Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells

Genome-wide association studies (GWASs) have uncovered hundreds of autoimmune disease-associated loci; however, the causal genetic variants within each locus are mostly unknown. Here, we perform high-throughput allele-specific reporter assays to prioritize disease-associated variants for five autoimmune diseases. By examining variants that both promote allele-specific reporter expression and are located in accessible chromatin, we identify 60 putatively causal variants that enrich for statistically fine-mapped variants by up to 57.8-fold. We introduced the risk allele of a prioritized variant (rs72928038) into a human T cell line and deleted the orthologous sequence in mice, both resulting in reduced BACH2 expression. Naive CD8 T cells from mice containing the deletion had reduced expression of genes that suppress activation and maintain stemness and, upon acute viral infection, displayed greater propensity to become effector T cells. Our results represent an example of an effective approach for prioritizing variants and studying their physiologically relevant effects.

Systematic identification of genomic elements that regulate FCGR2A expression and harbor variants linked with autoimmune disease

BACKGROUND

FCGR2A binds antibody-antigen complexes to regulate the abundance of circulating and deposited complexes along with downstream immune and autoimmune responses. Although the abundance of FCRG2A may be critical in immune-mediated diseases, little is known about whether its surface expression is regulated through cis genomic elements and non-coding variants. In the current study, we aimed to characterize the regulation of FCGR2A expression, the impact of genetic variation and its association with autoimmune disease.

METHODS

We applied CRISPR-based interference and editing to scrutinize 1.7 Mb of open chromatin surrounding the FCGR2A gene to identify regulatory elements. Relevant transcription factors (TFs) binding to these regions were defined through public databases. Genetic variants affecting regulation were identified using luciferase reporter assays and were verified in a cohort of 1996 genotyped healthy individuals using flow cytometry.

RESULTS

We identified a complex proximal region and five distal enhancers regulating FCGR2A. The proximal region split into subregions upstream and downstream of the transcription start site, was enriched in binding of inflammation-regulated TFs, and harbored a variant associated with FCGR2A expression in primary myeloid cells. One distal enhancer region was occupied by CCCTC-binding factor (CTCF) whose binding site was disrupted by a rare genetic variant, altering gene expression.

CONCLUSIONS

The FCGR2A gene is regulated by multiple proximal and distal genomic regions, with links to autoimmune disease. These findings may open up novel therapeutic avenues where fine-tuning of FCGR2A levels may constitute a part of treatment strategies for immune-mediated diseases.

MAUDE: inferring expression changes in sorting-based CRISPR screens

Improved methods are needed to model CRISPR screen data for interrogation of genetic elements that alter reporter gene expression readout. We create MAUDE (Mean Alterations Using Discrete Expression) for quantifying the impact of guide RNAs on a target gene's expression in a pooled, sorting-based expression screen. MAUDE quantifies guide-level effects by modeling the distribution of cells across sorting expression bins. It then combines guides to estimate the statistical significance and effect size of targeted genetic elements. We demonstrate that MAUDE outperforms previous approaches and provide experimental design guidelines to best leverage MAUDE, which is available on https://github.com/Carldeboer/MAUDE.

Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features

Genome-wide association studies have associated thousands of genetic variants with complex traits and diseases, but pinpointing the causal variant(s) among those in tight linkage disequilibrium with each associated variant remains a major challenge. Here, we use seven experimental assays to characterize all common variants at the multiple disease-associated TNFAIP3 locus in five disease-relevant immune cell lines, based on a set of features related to regulatory potential. Trait/disease-associated variants are enriched among SNPs prioritized based on either: (1) residing within CRISPRi-sensitive regulatory regions, or (2) localizing in a chromatin accessible region while displaying allele-specific reporter activity. Of the 15 trait/disease-associated haplotypes at TNFAIP3, 9 have at least one variant meeting one or both of these criteria, 5 of which are further supported by genetic fine-mapping. Our work provides a comprehensive strategy to characterize genetic variation at important disease-associated loci, and aids in the effort to identify trait causal genetic variants.

