A comprehensive atlas of immunological differences between humans, mice and non-human primates, bioRxiv, 2019-03-12
Animal models are an integral part of the drug development and evaluation process. However, they are unsurprisingly imperfect reflections of humans, and the extent and nature of many immunological differences are unknown. With the rise of targeted and biological therapeutics, it is increasingly important that we understand the molecular differences in immunological behavior of humans and model organisms. Thus, we profiled a large number of healthy humans, along with three of the model organisms most similar to humans rhesus and cynomolgus macaques and African green monkeys; and the most widely used mammalian model mice. Using cross-species, universal phenotyping and signaling panels, we measured immune cell signaling responses to an array of 15 stimuli using CyTOF mass cytometry. We found numerous instances of different cellular phenotypes and immune signaling events occurring within and between species with likely effects on evaluation of therapeutics, and detail three examples (double-positive T cell frequency and signaling; granulocyte response to Bacillus anthracis antigen; and B cell subsets). We also explore the correlation of herpes simian B virus serostatus on the immune profile. The full dataset is available online at <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpsflowrepository.org>httpsflowrepository.org<jatsext-link> (accession FR-FCM-Z2ZY) and <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpsimmuneatlas.org>httpsimmuneatlas.org<jatsext-link>.
biorxiv immunology 100-200-users 2019Variation of immune cell responses in humans reveals sex-specific coordinated signaling across cell types, bioRxiv, 2019-03-09
Assessing the health and competence of the immune system is central to evaluating vaccination responses, autoimmune conditions, cancer prognosis and treatment. With an increasing number of studies examining immune dysregulation, there is a growing need for a curated reference of variation in immune parameters in healthy individuals. We used mass cytometry (CyTOF) to profile blood from 86 humans in response to 15 ex vivo immune stimuli. We present reference ranges for cell-specific immune markers and highlight differences that appear across sex and age. We identified modules of immune features that suggests there exists and underlying structure to the immune system based on signaling pathway responses across cell types. We observed increased MAPK signaling in inflammatory pathways in innate immune cells and greater overall coordination of immune cell responses in women. In contrast, men exhibited stronger STAT1 and TBK1 responses. These reference data are publicly available as a resource for immune profiling studies.
biorxiv immunology 0-100-users 2019B cells engineered to express pathogen-specific antibodies using CRISPRCas9 protect against infection, bioRxiv, 2019-02-06
Effective vaccines inducing lifelong protection against many important infections such as respiratory syncytial virus (RSV), human immunodeficiency virus (HIV), influenza and Epstein-Barr virus (EBV) are not yet available despite decades of research. As an alternative to a protective vaccine we developed a genetic engineering strategy in which CRISPRCas9 was utilized to replace endogenously-encoded antibodies with antibodies protective against RSV, HIV, influenza or EBV in primary human or murine B cells. The engineered antibodies were expressed in up to 59% of primary B cells under the control of endogenous regulatory elements, which maintained normal antibody expression and secretion. Importantly, a single transfer of murine B cells engineered to express an antibody protective against RSV resulted in potent and durable protection against RSV infection in immunocompromised hosts. This approach offers the opportunity to achieve sterilizing immunity against pathogens for which traditional vaccination has failed to induce or maintain protective antibody responses.
biorxiv immunology 0-100-users 2019Conduit integrity is compromised during acute lymph node expansion, bioRxiv, 2019-01-24
Lymph nodes (LNs) work as filtering organs, constantly sampling peripheral cues. This is facilitated by the conduit network, a parenchymal tubular-like structure formed of bundles of aligned extracellular matrix (ECM) fibrils ensheathed by fibroblastic reticular cells (FRCs). LNs undergo 5-fold expansion with every adaptive immune response and yet these ECM-rich structures are not permanently damaged. Whether conduit integrity and filtering functions are affected during cycles of LN expansion and resolution is not known. Here we show that the conduit structure is disrupted during acute LN expansion but FRC-FRC contacts remain intact. In homeostasis, polarised FRCs adhere to the underlying substrate to deposit ECM ba-solaterally. ECM production by FRCs is regulated by the C-type lectin CLEC-2, expressed by dendritic cells (DCs), at transcriptional and secretory levels. Inflamed LNs maintain conduit size-exclusion, but flow becomes leaky, which allows soluble antigens to reach more antigen-presenting cells. We show how dynamic communication between peripheral tissues and LNs changes during immune responses, and describe a mechanism that enables LNs to prevent inflammation-induced fibrosis.Highlights<jatslist list-type=bullet><jatslist-item>FRCs use polarized microtubule networks to guide matrix deposition<jatslist-item><jatslist-item>CLEC-2PDPN controls matrix production at transcriptional and post-transcriptional levels<jatslist-item><jatslist-item>FRCs halt matrix production and decouple from conduits during acute LN expansion<jatslist-item><jatslist-item>Conduits leak soluble antigen during acute LN expansion<jatslist-item>
biorxiv immunology 100-200-users 2019Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy, bioRxiv, 2018-12-21
SummaryClinical benefits to cytokine blockade in ileal Crohn’s disease (iCD) have been limited to a subset of patients. Whether cellular and molecular heterogeneity contributes to variability in treatment responses has been unclear. Using single cell technologies combining scRNAseq, CyTOF and multiplex tissue imaging, we mapped the cellular landscape of inflamed ileum lesions, adjacent non-inflamed ileum and matched circulating blood cells of iCD patients. In inflamed tissues, we identified a pathogenic module characterized by an inflammatory mononuclear phagocyte (Inf.MNP)-associated cellular response organized around inflammatory macrophages and mature dendritic cells in a subset of iCD patients. We confirmed the Inf.MNP-associated cellular response in 4 independent iCD cohorts (n=441) and showed that presence of this pathogenic module at diagnosis correlated with primary resistance to anti-TNF therapy. Single cell mapping of iCD tissues identifies a complex cellular signature of anti-TNF resistance thereby revealing novel biomarkers of treatment response and tailored therapeutic opportunities.
biorxiv immunology 0-100-users 2018Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy, bioRxiv, 2018-12-13
SummaryThe success of immunotherapy has led to a myriad of new clinical trials. Connected to these trials are efforts to discover biomarkers providing mechanistic insight and predictive signatures for personalization. Still, the plethora of immune monitoring technologies can face investigator bias, missing unanticipated cellular responses in limited clinical material. We here present a mass cytometry workflow for standardized, systems-level biomarker discovery in immunotherapy trials. To broadly enumerate human immune cell identity and activity, we established and extensively assessed a reference panel of 33 antibodies to cover major cell subsets, simultaneously quantifying activation and immune checkpoint molecules in a single assay. The resulting assay enumerated ≥ 98% of peripheral immune cells with ≥ 4 positively identifying antigens. Robustness and reproducibility were demonstrated on multiple samples types, across research centers and by orthogonal measurements. Using automated analysis, we monitored complex immune dynamics, identifying signatures in bone-marrow transplantation associated graft-versus-host disease. This validated and available workflow ensures comprehensive immunophenotypic analysis, data comparability and will accelerate biomarker discovery in immunomodulatory therapeutics.
biorxiv immunology 100-200-users 2018