High-dimensional profiling of pediatric immune responses to solid organ transplantation

Cell Reports Medicine - Tập 4 - Trang 101147 - 2023
Mahil Rao1,2, Meelad Amouzgar3, James T. Harden2,3, M. Gay Lapasaran2, Amber Trickey4, Brian Armstrong5, Jonah Odim6, Tracia Debnam6, Carlos O. Esquivel2,4, Sean C. Bendall7,8, Olivia M. Martinez2,4,7, Sheri M. Krams2,4,7
1Department of Pediatrics, Division of Pediatric Critical Care Medicine, Stanford University School of Medicine, Palo Alto, CA 94304, USA
2Transplant Immunology Lab, Stanford University School of Medicine, Palo Alto, CA 94304, USA
3Immunology Graduate Program, Stanford University School of Medicine, Palo Alto, CA 94304, USA
4Department of Surgery, Division of Abdominal Transplant Surgery, Stanford University School of Medicine, Palo Alto, CA 94304, USA
5Rho Inc, Durham, NC, USA
6National Institutes of Health, Bethesda, MD, USA
7Program in Immunology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
8Department of Pathology, Stanford University School of Medicine, Palo Alto, CA 94304, USA

Tài liệu tham khảo

Alessiani, 1990, Infections with FK 506 immunosuppression: preliminary results with primary therapy, Transplant. Proc., 22, 44 Williams, 2006, Calcineurin nephrotoxicity, Adv. Chronic Kidney Dis., 13, 47, 10.1053/j.ackd.2005.11.001 Absalon, 2017, Post-transplant lymphoproliferative disorder after solid-organ transplant in children, Semin. Pediatr. Surg., 26, 257, 10.1053/j.sempedsurg.2017.07.002 Colvin, 2021, OPTN/SRTR 2019 Annual Data Report: Heart, Am. J. Transplant., 21, 356, 10.1111/ajt.16492 Horslen, 2021, OPTN/SRTR 2019 Annual Data Report: Intestine, Am. J. Transplant., 21, 316, 10.1111/ajt.16498 Hart, 2021, OPTN/SRTR 2019 Annual Data Report: Kidney, Am. J. Transplant., 21, 21, 10.1111/ajt.16502 Kwong, 2021, OPTN/SRTR 2019 Annual Data Report: Liver, Am. J. Transplant., 21, 208, 10.1111/ajt.16494 Mbiribindi, 2019, Natural killer cells as modulators of alloimmune responses, Curr. Opin. Organ Transplant., 24, 37, 10.1097/MOT.0000000000000590 Miyairi, 2021, Natural Killer Cells: Critical Effectors During Antibody-mediated Rejection of Solid Organ Allografts, Transplantation, 105, 284, 10.1097/TP.0000000000003298 Moreau, 2013, Effector mechanisms of rejection, Cold Spring Harb. Perspect. Med., 3, a015461, 10.1101/cshperspect.a015461 Chong, 2020, Mechanisms of organ transplant injury mediated by B cells and antibodies: Implications for antibody-mediated rejection, Am. J. Transplant., 20, 23, 10.1111/ajt.15844 Duneton, 2022, Activation and regulation of alloreactive T cell immunity in solid organ transplantation, Nat. Rev. Nephrol., 18, 663, 10.1038/s41581-022-00600-0 Neeland, 2020, Mass cytometry reveals cellular fingerprint associated with IgE+ peanut tolerance and allergy in early life, Nat. Commun., 11, 1091, 10.1038/s41467-020-14919-4 Lau, 2016, Mass cytometry reveals a distinct immunoprofile of operational tolerance in pediatric liver transplantation, Pediatr. Transplant., 20, 1072, 10.1111/petr.12795 Amouzgar, 2022, Supervised dimensionality reduction for exploration of single-cell data by HSS-LDA, Patterns, 3, 100536, 10.1016/j.patter.2022.100536 Hastie, 2009 Hoffman, 2016, variancePartition: interpreting drivers of variation in complex gene expression studies, BMC Bioinf., 17, 483, 10.1186/s12859-016-1323-z Xu, 2003, Measuring explained variation in linear mixed effects models, Stat. Med., 22, 3527, 10.1002/sim.1572 Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 550, 10.1186/s13059-014-0550-8 Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616 Seiler, 2021, CytoGLMM: conditional differential analysis for flow and mass cytometry experiments, BMC Bioinf., 22, 137, 10.1186/s12859-021-04067-x Fontenot, 2003, Foxp3 programs the development and function of CD4+CD25+ regulatory T cells, Nat. Immunol., 4, 330, 10.1038/ni904 Han, 2012 De Serres, 2012, Immune profile of pediatric renal transplant recipients following alemtuzumab induction, J. Am. Soc. Nephrol., 23, 174, 10.1681/ASN.2011040360 Schulz-Juergensen, 2013, Markers of operational immune tolerance after pediatric liver transplantation in patients under immunosuppression, Pediatr. Transplant., 17, 348, 10.1111/petr.12079 Stenard, 2009, Decreases in circulating CD4+CD25hiFOXP3+ cells and increases in intragraft FOXP3+ cells