Publications by authors named "David A Hafler"

214 Publications

Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells.

JCI Insight 2021 Jun 22;6(12). Epub 2021 Jun 22.

Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA.

The skin lesion erythema migrans (EM) is an initial sign of the Ixodes tick-transmitted Borreliella spirochetal infection known as Lyme disease. T cells and innate immune cells have previously been shown to predominate the EM lesion and promote the reaction. Despite the established importance of B cells and antibodies in preventing infection, the role of B cells in the skin immune response to Borreliella is unknown. Here, we used single-cell RNA-Seq in conjunction with B cell receptor (BCR) sequencing to immunophenotype EM lesions and their associated B cells and BCR repertoires. We found that B cells were more abundant in EM in comparison with autologous uninvolved skin; many were clonally expanded and had circulating relatives. EM-associated B cells upregulated the expression of MHC class II genes and exhibited preferential IgM isotype usage. A subset also exhibited low levels of somatic hypermutation despite a gene expression profile consistent with memory B cells. Our study demonstrates that single-cell gene expression with paired BCR sequencing can be used to interrogate the sparse B cell populations in human skin and reveals that B cells in the skin infection site in early Lyme disease expressed a phenotype consistent with local antigen presentation and antibody production.
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http://dx.doi.org/10.1172/jci.insight.148035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262471PMC
June 2021

Cutting Edge: Distinct B Cell Repertoires Characterize Patients with Mild and Severe COVID-19.

J Immunol 2021 May 28. Epub 2021 May 28.

Department of Pathology, Yale School of Medicine, New Haven, CT;

Protective immunity against COVID-19 likely depends on the production of SARS-CoV-2-specific plasma cells and memory B cells postinfection or postvaccination. Previous work has found that germinal center reactions are disrupted in severe COVID-19. This may adversely affect long-term immunity against reinfection. Consistent with an extrafollicular B cell response, patients with severe COVID-19 have elevated frequencies of clonally expanded, class-switched, unmutated plasmablasts. However, it is unclear whether B cell populations in individuals with mild COVID-19 are similarly skewed. In this study, we use single-cell RNA sequencing of B cells to show that in contrast to patients with severe COVID-19, subjects with mildly symptomatic COVID-19 have B cell repertoires enriched for clonally diverse, somatically hypermutated memory B cells ∼30 d after the onset of symptoms. This provides evidence that B cell responses are less disrupted in mild COVID-19 and result in the production of memory B cells.
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http://dx.doi.org/10.4049/jimmunol.2100135DOI Listing
May 2021

NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data.

Commun Biol 2021 May 26;4(1):629. Epub 2021 May 26.

Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA.

The increasing availability of single-cell data revolutionizes the understanding of biological mechanisms at cellular resolution. For differential expression analysis in multi-subject single-cell data, negative binomial mixed models account for both subject-level and cell-level overdispersions, but are computationally demanding. Here, we propose an efficient NEgative Binomial mixed model Using a Large-sample Approximation (NEBULA). The speed gain is achieved by analytically solving high-dimensional integrals instead of using the Laplace approximation. We demonstrate that NEBULA is orders of magnitude faster than existing tools and controls false-positive errors in marker gene identification and co-expression analysis. Using NEBULA in Alzheimer's disease cohort data sets, we found that the cell-level expression of APOE correlated with that of other genetic risk factors (including CLU, CST3, TREM2, C1q, and ITM2B) in a cell-type-specific pattern and an isoform-dependent manner in microglia. NEBULA opens up a new avenue for the broad application of mixed models to large-scale multi-subject single-cell data.
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http://dx.doi.org/10.1038/s42003-021-02146-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8155058PMC
May 2021

Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children.

Immunity 2021 05 13;54(5):1083-1095.e7. Epub 2021 Apr 13.

Department of Pediatrics, Yale University School of Medicine, New Haven, CT, 06520, USA.

Multisystem inflammatory syndrome in children (MIS-C) is a life-threatening post-infectious complication occurring unpredictably weeks after mild or asymptomatic SARS-CoV-2 infection. We profiled MIS-C, adult COVID-19, and healthy pediatric and adult individuals using single-cell RNA sequencing, flow cytometry, antigen receptor repertoire analysis, and unbiased serum proteomics, which collectively identified a signature in MIS-C patients that correlated with disease severity. Despite having no evidence of active infection, MIS-C patients had elevated S100A-family alarmins and decreased antigen presentation signatures, indicative of myeloid dysfunction. MIS-C patients showed elevated expression of cytotoxicity genes in NK and CD8 T cells and expansion of specific IgG-expressing plasmablasts. Clinically severe MIS-C patients displayed skewed memory T cell TCR repertoires and autoimmunity characterized by endothelium-reactive IgG. The alarmin, cytotoxicity, TCR repertoire, and plasmablast signatures we defined have potential for application in the clinic to better diagnose and potentially predict disease severity early in the course of MIS-C.
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http://dx.doi.org/10.1016/j.immuni.2021.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043654PMC
May 2021

Clinical Significance of PDCD4 in Melanoma by Subcellular Expression and in Tumor-Associated Immune Cells.

