened ex vivo tissue frequencies of T helper (Th)1 cells emerged as both a predictor and a correlate of neutralizing antibody responses to inactivated influenza vaccines (IIVs). Secondary analysis of human public data confirmed that elevated Th1 signatures are associated with antibody responses following in vivo vaccination. These findings demonstrate the utility of human in vitro models for identifying in vivo correlates of protection and establish a role for Th1 functions in influenza vaccination.
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Affiliation(s)
- Zachary W Wagoner
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA; Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Center for Virus Research, University of California, Irvine, Irvine, CA, USA; Vaccine R&D Center, University of California, Irvine, Irvine, CA, USA
| | - Timothy B Yates
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA; Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Center for Virus Research, University of California, Irvine, Irvine, CA, USA; Vaccine R&D Center, University of California, Irvine, Irvine, CA, USA
| | - Jenny E Hernandez-Davies
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA; Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Center for Virus Research, University of California, Irvine, Irvine, CA, USA; Vaccine R&D Center, University of California, Irvine, Irvine, CA, USA
| | - Suhas Sureshchandra
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA; Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Center for Virus Research, University of California, Irvine, Irvine, CA, USA; Vaccine R&D Center, University of California, Irvine, Irvine, CA, USA
| | - Erika M Joloya
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA; Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Center for Virus Research, University of California, Irvine, Irvine, CA, USA; Vaccine R&D Center, University of California, Irvine, Irvine, CA, USA
| | - Aarti Jain
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA; Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Vaccine R&D Center, University of California, Irvine, Irvine, CA, USA
| | - Rafael de Assis
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA; Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Vaccine R&D Center, University of California, Irvine, Irvine, CA, USA
| | - Jenna M Kastenschmidt
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA; Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Center for Virus Research, University of California, Irvine, Irvine, CA, USA; Vaccine R&D Center, University of California, Irvine, Irvine, CA, USA
| | - Andrew M Sorn
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA; Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Center for Virus Research, University of California, Irvine, Irvine, CA, USA; Vaccine R&D Center, University of California, Irvine, Irvine, CA, USA
| | - Mahina Tabassum Mitul
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA; Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Center for Virus Research, University of California, Irvine, Irvine, CA, USA; Vaccine R&D Center, University of California, Irvine, Irvine, CA, USA
| | - Ian Tamburini
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA; Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, CA, USA
| | - Gurpreet Ahuja
- Department of Pediatric Otolaryngology, Children's Hospital of Orange County, Orange, CA, USA; Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, CA, USA
| | - Qiu Zhong
- Department of Pediatric Otolaryngology, Children's Hospital of Orange County, Orange, CA, USA; Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, CA, USA
| | - Douglas Trask
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, Orange, CA, USA
| | - Marcus Seldin
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA; Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, CA, USA
| | - D Huw Davies
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA; Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Center for Virus Research, University of California, Irvine, Irvine, CA, USA; Vaccine R&D Center, University of California, Irvine, Irvine, CA, USA
| | - Lisa E Wagar
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA; Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Center for Virus Research, University of California, Irvine, Irvine, CA, USA; Vaccine R&D Center, University of California, Irvine, Irvine, CA, USA.
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Wolf J, Reinhard T, Hajdu RI, Schlunck G, Auw-Haedrich C, Lange C. Transcriptional Profiling Identifies Prognostic Gene Signatures for Conjunctival Extranodal Marginal Zone Lymphoma. Biomolecules 2023; 13:115. [PMID: 36671500 PMCID: PMC9855408 DOI: 10.3390/biom13010115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/11/2023] Open
Abstract
This study characterizes the transcriptional profile and the cellular tumor microenvironment of conjunctival extranodal marginal zone lymphoma (EMZL) and identifies prognostically relevant biomarkers. Ten formalin-fixed and paraffin-embedded conjunctival EMZL and eight healthy conjunctival specimens were analyzed by Massive Analysis of cDNA Ends (MACE) RNA sequencing. The 3417 upregulated genes in conjunctival EMZL were involved in processes such as B cell proliferation and Rac protein signaling, whereas the 1188 downregulated genes contributed most significantly to oxidative phosphorylation and UV protection. The tumor microenvironment, as determined by deconvolution analysis, was mainly composed of multiple B cell subtypes which reflects the tumor's B cell lineage. However, several T cell types, including T helper 2 cells and regulatory T cells, as well as innate immune cell types, such as anti-inflammatory macrophages and plasmacytoid dendritic cells, were also strongly enriched in conjunctival EMZL. A 13-biomarker prognostic panel, including S100A8 and S100A9, classified ocular and extraocular tumor recurrence, exceeded prognostic accuracy of Ann Arbor and American Joint Committee on Cancer (AJCC) staging, and demonstrated prognostic value for patient survival in 21 different cancer types in a database of 12,332 tumor patients. These findings may lead to new options of targeted therapy and may improve prognostic prediction for conjunctival EMZL.