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

Treatment of cancer has been revolutionized by immune checkpoint blockade therapies. Despite the high rate of response in advanced melanoma, the majority of patients succumb to disease. To identify factors associated with success or failure of checkpoint therapy, we profiled transcriptomes of 16,291 individual immune cells from 48 tumor samples of melanoma patients treated with checkpoint inhibitors. Two distinct states of CD8+ T cells were defined by clustering and associated with patient tumor regression or progression. A single transcription factor, TCF7, was visualized within CD8+ T cells in fixed tumor samples and predicted positive clinical outcome in an independent cohort of checkpoint-treated patients. We delineated the epigenetic landscape and clonality of these T cell states and demonstrated enhanced antitumor immunity by targeting novel combinations of factors in exhausted cells. Our study of immune cell transcriptomes from tumors demonstrates a strategy for identifying predictors, mechanisms, and targets for enhancing checkpoint immunotherapy.

Resistance to checkpoint blockade therapy through inactivation of antigen presentation

Treatment with immune checkpoint blockade (CPB) therapies often leads to prolonged responses in patients with metastatic melanoma, but the common mechanisms of primary and acquired resistance to these agents remain incompletely characterized and have yet to be validated in large cohorts. By analyzing longitudinal tumor biopsies from 17 metastatic melanoma patients treated with CPB therapies, we observed point mutations, deletions or loss of heterozygosity (LOH) in beta-2-microglobulin (B2M), an essential component of MHC class I antigen presentation, in 29.4% of patients with progressing disease. In two independent cohorts of melanoma patients treated with anti-CTLA4 and anti-PD1, respectively, we find that B2M LOH is enriched threefold in non-responders (~30%) compared to responders (~10%) and associated with poorer overall survival. Loss of both copies of B2M is found only in non-responders. B2M loss is likely a common mechanism of resistance to therapies targeting CTLA4 or PD1.

The Interleukin-2-mTORc1 Kinase Axis Defines the Signaling, Differentiation, and Metabolism of T Helper 1 and Follicular B Helper T Cells

The differentiation of CD4(+) helper T cell subsets with diverse effector functions is accompanied by changes in metabolism required to meet their bioenergetic demands. We find that follicular B helper T (Tfh) cells exhibited less proliferation, glycolysis, and mitochondrial respiration, accompanied by reduced mTOR kinase activity compared to T helper 1 (Th1) cells in response to acute viral infection. IL-2-mediated activation of the Akt kinase and mTORc1 signaling was both necessary and sufficient to shift differentiation away from Tfh cells, instead promoting that of Th1 cells. These findings were not the result of generalized signaling attenuation in Tfh cells, because they retained the ability to flux calcium and activate NFAT-transcription-factor-dependent cytokine production. These data identify the interleukin-2 (IL-2)-mTORc1 axis as a critical orchestrator of the reciprocal balance between Tfh and Th1 cell fates and their respective metabolic activities after acute viral infection.

Impact of autoimmune risk alleles on the immune system

Genetic analyses of autoimmune diseases have revealed hundreds of disease-associated DNA variants, but the identity and function of the causal variants are understudied and warrant deeper mechanistic studies. Here, we highlight methods for deciphering how alleles that are associated with autoimmune disease alter the human immune system, and suggest strategies for future autoimmune genetic research.

The transforming growth factor beta signaling pathway is critical for the formation of CD4 T follicular helper cells and isotype-switched antibody responses in the lung mucosa

T follicular helper cells (Tfh) are crucial for the initiation and maintenance of germinal center (GC) reactions and high affinity, isotype-switched antibody responses. In this study, we demonstrate that direct TGF-β signaling to CD4 T cells is important for the formation of influenza-specific Tfh cells, GC reactions, and development of isotype-switched, flu-specific antibody responses. Early during infection, TGF-β signaling suppressed the expression of the high affinity IL-2 receptor α chain (CD25) on virus-specific CD4 T cells, which tempered IL-2 signaling and STAT5 and mammalian target of rapamycin (mTOR) activation in Tfh precursor CD4 T cells. Inhibition of mTOR allowed for the differentiation of Tfh cells in the absence of TGF-βR signaling, suggesting that TGF-β insulates Tfh progenitor cells from IL-2-delivered mTOR signals, thereby promoting Tfh differentiation during acute viral infection. These findings identify a new pathway critical for the generation of Tfh cells and humoral responses during respiratory viral infections.