Cancers (Basel) 2021 Mar 2;13(5). Epub 2021 Mar 2.

Department of Medicine (Medical Oncology), Yale University School of Medicine, New Haven, CT 06510, USA.

Little is known about the subcellular localization and function of programmed cell death 4 (PDCD4) in melanoma. Our past studies suggest PDCD4 interacts with Pleckstrin Homology Domain Containing A5 (PLEKHA5) to influence melanoma brain metastasis outcomes, as high intracranial PDCD4 expression leads to improved survival. We aimed to define the subcellular distribution of PDCD4 in melanoma and in the tumor microenvironment during neoplastic progression and its impact on clinical outcomes. We analyzed multiple tissue microarrays with well-annotated clinicopathological variables using quantitative immunofluorescence and evaluated single-cell RNA-sequencing on a brain metastasis sample to characterize PDCD4+ immune cell subsets. We demonstrate differences in PDCD4 expression during neoplastic progression, with high tumor and stromal PDCD4 levels associated with improved survival in primary melanomas and in intracranial metastases, but not in extracranial metastatic disease. While the expression of PDCD4 is well-documented on CD8+ T cells and natural killer cells, we show that it is also found on B cells and mast cells. PDCD4 expression in the tumor microenvironment is associated with increased immune cell infiltration. Further studies are needed to define the interaction of PDCD4 and PLEKHA5 and to evaluate the utility of this pathway as a therapeutic target in melanoma brain metastasis.
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http://dx.doi.org/10.3390/cancers13051049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7958624PMC
March 2021

Circulating clonally expanded T cells reflect functions of tumor-infiltrating T cells.

J Exp Med 2021 Apr;218(4)

Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT.

Understanding the relationship between tumor and peripheral immune environments could allow longitudinal immune monitoring in cancer. Here, we examined whether T cells that share the same TCRαβ and are found in both tumor and blood can be interrogated to gain insight into the ongoing tumor T cell response. Paired transcriptome and TCRαβ repertoire of circulating and tumor-infiltrating T cells were analyzed at the single-cell level from matched tumor and blood from patients with metastatic melanoma. We found that in circulating T cells matching clonally expanded tumor-infiltrating T cells (circulating TILs), gene signatures of effector functions, but not terminal exhaustion, reflect those observed in the tumor. In contrast, features of exhaustion are displayed predominantly by tumor-exclusive T cells. Finally, genes associated with a high degree of blood-tumor TCR sharing were overexpressed in tumor tissue after immunotherapy. These data demonstrate that circulating TILs have unique transcriptional patterns that may have utility for the interrogation of T cell function in cancer immunotherapy.
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http://dx.doi.org/10.1084/jem.20200921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7933991PMC
April 2021

Post-infectious inflammatory disease in MIS-C features elevated cytotoxicity signatures and autoreactivity that correlates with severity.

medRxiv 2020 Dec 4. Epub 2020 Dec 4.

Multisystem inflammatory syndrome in children (MIS-C) is a life-threatening post-infectious complication occurring unpredictably weeks after mild or asymptomatic SARS-CoV2 infection in otherwise healthy children. Here, we define immune abnormalities in MIS-C compared to adult COVID-19 and pediatric/adult healthy controls using single-cell RNA sequencing, antigen receptor repertoire analysis, unbiased serum proteomics, and in vitro assays. Despite no evidence of active infection, we uncover elevated S100A-family alarmins in myeloid cells and marked enrichment of serum proteins that map to myeloid cells and pathways including cytokines, complement/coagulation, and fluid shear stress in MIS-C patients. Moreover, NK and CD8 T cell cytotoxicity genes are elevated, and plasmablasts harboring IgG1 and IgG3 are expanded. Consistently, we detect elevated binding of serum IgG from severe MIS-C patients to activated human cardiac microvascular endothelial cells in culture. Thus, we define immunopathology features of MIS-C with implications for predicting and managing this SARS-CoV2-induced critical illness in children.
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http://dx.doi.org/10.1101/2020.12.01.20241364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7724682PMC
December 2020

Oleic acid restores suppressive defects in tissue-resident FOXP3 Tregs from patients with multiple sclerosis.

J Clin Invest 2021 Jan;131(2)

Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA.