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Affiliation(s)
- Julian Wolf
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Molecular Surgery Laboratory, Stanford University, Palo Alto, CA 94304, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Thomas Reinhard
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Rozina Ida Hajdu
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Department of Ophthalmology, Semmelweis University, 1085 Budapest, Hungary
| | - Günther Schlunck
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Claudia Auw-Haedrich
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Clemens Lange
- Ophtha-Lab, Department of Ophthalmology, St. Franziskus Hospital, 48145 Münster, Germany
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Wang Y, Lei Y, Gu Y, Kong X, Bian Z, Ji F. Effect of dexmedetomidine on CD4+ T cells and programmed cell death protein-1 in postoperative analgesia: a prospective, randomized, controlled study. Minerva Anestesiol 2021; 87:423-431. [PMID: 33432790 DOI: 10.23736/s0375-9393.20.14581-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Surgical trauma inhibits cellular immunity. Dexmedetomidine produces opioid-sparing effect and an impact on immune response. METHODS Eighty-six surgical patients were enrolled and received postoperative patient-controlled intravenous analgesia (PCIA) with either fentanyl alone (fentanyl group) or combined with dexmedetomidine (dexmedetomidine group). The percentages of T helper cells (Th1, Th2, and Th17) and regulatory T (Treg) cells, expression levels of programmed cell death protein-1 (PD-1) and its ligand (PD-L1) on the CD4+ T cells, and plasma levels of the cytokines were tested. Postoperative pain was measured by numerical rating scale (NRS), including NRS at rest (NRSR) and movement (NRSM). RESULTS In dexmedetomidine group, Th1 cells were increased significantly at 24 and 48 h following surgery (P=0.011 and P=0.013, respectively) and Treg cells were significantly higher at 48 h postoperatively (P=0.013). PD-1 was significantly lower in dexmedetomidine group at 24 h postoperatively (P=0.046) and interleukin 4 (IL-4) and IL-6 were significantly decreased at 48 h postoperatively (P=0.024 and P=0.035, respectively). Compared with fentanyl group, NRSR scores were lower in dexmedetomidine group at 24 h following surgery (P=0.018) and NRSR and NRSM scores were lower at 48 h postoperatively (P=0.007 and P=0.011, respectively). NRSR exhibited negative correlations with Th1 cells in fentanyl group and dexmedetomidine group (P=0.003 and P=0.005, respectively). CONCLUSIONS Dexmedetomidine increases the differentiation of Th1 and Treg cells and reduces the expression of PD-1 on CD4+ T cells. Dexmedetomidine may assist to ameliorate postoperative pain and attenuate proinflammatory response. There might be a negative correlation between pain and Th1 cells.
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Affiliation(s)
- Yulan Wang
- Department of Anesthesiology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yishan Lei
- Department of Anesthesiology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yanzheng Gu
- Clinical Immunology Institute of Jiangsu Province, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaoqi Kong
- Department of Anesthesiology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhen Bian
- Department of Anesthesiology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fuhai Ji
- Department of Anesthesiology, The First Affiliated Hospital of Soochow University, Suzhou, China -
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Hollern DP, Contreras CM, Dance-Barnes S, Silva GO, Pfefferle AD, Xiong J, Darr DB, Usary J, Mott KR, Perou CM. A mouse model featuring tissue-specific deletion of p53 and Brca1 gives rise to mammary tumors with genomic and transcriptomic similarities to human basal-like breast cancer. Breast Cancer Res Treat 2018; 174:143-155. [PMID: 30484104 PMCID: PMC6418066 DOI: 10.1007/s10549-018-5061-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022]
Abstract
Purpose and methods In human basal-like breast cancer, mutations and deletions in TP53 and BRCA1 are frequent oncogenic events. Thus, we interbred mice expressing the CRE-recombinase with mice harboring loxP sites at TP53 and BRCA1 (K14-Cre; p53f/f Brca1f/f) to test the hypothesis that tissue-specific deletion of TP53 and BRCA1 would give rise to tumors reflective of human basal-like breast cancer. Results In support of our hypothesis, these transgenic mice developed tumors that express basal-like cytokeratins and demonstrated intrinsic gene expression features similar to human basal-like tumors. Array comparative genomic hybridization revealed a striking conservation of copy number alterations between the K14-Cre; p53f/f Brca1f/f mouse model and human basal-like breast cancer. Conserved events included MYC amplification, KRAS amplification, and RB1 loss. Microarray analysis demonstrated that these DNA copy number events also led to corresponding changes in signatures of pathway activation including high proliferation due to RB1 loss. K14-Cre; p53f/f Brca1f/f also matched human basal-like breast cancer for a propensity to have immune cell infiltrates. Given the long latency of K14-Cre; p53f/f Brca1f/f tumors (~ 250 days), we created tumor syngeneic transplant lines, as well as in vitro cell lines, which were tested for sensitivity to carboplatin and paclitaxel. These therapies invoked acute regression, extended overall survival, and resulted in gene expression signatures of an anti-tumor immune response. Conclusion These findings demonstrate that this model is a valuable preclinical resource for the study of human basal-like breast cancer. Electronic supplementary material The online version of this article (10.1007/s10549-018-5061-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel P Hollern
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB#7264, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Cristina M Contreras
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB#7264, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Stephanie Dance-Barnes
- Department of Biological Sciences, Winston Salem State University, Winston-Salem, NC, 27110, USA
| | - Grace O Silva
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB#7264, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Adam D Pfefferle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB#7264, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jessie Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB#7264, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - David B Darr
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB#7264, Chapel Hill, NC, 27599, USA
| | - Jerry Usary
- Arrow Genomics LLC, Chapel Hill, NC, 27517, USA
| | - Kevin R Mott
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB#7264, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB#7264, Chapel Hill, NC, 27599, USA. .,Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.
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