DOI:http://dx.doi.org/10.7554/eLife.04851.001

The influenza virus is thought to cause illness in up to 10% of adults and 30% of children each year worldwide. Most of these cases resolve on their own and don’t require treatment, but three to five million people are hospitalized and up to half a million people die each year.

Unfortunately, the vaccines currently available to protect against influenza only target particular varieties or “strains” of the virus. The strains that circulate vary from year-to-year so it is necessary to develop new influenza vaccines every year. However, it is difficult to correctly predict which strains will circulate, so a more effective solution would be to develop a new vaccine that can help the body defend itself against many, or ideally any influenza strain.

During a viral infection, a type of immune cell in the host can specialize into two different types of cells to help fight the virus: T helper 1 cells and CD4 T follicular helper cells. T helper 1 cells help to kill host cells that have become infected. CD4 T follicular helper cells promote the production of proteins called antibodies, which identify and neutralize the virus.

Here, Marshall et al. studied how T helper 1 cells and CD4 T follicular helper cells form in mice suffering from a lung infection similar to influenza. It was already known that a protein called transforming growth factor beta (TGF-β) helps the immune response to mount an effective defense against an infection without causing too much harm to the host. Marshall et al. show that TGF-β increases the number of CD4 T follicular helper cells in the mice by suppressing the production of another protein—called IL-2—on the surface of CD4 T cells. Treating mice lacking the ability to detect TGF-β with a drug that blocks a protein controlled by IL-2 also allows more CD4 T follicular helper cells to be produced.

Marshall et al.’s findings reveal that TGF-β is involved in controlling the balance of T helper 1 cells and CD4 T follicular helper cells produced during viral infections of the respiratory tract. Since TGF-β also has other roles in immune responses against viruses, it is now an attractive target for the development of a vaccine that may protect us against all strains of the influenza virus.

DOI:http://dx.doi.org/10.7554/eLife.04851.002

An enzyme that inactivates the inflammatory mediator leukotriene b4 restricts mycobacterial infection

While tuberculosis susceptibility has historically been ascribed to failed inflammation, it is now known that an excess of leukotriene A4 hydrolase (LTA4H), which catalyzes the final step in leukotriene B4 (LTB4) synthesis, produces a hyperinflammatory state and tuberculosis susceptibility. Here we show that the LTB4-inactivating enzyme leukotriene B4 dehydrogenase/prostaglandin reductase 1 (LTB4DH/PTGR1) restricts inflammation and independently confers resistance to tuberculous infection. LTB4DH overexpression counters the susceptibility resulting from LTA4H excess while ltb4dh-deficient animals can be rescued pharmacologically by LTB4 receptor antagonists. These data place LTB4DH as a key modulator of TB susceptibility and suggest new tuberculosis therapeutic strategies.

Host genotype-specific therapies can optimize the inflammatory response to mycobacterial infections

Susceptibility to tuberculosis is historically ascribed to an inadequate immune response that fails to control infecting mycobacteria. In zebrafish, we find that susceptibility to Mycobacterium marinum can result from either inadequate or excessive acute inflammation. Modulation of the leukotriene A(4) hydrolase (LTA4H) locus, which controls the balance of pro- and anti-inflammatory eicosanoids, reveals two distinct molecular routes to mycobacterial susceptibility converging on dysregulated TNF levels: inadequate inflammation caused by excess lipoxins and hyperinflammation driven by excess leukotriene B(4). We identify therapies that specifically target each of these extremes. In humans, we identify a single nucleotide polymorphism in the LTA4H promoter that regulates its transcriptional activity. In tuberculous meningitis, the polymorphism is associated with inflammatory cell recruitment, patient survival and response to adjunctive anti-inflammatory therapy. Together, our findings suggest that host-directed therapies tailored to patient LTA4H genotypes may counter detrimental effects of either extreme of inflammation.