FOXP3+ Tregs rely on fatty acid β-oxidation-driven (FAO-driven) oxidative phosphorylation (OXPHOS) for differentiation and function. Recent data demonstrate a role for Tregs in the maintenance of tissue homeostasis, with tissue-resident Tregs possessing tissue-specific transcriptomes. However, specific signals that establish tissue-resident Treg programs remain largely unknown. Tregs metabolically rely on FAO, and considering the lipid-rich environments of tissues, we hypothesized that environmental lipids drive Treg homeostasis. First, using human adipose tissue to model tissue residency, we identified oleic acid as the most prevalent free fatty acid. Mechanistically, oleic acid amplified Treg FAO-driven OXPHOS metabolism, creating a positive feedback mechanism that increased the expression of FOXP3 and phosphorylation of STAT5, which enhanced Treg-suppressive function. Comparing the transcriptomic program induced by oleic acid with proinflammatory arachidonic acid, we found that Tregs sorted from peripheral blood and adipose tissue of healthy donors transcriptomically resembled the Tregs treated in vitro with oleic acid, whereas Tregs from patients with multiple sclerosis (MS) more closely resembled an arachidonic acid transcriptomic profile. Finally, we found that oleic acid concentrations were reduced in patients with MS and that exposure of MS Tregs to oleic acid restored defects in their suppressive function. These data demonstrate the importance of fatty acids in regulating tissue inflammatory signals.
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http://dx.doi.org/10.1172/JCI138519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7810477PMC
January 2021

Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells.

bioRxiv 2020 Oct 31. Epub 2020 Oct 31.

While inhibition of T cell co-inhibitory receptors has revolutionized cancer therapy, the mechanisms governing their expression on human T cells have not been elucidated. Type 1 interferon (IFN-I) modulates T cell immunity in viral infection, autoimmunity, and cancer, and may facilitate induction of T cell exhaustion in chronic viral infection . Here we show that IFN-I regulates co-inhibitory receptors expression on human T cells, inducing PD-1/TIM-3/LAG-3 while surprisingly inhibiting TIGIT expression. High-temporal-resolution mRNA profiling of IFN-I responses enabled the construction of dynamic transcriptional regulatory networks uncovering three temporal transcriptional waves. Perturbation of key transcription factors on human primary T cells revealed both canonical and non-canonical IFN-I transcriptional regulators, and identified unique regulators that control expression of co-inhibitory receptors. To provide direct in vivo evidence for the role of IFN-I on co-inhibitory receptors, we then performed single cell RNA-sequencing in subjects infected with SARS-CoV-2, where viral load was strongly associated with T cell IFN-I signatures. We found that the dynamic IFN-I response in vitro closely mirrored T cell features with acute IFN-I linked viral infection, with high LAG3 and decreased TIGIT expression. Finally, our gene regulatory network identified SP140 as a key regulator for differential LAG3 and TIGIT expression. The construction of co-inhibitory regulatory networks induced by IFN-I with identification of unique transcription factors controlling their expression may provide targets for enhancement of immunotherapy in cancer, infectious diseases, and autoimmunity.
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http://dx.doi.org/10.1101/2020.10.30.362947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605554PMC
October 2020

Two genetic variants explain the association of European ancestry with multiple sclerosis risk in African-Americans.

Sci Rep 2020 10 9;10(1):16902. Epub 2020 Oct 9.

Department of Genetics, Harvard Medical School, New Research Building, Boston, MA, 02115, USA.

Epidemiological studies have suggested differences in the rate of multiple sclerosis (MS) in individuals of European ancestry compared to African ancestry, motivating genetic scans to identify variants that could contribute to such patterns. In a whole-genome scan in 899 African-American cases and 1155 African-American controls, we confirm that African-Americans who inherit segments of the genome of European ancestry at a chromosome 1 locus are at increased risk for MS [logarithm of odds (LOD) = 9.8], although the signal weakens when adding an additional 406 cases, reflecting heterogeneity in the two sets of cases [logarithm of odds (LOD) = 2.7]. The association in the 899 individuals can be fully explained by two variants previously associated with MS in European ancestry individuals. These variants tag a MS susceptibility haplotype associated with decreased CD58 gene expression (odds ratio of 1.37; frequency of 84% in Europeans and 22% in West Africans for the tagging variant) as well as another haplotype near the FCRL3 gene (odds ratio of 1.07; frequency of 49% in Europeans and 8% in West Africans). Controlling for all other genetic and environmental factors, the two variants predict a 1.44-fold higher rate of MS in European-Americans compared to African-Americans.
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http://dx.doi.org/10.1038/s41598-020-74035-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7547691PMC
October 2020

Epigenetic fine-mapping: identification of causal mechanisms for autoimmunity.

Curr Opin Immunol 2020 12 23;67:50-56. Epub 2020 Sep 23.

Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.