accompany allograft rejection in pediatric liver allograft recipients, Pediatr. Transplant., 13, 70, 10.1111/j.1399-3046.2008.00917.x Kumar, 2022, Pro-Inflammatory Derangement of the Immuno-Interactome in Heart Failure, Front. Immunol., 13, 817514, 10.3389/fimmu.2022.817514 Kim, 2022, Alterations in the immune phenotype of thymectomized children and the development of atopic disorders after heart transplantation, Pediatr. Transplant., 26, e14252, 10.1111/petr.14252 Porcu, 2021, Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome, Nat. Commun., 12, 5647, 10.1038/s41467-021-25805-y Brouard, 2012, The natural history of clinical operational tolerance after kidney transplantation through twenty-seven cases, Am. J. Transplant., 12, 3296, 10.1111/j.1600-6143.2012.04249.x Chandrasekharan, 2013, Achieving operational tolerance in transplantation: how can lessons from the clinic inform research directions?, Transpl. Int., 26, 576, 10.1111/tri.12081 Feng, 2012, Complete immunosuppression withdrawal and subsequent allograft function among pediatric recipients of parental living donor liver transplants, JAMA, 307, 283, 10.1001/jama.2011.2014 Kim, 2018, Clinical significance of CCR7(+)CD8(+) T cells in kidney transplant recipients with allograft rejection, Sci. Rep., 8, 8827, 10.1038/s41598-018-27141-6 Betjes, 2020, High numbers of differentiated CD28null CD8+ T cells are associated with a lowered risk for late rejection and graft loss after kidney transplantation, PLoS One, 15, e0228096, 10.1371/journal.pone.0228096 Morgun, 2006, Molecular profiling improves diagnoses of rejection and infection in transplanted organs, Circ. Res., 98, e74, 10.1161/01.RES.0000228714.15691.8a Khatri, 2013, A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation, J. Exp. Med., 210, 2205, 10.1084/jem.20122709 Liu, 2023, Liver graft injury caused by de novo donor-specific HLA antibodies in pediatric liver transplant recipients with low, moderate, and high immunologic risk, Am. J. Surg., 225, 275, 10.1016/j.amjsurg.2022.09.007 Webber, 2018, Pediatric heart transplantation across a positive crossmatch: First year results from the CTOTC-04 multi-institutional study, Am. J. Transplant., 18, 2148, 10.1111/ajt.14876 Chen, 2019, Acute cellular rejection treatment outcomes stratified by Banff grade in pediatric kidney transplant, Pediatr. Transplant., 23, e13334, 10.1111/petr.13334 Twombley, 2013, Acute antibody-mediated rejection in pediatric kidney transplants: a single center experience, Pediatr. Transplant., 17, E149, 10.1111/petr.12129 Bettelli, 2006, Reciprocal developmental pathways for the generation of pathogenic effector TH17 and regulatory T cells, Nature, 441, 235, 10.1038/nature04753 Du, 2008, Isoform-specific inhibition of ROR alpha-mediated transcriptional activation by human FOXP3, J. Immunol., 180, 4785, 10.4049/jimmunol.180.7.4785 Zhou, 2008, TGF-beta-induced Foxp3 inhibits T(H)17 cell differentiation by antagonizing RORgammat function, Nature, 453, 236, 10.1038/nature06878 Laurence, 2007, Interleukin-2 signaling via STAT5 constrains T helper 17 cell generation, Immunity, 26, 371, 10.1016/j.immuni.2007.02.009 2019 Braza, 2015, Central Role of CD45RA- Foxp3hi Memory Regulatory T Cells in Clinical Kidney Transplantation Tolerance, J. Am. Soc. Nephrol., 26, 1795, 10.1681/ASN.2014050480 Fribourg, 2019, T-cell exhaustion correlates with improved outcomes in kidney transplant recipients, Kidney Int., 96, 436, 10.1016/j.kint.2019.01.040 Ishiyama, 2022, Mass cytometry reveals single-cell kinetics of cytotoxic lymphocyte evolution in CMV-infected renal transplant patients, Proc. Natl. Acad. Sci. USA, 119, 10.1073/pnas.2116588119 Stern, 2022, Immunoprofiling reveals cell subsets associated with the trajectory of cytomegalovirus reactivation post stem cell transplantation, Nat. Commun., 13, 2603, 10.1038/s41467-022-29943-9 Ung, 2022, Adaptation of Imaging Mass Cytometry to Explore the Single Cell Alloimmune Landscape of Liver Transplant Rejection, Front. Immunol., 13, 831103, 10.3389/fimmu.2022.831103 Schuyler, 2019, Minimizing Batch Effects in Mass Cytometry Data, Front. Immunol., 10, 2367, 10.3389/fimmu.2019.02367 Ellis, 2022 Melville, 2021 Ripley, 2022 Venables, 2002 Bendall, 2011, Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum, Science, 332, 687, 10.1126/science.1198704