The lta4h locus modulates susceptibility to mycobacterial infection in zebrafish and humans

Exposure to Mycobacterium tuberculosis produces varied early outcomes, ranging from resistance to infection to progressive disease. Here we report results from a forward genetic screen in zebrafish larvae that identify multiple mutant classes with distinct patterns of innate susceptibility to Mycobacterium marinum. A hypersusceptible mutant maps to the lta4h locus encoding leukotriene A(4) hydrolase, which catalyzes the final step in the synthesis of leukotriene B(4) (LTB(4)), a potent chemoattractant and proinflammatory eicosanoid. lta4h mutations confer hypersusceptibility independent of LTB(4) reduction, by redirecting eicosanoid substrates to anti-inflammatory lipoxins. The resultant anti-inflammatory state permits increased mycobacterial proliferation by limiting production of tumor necrosis factor. In humans, we find that protection from both tuberculosis and multibacillary leprosy is associated with heterozygosity for LTA4H polymorphisms that have previously been correlated with differential LTB(4) production. Our results suggest conserved roles for balanced eicosanoid production in vertebrate resistance to mycobacterial infection.

Innate immunity to tuberculosis: a forward genetic approach (133.15)

We have developed a forward genetic screen in the zebrafish to identify host genes that control resistance and susceptibility to tuberculosis. Using facile live imaging techniques to screen mutant larvae for alterations in the pathogenesis of Mycobacterium marinum, we have identified multiple genetic loci that alter myeloid development and functions, including macrophage microbicidal capacity, migration and aggregation. Through a positional cloning approach, we have identified genes affected by three mutations causing hypersusceptibility to M. marinum. One of these mutations lies in the gene encoding leukotriene A4 hydrolase (LTA4H), the biosynthetic enzyme that produces leukotriene B4 (LTB4). In spite of LTB4's role as a potent leukocyte chemoattractant, the mutant is not compromised in the initial migration of macrophages to the site of infection. Rather mutant macrophages are defective in limiting intracellular bacterial growth and are quickly killed by the infection. Chemical inhibitors of this pathway mimic the mutant phenotype. Finally, we show that the protective effect of LTA4H in limiting mycobacterial growth may be attributable to a role in the regulation of TNF, as mutant fish fail to induce TNF transcription in response to infection.

The organization of projections from the mediodorsal nucleus of the thalamus to orbital and medial prefrontal cortex in macaque monkeys

The organization of interconnections between the mediodorsal nucleus of the thalamus (MD) and the orbital and medial prefrontal cortex and the agranular insular cortex in the monkey was studied by retrograde and anterograde tracing techniques. In addition to the magnocellular and parvicellular divisions of MD, three other subdivisions can be recognized on the basis of myeloarchitecture, cytoarchitecture, and connections. The first two of these represent a parcellation of the magnocellular division into a lateral, fiber-rich MD pars fibrosa and a medial, poorly myelinated MD pars paramediana adjacent to the midline. The third is a small, poorly myelinated area located at the caudomedial and dorsal edges of MD; it is referred to as MD pars caudodorsalis. MD pars fibrosa is reciprocally interconnected primarily with areas 11, 12 and 13 in the central and lateral part of the orbital cortex. There is a general organization within this projection, with the rostrocaudal axis of the cortex represented from dorsal to ventral in the pars fibrosa, and the mediolateral cortical axis represented from medial to lateral. Cells that project to area 12 also extend laterally into the adjacent pars parvicellularis. MD pars paramediana is more heavily interconnected with the caudal and medial portions of the orbital region, particularly the agranular insular areas and the caudal parts of areas 13 and 14. Cells that project to two caudal areas, 13a and Iad, do not fit with the general organization, in that they are located in the dorsomedial parts of the pars fibrosa and pars paramediana, where they overlap with cells that project to area 14. The pars fibrosa and pars paramediana receive inputs from areas of the ventral forebrain such as the amygdala, piriform (olfactory) cortex, and entorhinal cortex, which project directly to the orbital and agranular insular cortex, as well as from the ventral pallidum. MD pars caudodorsalis is reciprocally interconnected with areas 14, 24, and 32 on the medial surface of the prefrontal cortex. In this part of the nucleus the dorsoventral axis of the medial prefrontal cortex is represented from caudal to rostral in the thalamus. The amygdala and other ventral forebrain structures do not send fibers into the pars caudodorsalis, even though some of these structures project directly to the medial prefrontal cortex. Ventral to MD, and separated from it by the internal medullary lamina, a small region was recognized that appears to be comparable to the anteroventral part of the submedial nucleus previously defined in the rat and cat.(ABSTRACT TRUNCATED AT 400 WORDS)