Genome-wide association studies (GWAS) have identified genetic susceptibility loci for a variety of autoimmune and inflammatory diseases. These studies confirm the fundamental genetic basis of individual autoimmune diseases, and also point to shared etiological mechanisms across the spectrum of autoimmunity. While hundreds of genetic loci have been implicated in autoimmune diseases, the translation of individual susceptibility loci into specific molecular mechanisms for individual diseases remains difficult. This review highlights recent advances in the genetics of autoimmune disease, and the emerging use of epigenetic techniques to identify pathogenic cell types and causal molecular mechanisms of autoimmunity.
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http://dx.doi.org/10.1016/j.coi.2020.09.002DOI Listing
December 2020

Transcriptomic and clonal characterization of T cells in the human central nervous system.

Sci Immunol 2020 09;5(51)

Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA.

T cells provide critical immune surveillance to the central nervous system (CNS), and the cerebrospinal fluid (CSF) is thought to be a main route for their entry. Further characterization of the state of T cells in the CSF in healthy individuals is important for understanding how T cells provide protective immune surveillance without damaging the delicate environment of the CNS and providing tissue-specific context for understanding immune dysfunction in neuroinflammatory disease. Here, we have profiled T cells in the CSF of healthy human donors and have identified signatures related to cytotoxic capacity and tissue adaptation that are further exemplified in clonally expanded CSF T cells. By comparing profiles of clonally expanded T cells obtained from the CSF of patients with multiple sclerosis (MS) and healthy donors, we report that clonally expanded T cells from the CSF of patients with MS have heightened expression of genes related to T cell activation and cytotoxicity.
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http://dx.doi.org/10.1126/sciimmunol.abb8786DOI Listing
September 2020

CXCR3+ T cells in multiple sclerosis correlate with reduced diversity of the gut microbiome.

J Transl Autoimmun 2020 20;3:100032. Epub 2019 Dec 20.

Department of Neurology, Yale University School of Medicine, New Haven, CT, 06511, USA.

Multiple sclerosis (MS) is a genetically mediated autoimmune disease characterized by inflammation in the central nervous system (CNS). Disease onset is thought to occur when autoreactive T cells orchestrate a cascade of events in the CNS resulting in white and grey matter inflammation and axonal degeneration. It is unclear what triggers the activation of CNS-reactive T cells and their polarization into inflammatory subsets. Mounting evidence from animal and human studies supports the hypothesis that the gut microbiome affects MS pathogenesis. We investigated the association between the gut microbiome and inflammatory T cell subsets in relapsing-remitting MS patients and healthy controls. Gut microbiome composition was characterized by sequencing the V4 region of the 16S rRNA gene from fecal DNA, and inflammatory T cell subsets were characterized by flow cytometry. We identified an altered gut microbiome in MS patients, including decreased abundance of and an unidentified genus. Among circulating immune cells, patients had increased expression of CXCR3 in both CD4 and CD8 T cells, and both CD4CXCR3 and CD8CXCR3 populations expressing the gut-homing α4β7 integrin receptor were increased. Finally, we show that alpha diversity inversely correlated with a CXCR3 Th1 phenotype in MS. These findings indicate the presence of an aberrant gut-immune axis in patients with MS.
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http://dx.doi.org/10.1016/j.jtauto.2019.100032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7388357PMC
December 2019

Differential expression of the T-cell inhibitor TIGIT in glioblastoma and MS.

Neurol Neuroimmunol Neuroinflamm 2020 05 8;7(3). Epub 2020 Apr 8.

From the Departments of Neurology (L.E.L., B.A.L., C.P., D.D., B.H., V.P.K., G.P., K.R., D.A.H., D.P.); Immunobiology (L.E.L., B.A.L., B.H., K.R., D.A.H.); and Pathology (A.H.), Yale School of Medicine, New Haven, CT.

Objective: To identify coinhibitory immune pathways important in the brain, we hypothesized that comparison of T cells in lesions from patients with MS with tumor-infiltrating T cells (TILs) from patients with glioblastoma multiforme may reveal novel targets for immunotherapy.

Methods: We collected fresh surgical resections and matched blood from patients with glioblastoma, blood and unmatched postmortem CNS tissue from patients with MS, and blood from healthy donors. The expression of TIGIT, CD226, and their shared ligand CD155 as well as PD-1 and PDL1 was assessed by both immunohistochemistry and flow cytometry.

Results: We found that TIGIT was highly expressed on glioblastoma-infiltrating T cells, but was near-absent from MS lesions. Conversely, lymphocytic expression of PD-1/PD-L1 was comparable between the 2 diseases. Moreover, TIGIT was significantly upregulated in circulating lymphocytes of patients with glioblastoma compared with healthy controls, suggesting recirculation of TILs. Expression of CD226 was also increased in glioblastoma, but this costimulatory receptor was expressed alongside TIGIT in the majority of tumor-infiltrating T cells, suggesting functional counteraction.

Conclusions: The opposite patterns of TIGIT expression in the CNS between MS and glioblastoma reflects the divergent features of the immune response in these 2 CNS diseases. These data raise the possibility that anti-TIGIT therapy may be beneficial for patients with glioblastoma.
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http://dx.doi.org/10.1212/NXI.0000000000000712DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7188477PMC
May 2020

Siponimod Chips Away at Progressive MS.

Cell 2019 Dec 12;179(7):1440. Epub 2019 Dec 12.

Yale University, New Haven, CT, USA.

Progressive multiple sclerosis (PMS) causes slow accumulation of neurologic disability and has been refractory to treatment with the immunomodulatory medications that effectively control relapsing MS. Siponimod modestly slowed the rate of disability progression among PMS patients who had inflammatory disease activity, evidenced by new or gadolinium-enhancing MRI lesions. To view this Bench to Bedside, open or download the PDF.
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http://dx.doi.org/10.1016/j.cell.2019.11.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8023412PMC
December 2019

Author Correction: Activated β-catenin in Foxp3 regulatory T cells links inflammatory environments to autoimmunity.

Nat Immunol 2019 07;20(7):943

Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41590-019-0438-6DOI Listing
July 2019

Corrigendum to "Fingolimod modulates T cell phenotype and regulatory T cell plasticity in vivo" [Yjaut 96C (2019) 40-49].

J Autoimmun 2019 Aug 18;102:179. Epub 2019 May 18.

Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jaut.2019.05.008DOI Listing
August 2019

Latent autoimmunity across disease-specific boundaries in at-risk first-degree relatives of SLE and RA patients.

EBioMedicine 2019 Apr 3;42:76-85. Epub 2019 Apr 3.

University of Colorado, Aurora, CO, USA.

Background: Autoimmune disease prevention requires tools to assess an individual's risk of developing a specific disease. One tool is disease-associated autoantibodies, which accumulate in an asymptomatic preclinical period. However, patients sometimes exhibit autoantibodies associated with a different disease classification. When and how these alternative autoantibodies first appear remain unknown. This cross-sectional study characterizes alternative autoimmunity, and associated genetic and environmental factors, in unaffected first-degree relatives (FDRs) of patients, who exhibit increased future risk for the same disease.

Methods: Samples (n = 1321) from disease-specific autoantibody-positive (aAb+) systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and type 1 diabetes (T1D) patients; and unaffected aAb+ and autoantibody-negative (aAb-) SLE and RA FDRs were tested for SLE, RA, and T1D aAbs, as well as anti-tissue transglutaminase, anti-cardiolipin and anti-thyroperoxidase. FDR SLE and RA genetic risk scores (GRS) were calculated.

Findings: Alternative autoimmunity occurred in SLE patients (56%) and FDRs (57·4%), RA patients (32·6%) and FDRs (34·8%), and T1D patients (43%). Expanded autoimmunity, defined as autoantibodies spanning at least two other diseases, occurred in 18·5% of SLE patients, 16·4% of SLE FDRs, 7·8% of RA patients, 5·3% of RA FDRs, and 10·8% of T1D patients. SLE FDRs were more likely to have alternative (odds ratio [OR] 2·44) and expanded (OR 3·27) autoimmunity than RA FDRs. Alternative and expanded autoimmunity were associated with several environmental exposures. Alternative autoimmunity was associated with a higher RA GRS in RA FDRs (OR 1·41), and a higher SLE GRS in aAb+ RA FDRs (OR 1·87), but not in SLE FDRs.

Interpretation: Autoimmunity commonly crosses disease-specific boundaries in systemic (RA, SLE) and organ-specific (T1D) autoimmune diseases. Alternative autoimmunity is more common in SLE FDRs than RA FDRs, and is influenced by genetic and environmental factors. These findings have substantial implications for preclinical disease pathogenesis and autoimmune disease prevention studies. FUND: NIH U01AI101981, R01AR051394, U19AI082714, P30AR053483, P30GM103510, U54GM104938, U01AI101934, R01AI024717, U01AI130830, I01BX001834, & U01HG008666.
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http://dx.doi.org/10.1016/j.ebiom.2019.03.063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6491794PMC
April 2019

From Big Data to Precision Medicine.

Front Med (Lausanne) 2019 1;6:34. Epub 2019 Mar 1.

Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom.