The organization of the thalamocortical connections of the mediodorsal thalamic nucleus in the rat, related to the ventral forebrain-prefrontal cortex topography

The medial and central segments of the mediodorsal nucleus of the thalamus (MD) receive afferents from the ventral forebrain, including the piriform cortex, the ventral pallidum, and the amygdaloid complex. Because MD is reciprocally interconnected with prefrontal and agranular insular cortical areas, it provides a relay of ventral forebrain activity to these cortical areas. However, there are also direct projections from the piriform cortex and the amygdala to the prefrontal and agranular insular cortices. This study addresses whether this system has a "triangular" organization, such that structures in the ventral forebrain project to interconnected areas in MD and the prefrontal/insular cortex. The thalamocortical projections of MD have been studied in experiments with injections of retrograde tracers into prefrontal or agranular insular cortical areas. In many of the same experiments, projections from the ventral forebrain to MD and to the prefrontal/insular cortex have been demonstrated with anterograde axonal tracers. The connections of the piriform cortex (PC) with MD and the prefrontal/insular cortex form an organized triangular system. The PC projections to the central and medial segments of MD and to the lateral orbital cortex (LO) and the ventral and posterior agranular insular cortices (AIv and AIp) are topographically organized, such that more caudal parts of PC tend to project more medially in MD and more caudally within the orbital/insular cortex. The central and medial portions of MD also send matching, topographically organized projections to LO, AIv and AIp, with more medial parts of MD projecting further caudally. The anterior cortical nucleus of the amygdala (COa) also projects to the dorsal part of the medial segment of MD and to its cortical targets, the medial orbital area (MO) and AIp. The projections of the basal/accessory basal amygdaloid nuclei to MD and to prefrontal cortex, and from MD to amygdaloceptive parts of prefrontal cortex, are not as tightly organized. Amygdalothalamic afferents in MD are concentrated in the dorsal half of the medial segment. Cells in this part of the nucleus project to the amygdaloceptive prelimbic area (PL) and AIp. However, other amygdaloceptive prefrontal areas are connected to parts of MD that do not receive fibers from the amygdala. Ventral pallidal afferents are distributed to all parts of the central and medial segments of MD, overlapping with the fibers from the amygdala and piriform cortex. Fibers from other parts of the pallidum, or related areas such as the substantia nigra, pars reticulata, terminate in the lateral and ventral parts of MD, where they overlap with inputs from the superior colliculus and other brainstem structures.(ABSTRACT TRUNCATED AT 400 WORDS)

Sources of presumptive glutamatergic/aspartatergic afferents to the mediodorsal nucleus of the thalamus in the rat

The distribution of presumptive glutamatergic and/or aspartatergic neurons retrogradely labeled following injections of 3HD-aspartate into the mediodorsal nucleus of the thalamus (MD) in the rat was compared to the distribution of neurons labeled by comparable injections of the nonspecific retrograde tracer wheat germ agglutinin conjugated horseradish peroxidase (WGA-HRP). Cells retrogradely labeled by WGA-HRP were found in the prefrontal and agranular insular cortices; in forebrain structures such as the amygdaloid complex, the piriform cortex, the ventral pallidum and the reticular nucleus of the thalamus; and in several different parts of the brainstem, such as the superior colliculus, central grey, and substantia nigra, pars reticulata. Some, but not all, of these projections are presumably glutamatergic and/or aspartatergic. The projections to MD from the prefrontal and agranular insular cortices are well labeled with 3H-D-aspartate, as are projections from the anterior cortical amygdaloid nucleus. Projections from the superior colliculus to the lateral portion of MD also label with this tracer. However, other forebrain and brainstem projections to MD are not labeled with 3H-D-aspartate, and apparently do not use glutamate or aspartate as a neurotransmitter. These include the projections from the basal and accessory basal amygdaloid nuclei, as well as possibly GABAergic projections from the ventral pallidum and the substantia nigra, pars reticulata. A small fraction of the cells in the piriform cortex that project to MD label with 3H-D-aspartate, suggesting that this projection may be heterogeneous. In other experiments, presumptive GABAergic projections to MD were studied by using 3H-GABA as a retrograde tracer. Although in these cases the thalamic reticular nucleus is well labeled, the ventral pallidum and the substantia nigra, pars reticulata are only poorly labeled. Pallidal projections to the ventromedial thalamic nucleus (VM), which are likely to be GABAergic, were also studied with this technique. After injections of 3H-GABA into VM, only a few cells in the substantia nigra, pars reticulata, or entopeduncular nucleus were labeled. This result suggests 3H-GABA has limited usefulness as a transmitter-specific retrograde tracer.