For over a decade the term "Big data" has been used to describe the rapid increase in volume, variety and velocity of information available, not just in medical research but in almost every aspect of our lives. As scientists, we now have the capacity to rapidly generate, store and analyse data that, only a few years ago, would have taken many years to compile. However, "Big data" no longer means what it once did. The term has expanded and now refers not to just large data volume, but to our increasing ability to analyse and interpret those data. Tautologies such as "data analytics" and "data science" have emerged to describe approaches to the volume of available information as it grows ever larger. New methods dedicated to improving data collection, storage, cleaning, processing and interpretation continue to be developed, although not always by, or for, medical researchers. Exploiting new tools to extract meaning from large volume information has the potential to drive real change in clinical practice, from personalized therapy and intelligent drug design to population screening and electronic health record mining. As ever, where new technology promises "Big Advances," significant challenges remain. Here we discuss both the opportunities and challenges posed to biomedical research by our increasing ability to tackle large datasets. Important challenges include the need for standardization of data content, format, and clinical definitions, a heightened need for collaborative networks with sharing of both data and expertise and, perhaps most importantly, a need to reconsider how and when analytic methodology is taught to medical researchers. We also set "Big data" analytics in context: recent advances may appear to promise a revolution, sweeping away conventional approaches to medical science. However, their real promise lies in their synergy with, not replacement of, classical hypothesis-driven methods. The generation of novel, data-driven hypotheses based on interpretable models will always require stringent validation and experimental testing. Thus, hypothesis-generating research founded on large datasets adds to, rather than replaces, traditional hypothesis driven science. Each can benefit from the other and it is through using both that we can improve clinical practice.
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http://dx.doi.org/10.3389/fmed.2019.00034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6405506PMC
March 2019

Aedes aegypti AgBR1 antibodies modulate early Zika virus infection of mice.

Nat Microbiol 2019 06 11;4(6):948-955. Epub 2019 Mar 11.

Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA.

A recent epidemic of Zika virus in the Americas, affecting well over a million people, caused substantial mortality and morbidity, including Guillain-Barre syndrome, microcephaly and other fetal developmental defects. Preventive and therapeutic measures that specifically target the virus are not readily available. The transmission of Zika virus is predominantly mosquito-borne, and Aedes aegypti mosquitoes serve as a key vector for Zika virus. Here, to identify salivary factors that modulate mosquito-borne Zika virus infection, we focused on antigenic proteins in mice that were repeatedly bitten by mosquitoes and developed antibodies against salivary proteins. Using a yeast surface display screen, we identified five antigenic A. aegypti salivary proteins in mice. Antiserum against one of these five proteins-A. aegypti bacteria-responsive protein 1 (AgBR1)-suppressed early inflammatory responses in the skin of mice bitten by Zika-virus-infected mosquitoes. AgBR1 antiserum also partially protected mice from lethal mosquito-borne-but not needle-injected-Zika virus infection. These data suggest that AgBR1 is a target for the prevention of mosquito-transmitted Zika virus infection.
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http://dx.doi.org/10.1038/s41564-019-0385-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6533137PMC
June 2019

Autoantibodies against Neurologic Antigens in Nonneurologic Autoimmunity.

J Immunol 2019 04 1;202(8):2210-2219. Epub 2019 Mar 1.

Department of Neurology, Yale School of Medicine, New Haven, CT 06511;

The aim of this study was to test whether autoantibodies against neurologic surface Ags are found in nonneurologic autoimmune diseases, indicating a broader loss of tolerance. Patient and matched healthy donor (HD) sera were derived from four large cohorts: 1) rheumatoid arthritis (RA) ( = 194, HD = 64), 2) type 1 diabetes (T1D) ( = 200, HD = 200), 3) systemic lupus erythematosus (SLE) ( = 200, HD = 67; neuro-SLE = 49, HD = 33), and 4) a control cohort of neurologic autoimmunity (relapsing-remitting multiple sclerosis [MS] = 110, HD = 110; primary progressive MS = 9; secondary progressive MS = 10; neuromyelitis optica spectrum disorders = 15; and other neurologic disorders = 26). Screening of 1287 unique serum samples against four neurologic surface Ags (myelin oligodendrocyte glycoprotein, aquaporin 4, acetylcholine receptor, and muscle-specific kinase) was performed with live cell-based immunofluorescence assays using flow cytometry. Positive samples identified in the screening were further validated using autoantibody titer quantification by serial dilutions or radioimmunoassay. Autoantibodies against neurologic surface Ags were not observed in RA and T1D patients, whereas SLE patients harbored such autoantibodies in rare cases (2/200, 1%). Within the CNS autoimmunity control cohort, autoantibodies against aquaporin 4 and high-titer Abs against myelin oligodendrocyte glycoprotein were, as expected, specific for neuromyelitis optica spectrum disorders. We conclude that neurologic autoantibodies do not cross disease barriers in RA and T1D. The finding of mildly increased neurologic autoantibodies in SLE may be consistent with a broader loss of B cell tolerance in this form of systemic autoimmunity.
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http://dx.doi.org/10.4049/jimmunol.1801295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6452031PMC
April 2019

Multiple sclerosis enters a grey area.