An ultrastructural study of neurotensin-like immunoreactive terminals in the mediodorsal thalamic nucleus of the rat

Neurotensin-like immunoreactive (NTir) axon terminals in the mediodorsal nucleus of the thalamus (MD) in the adult rat were demonstrated by electron microscopic immunohistochemistry. Most NTir terminals were large (greater than 2 microns in diameter) with round synaptic vesicles and asymmetrical synaptic contacts although smaller (less than 1.5 microns in diameter) axon terminals were also labeled. Both types of terminals were found in the medial and central parts of MD with the greatest density in the medial part. These NTir boutons have similar ultrastructural features as anterogradely labeled terminals from the piriform cortex and the preoptic area, which have previously been identified as sources of NTir axons in MD. A few NTir boutons were also found in the medial part of MD with pleomorphic vesicles and symmetrical synaptic contacts.

Postnatal changes in the density and distribution of neurotensin-like immunoreactive fibers in the mediodorsal nucleus of the thalamus in the rat

A previous report (Inagaki et al., Brain Res. 260:143-146, '83) suggested that the peptide neurotensin is contained in neurons of the piriform cortex that project to the mediodorsal thalamic nucleus (MD) in young rats. To confirm this, we have studied the distribution of neurotensin-like immunoreactive (NTIR) fibers in MD during development, using three antisera directed at different parts of the neurotensin molecule (Emson et al., J. Neurochem. 38:992-999, '82). In adult rats, NTIR fibers in MD are sparse. They are located mostly at the medial edge of MD and in the adjacent midline thalamic nuclei, with a few poorly stained NTIR fibers in the central part of MD. In contrast, during the first postnatal week, both the medial and central portions of MD stain heavily for neurotensin. The density of NTIR fibers in MD then progressively decreases until the density typical of adult rats is reached, at about 5 weeks. Changes in the distribution of NTIR fibers in MD also occur. In 7-day-old rats, the patches of NTIR fibers in the medial and central parts of MD are contiguous, but by 10 days a sparsely immunoreactive zone forms between them. With maturation, this zone enlarges as the density of neurotensin staining decreases, until the medial contingent of NTIR fibers reaches its adult position at the medial edge of MD. From a comparison of the distribution of NTIR cells with that of cells that can be retrogradely labeled from MD or the midline thalamus, the probable source of the NTIR fibers to the central part of MD is in the deep layer of the piriform cortex, while the NTIR fibers to the medial edge of MD and the midline nuclei may arise from the preoptic region and the medial amygdala. In neonatal rats, neurons are found in the piriform cortex, the preoptic region, and the medial amygdala, which can be double-labeled both for neurotensin and with a retrograde tracer injected into MD and the midline thalamus. Projections of the preoptic region to the thalamus have a distribution similar to that of the medial population of NTIR fibers, whereas the distribution of piriform cortical afferents in central MD matches the central patch of NTIR fibers.

The stokes radius of the CHAPS-solubilized benzodiazepine receptor complex

The Stokes radii and the apparent molecular weights of the CHAPS or Triton X-100 solubilized benzodiazepine receptors are calculated by gel exclusion chromatography. The results suggest that the molecular receptor complex solubilized by CHAPS is much larger than the complex solubilized by Triton X-100.