Nature 2019 02;566(7745):465-466

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http://dx.doi.org/10.1038/d41586-019-00563-6DOI Listing
February 2019

TIGIT signaling restores suppressor function of Th1 Tregs.

JCI Insight 2019 Feb 7;4(3). Epub 2019 Feb 7.

Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA.

Th1 Tregs are characterized by the acquisition of proinflammatory cytokine secretion and reduced suppressor activity. Th1 Tregs are found at increased frequency in autoimmune diseases, including type 1 diabetes and multiple sclerosis (MS). We have previously reported that in vitro stimulation with IL-12 recapitulates the functional and molecular features of MS-associated Th1 Tregs, revealing a central role for hyperactivation of the Akt pathway in their induction. TIGIT is a newly identified coinhibitory receptor that marks Tregs that specifically control Th1 and Th17 responses. Here, we report that signaling through TIGIT counteracts the action of IL-12 in inducing the Th1 program. Specifically, TIGIT signaling represses production of IFN-γ and T-bet expression and restores suppressor function in Tregs treated with IL-12. FoxO1 functional inhibition abolishes the protective effect of TIGIT, indicating that TIGIT signaling promotes FoxO1 nuclear localization. Consistent with this observation, signaling through TIGIT leads to a rapid suppression of Akt function and FoxO1 phosphorylation. Finally, TIGIT stimulation reduces the production of IFN-γ and corrects the suppressor defect of Tregs from patients with MS. Our results indicate an important role for TIGIT in controlling the functional stability of Tregs through repression of Akt, suggesting that the TIGIT pathway could be targeted for immunomodulatory therapies in human autoimmune disorders.
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http://dx.doi.org/10.1172/jci.insight.124427DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6413794PMC
February 2019

Enhanced astrocyte responses are driven by a genetic risk allele associated with multiple sclerosis.

Nat Commun 2018 12 17;9(1):5337. Epub 2018 Dec 17.

Department of Neurology, Yale School of Medicine, New Haven, CT, 06511, USA.

Epigenetic annotation studies of genetic risk variants for multiple sclerosis (MS) implicate dysfunctional lymphocytes in MS susceptibility; however, the role of central nervous system (CNS) cells remains unclear. We investigated the effect of the risk variant, rs7665090, located near NFKB1, on astrocytes. We demonstrated that chromatin is accessible at the risk locus, a prerequisite for its impact on astroglial function. The risk variant was associated with increased NF-κB signaling and target gene expression, driving lymphocyte recruitment, in cultured human astrocytes and astrocytes within MS lesions, and with increased lesional lymphocytic infiltrates and lesion sizes. Thus, our study establishes a link between genetic risk for MS (rs7665090) and dysfunctional astrocyte responses associated with increased CNS access for peripheral immune cells. MS may therefore result from variant-driven dysregulation of the peripheral immune system and of the CNS, where perturbed CNS cell function aids in establishing local autoimmune inflammation.
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http://dx.doi.org/10.1038/s41467-018-07785-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297228PMC
December 2018

Activated β-catenin in Foxp3 regulatory T cells links inflammatory environments to autoimmunity.

Nat Immunol 2018 12 29;19(12):1391-1402. Epub 2018 Oct 29.

Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA.

Foxp3 regulatory T cells (T cells) are the central component of peripheral immune tolerance. Whereas a dysregulated T cytokine signature has been observed in autoimmune diseases, the regulatory mechanisms underlying pro- and anti-inflammatory cytokine production are elusive. Here, we identify an imbalance between the cytokines IFN-γ and IL-10 as a shared T signature present in patients with multiple sclerosis and under high-salt conditions. RNA-sequencing analysis on human T subpopulations revealed β-catenin as a key regulator of IFN-γ and IL-10 expression. The activated β-catenin signature was enriched in human IFN-γ T cells, as confirmed in vivo with T-specific β-catenin-stabilized mice exhibiting lethal autoimmunity with a dysfunctional T phenotype. Moreover, we identified prostaglandin E receptor 2 (PTGER2) as a regulator of IFN-γ and IL-10 production under a high-salt environment, with skewed activation of the β-catenin-SGK1-Foxo axis. Our findings reveal a novel PTGER2-β-catenin loop in T cells linking environmental high-salt conditions to autoimmunity.
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http://dx.doi.org/10.1038/s41590-018-0236-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240373PMC
December 2018

Single-cell RNA sequencing reveals microglia-like cells in cerebrospinal fluid during virologically suppressed HIV.

JCI Insight 2018 09 20;3(18). Epub 2018 Sep 20.

Department of Neurology.

Central nervous system (CNS) immune activation is an important driver of neuronal injury during several neurodegenerative and neuroinflammatory diseases. During HIV infection, CNS immune activation is associated with high rates of neurocognitive impairment, even during sustained long-term suppressive antiretroviral therapy (ART). However, the cellular subsets that drive immune activation and neuronal damage in the CNS during HIV infection and other neurological conditions remain unknown, in part because CNS cells are difficult to access in living humans. Using single-cell RNA sequencing (scRNA-seq) on cerebrospinal fluid (CSF) and blood from adults with and without HIV, we identified a rare (<5% of cells) subset of myeloid cells that are found only in CSF and that present a gene expression signature that overlaps significantly with neurodegenerative disease-associated microglia. This highlights the power of scRNA-seq of CSF to identify rare CNS immune cell subsets that may perpetuate neuronal injury during HIV infection and other conditions.
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http://dx.doi.org/10.1172/jci.insight.121718DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237230PMC
September 2018

Fingolimod modulates T cell phenotype and regulatory T cell plasticity in vivo.

J Autoimmun 2019 01 16;96:40-49. Epub 2018 Aug 16.

Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA. Electronic address:

Fingolimod is an approved therapeutic option for patients with relapsing-remitting multiple sclerosis that primarily functions by sequestering T cells in lymph nodes inhibiting their egress to the central nervous system. However, recent data suggests that Fingolimod may also directly affect the immune cell function. Here we examined the in vivo effects of Fingolimod in modulating the phenotype and function of T cell and Foxp3 regulatory T cell populations in patients with multiple sclerosis under Fingolimod treatment. Besides decreasing the cell numbers in peripheral blood and sera levels of pro-inflammatory cytokines, Fingolimod inhibited the expression of Th1 and Th17 cytokines on CD4 T cells and increased the expression of exhaustion markers. Furthermore, treatment increased the frequency of regulatory T cells in blood and inhibited the Th1-like phenotype that is characteristic of patients with multiple sclerosis, augmenting the expression of markers associated with increased suppressive function. Overall, our data suggest that Fingolimod performs other important immunomodulatory functions besides altering T cell migratory capacities, with consequences for other autoimmune pathologies characterized by excessive Th1/Th17 responses and Th1-like regulatory T cell effector phenotypes.
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http://dx.doi.org/10.1016/j.jaut.2018.08.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7882197PMC
January 2019

Regulatory T cells in autoimmune disease.

Nat Immunol 2018 07 20;19(7):665-673. Epub 2018 Jun 20.

Department of Neurology, Yale School of Medicine, New Haven, CN, USA.

In recent years, the understanding of regulatory T cell (T cell) biology has expanded considerably. Key observations have challenged the traditional definition of T cells and have provided insight into the underlying mechanisms responsible for the development of autoimmune diseases, with new therapeutic strategies that improve disease outcome. This Review summarizes the newer concepts of T cell instability, T cell plasticity and tissue-specific T cells, and their relationship to autoimmunity. Those three main concepts have changed the understanding of T cell biology: how they interact with other immune and non-immune cells; their functions in specific tissues; and the implications of this for the pathogenesis of autoimmune diseases.
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http://dx.doi.org/10.1038/s41590-018-0120-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7882196PMC
July 2018

Minimum Information about T Regulatory Cells: A Step toward Reproducibility and Standardization.

Front Immunol 2017 15;8:1844. Epub 2018 Jan 15.

Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboudumc, Nijmegen, Netherlands.

Cellular therapies with CD4+ T regulatory cells (Tregs) hold promise of efficacious treatment for the variety of autoimmune and allergic diseases as well as posttransplant complications. Nevertheless, current manufacturing of Tregs as a cellular medicinal product varies between different laboratories, which in turn hampers precise comparisons of the results between the studies performed. While the number of clinical trials testing Tregs is already substantial, it seems to be crucial to provide some standardized characteristics of Treg products in order to minimize the problem. We have previously developed reporting guidelines called minimum information about tolerogenic antigen-presenting cells, which allows the comparison between different preparations of tolerance-inducing antigen-presenting cells. Having this experience, here we describe another minimum information about Tregs (MITREG). It is important to note that MITREG does not dictate how investigators should generate or characterize Tregs, but it does require investigators to report their Treg data in a consistent and transparent manner. We hope this will, therefore, be a useful tool facilitating standardized reporting on the manufacturing of Tregs, either for research purposes or for clinical application. This way MITREG might also be an important step toward more standardized and reproducible testing of the Tregs preparations in clinical applications.
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http://dx.doi.org/10.3389/fimmu.2017.01844DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5775516PMC
January 2018
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