Integrating population and single-cell variations in vaccine responses identifies a naturally adjuvanted human immune setpoint

Multimodal single-cell profiling methods can capture immune cell variations unfolding over time at the molecular, cellular, and population levels. Transforming these data into biological insights remains challenging. Here, we introduce a framework to integrate variations at the human population and single-cell levels in vaccination responses. Comparing responses following AS03-adjuvanted versus unadjuvanted influenza vaccines with CITE-seq revealed AS03-specific early (day 1) response phenotypes, including a B cell signature of elevated germinal center competition. A correlated network of cell-type-specific transcriptional states defined the baseline immune status associated with high antibody responders to the unadjuvanted vaccine. Certain innate subsets in the network appeared "naturally adjuvanted," with transcriptional states resembling those induced uniquely by AS03-adjuvanted vaccination. Consistently, CD14+ monocytes from high responders at baseline had elevated phospho-signaling responses to lipopolysaccharide stimulation. Our findings link baseline immune setpoints to early vaccine responses, with positive implications for adjuvant development and immune response engineering.

Human transcriptional signature of protection after Plasmodium falciparum immunization and infectious challenge via mosquito bites

The identification of immune correlates of protection against infectious pathogens will accelerate the design and optimization of recombinant and subunit vaccines. Systematic analyses such as immunoprofiling including serological, cellular, and molecular assessments supported by computational tools are key to not only identify correlates of protection but also biomarkers of disease susceptibility. The current study expands our previous cellular and serological profiling of vaccine-induced responses to a whole parasite malaria vaccine. The irradiated sporozoite model was chosen as it is considered the most effective vaccine against malaria. In contrast to whole blood transcriptomics analysis, we stimulated peripheral blood mononuclear cells (PBMC) with sporozoites and enriched for antigen-specific cells prior to conducting transcriptomics analysis. By focusing on transcriptional events triggered by antigen-specific stimulation, we were able to uncover quantitative and qualitative differences between protected and non-protected individuals to controlled human malaria infections and identified differentially expressed genes associated with sporozoite-specific responses. Further analyses including pathway and gene set enrichment analysis revealed that vaccination with irradiated sporozoites induced a transcriptomic profile associated with Th1-responses, Interferon-signaling, antigen-presentation, and inflammation. Analyzing longitudinal time points not only post-vaccination but also post-controlled human malaria infection further revealed that the transcriptomic profile of protected vs non-protected individuals was not static but continued to diverge over time. The results lay the foundation for comparing protective immune signatures induced by various vaccine platforms to uncover immune correlates of protection that are common across platforms.

Tracking B cell responses to the SARS-CoV-2 mRNA-1273 vaccine

Protective immunity following vaccination is sustained by long-lived antibody-secreting cells and resting memory B cells (MBCs). Responses to two-dose SARS-CoV-2 mRNA-1273 vaccination are evaluated longitudinally by multimodal single-cell analysis in three infection-naïve individuals. Integrated surface protein, transcriptomics, and B cell receptor (BCR) repertoire analysis of sorted plasmablasts and spike+ (S-2P+) and S-2P- B cells reveal clonal expansion and accumulating mutations among S-2P+ cells. These cells are enriched in a cluster of immunoglobulin G-expressing MBCs and evolve along a bifurcated trajectory rooted in CXCR3+ MBCs. One branch leads to CD11c+ atypical MBCs while the other develops from CD71+ activated precursors to resting MBCs, the dominant population at month 6. Among 12 evolving S-2P+ clones, several are populated with plasmablasts at early timepoints as well as CD71+ activated and resting MBCs at later timepoints, and display intra- and/or inter-cohort BCR convergence. These relationships suggest a coordinated and predictable evolution of SARS-CoV-2 vaccine-generated MBCs.

Multiscale integration of human and single-cell variations reveals unadjuvanted vaccine high responders are naturally adjuvanted

Advances in multimodal single cell analysis can empower high-resolution dissection of human vaccination responses. The resulting data capture multiple layers of biological variations, including molecular and cellular states, vaccine formulations, inter- and intra-subject differences, and responses unfolding over time. Transforming such data into biological insight remains a major challenge. Here we present a systematic framework applied to multimodal single cell data obtained before and after influenza vaccination without adjuvants or pandemic H5N1 vaccination with the AS03 adjuvant. Our approach pinpoints responses shared across or unique to specific cell types and identifies adjuvant specific signatures, including pro-survival transcriptional states in B lymphocytes that emerged one day after vaccination. We also reveal that high antibody responders to the unadjuvanted vaccine have a distinct baseline involving a rewired network of cell type specific transcriptional states. Remarkably, the status of certain innate immune cells in this network in high responders of the unadjuvanted vaccine appear "naturally adjuvanted": they resemble phenotypes induced early in the same cells only by vaccination with AS03. Furthermore, these cell subsets have elevated frequency in the blood at baseline and increased cell-intrinsic phospho-signaling responses after LPS stimulation ex vivo in high compared to low responders. Our findings identify how variation in the status of multiple immune cell types at baseline may drive robust differences in innate and adaptive responses to vaccination and thus open new avenues for vaccine development and immune response engineering in humans.

Multiomics integration of 22 immune-mediated monogenic diseases reveals an emergent axis of human immune health

Monogenic diseases are often studied in isolation due to their rarity. Here we utilize multiomics to assess 22 monogenic immune-mediated conditions with age- and sex-matched healthy controls. Despite clearly detectable disease-specific and "pan-disease" signatures, individuals possess stable personal immune states over time. Temporally stable differences among subjects tend to dominate over differences attributable to disease conditions or medication use. Unsupervised principal variation analysis of personal immune states and machine learning classification distinguishing between healthy controls and patients converge to a metric of immune health (IHM). The IHM discriminates healthy from multiple polygenic autoimmune and inflammatory disease states in independent cohorts, marks healthy aging, and is a pre-vaccination predictor of antibody responses to influenza vaccination in the elderly. We identified easy-to-measure circulating protein biomarker surrogates of the IHM that capture immune health variations beyond age. Our work provides a conceptual framework and biomarkers for defining and measuring human immune health.

Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19

Acute viral infections can have durable functional impacts on the immune system long after recovery, but how they affect homeostatic immune states and responses to future perturbations remain poorly understood1-4. Here we use systems immunology approaches, including longitudinal multimodal single-cell analysis (surface proteins, transcriptome and V(D)J sequences) to comparatively assess baseline immune statuses and responses to influenza vaccination in 33 healthy individuals after recovery from mild, non-hospitalized COVID-19 (mean, 151 days after diagnosis) and 40 age- and sex-matched control individuals who had never had COVID-19. At the baseline and independent of time after COVID-19, recoverees had elevated T cell activation signatures and lower expression of innate immune genes including Toll-like receptors in monocytes. Male individuals who had recovered from COVID-19 had coordinately higher innate, influenza-specific plasmablast, and antibody responses after vaccination compared with healthy male individuals and female individuals who had recovered from COVID-19, in part because male recoverees had monocytes with higher IL-15 responses early after vaccination coupled with elevated prevaccination frequencies of 'virtual memory'-like CD8+ T cells poised to produce more IFNγ after IL-15 stimulation. Moreover, the expression of the repressed innate immune genes in monocytes increased by day 1 to day 28 after vaccination in recoverees, therefore moving towards the prevaccination baseline of the healthy control individuals. By contrast, these genes decreased on day 1 and returned to the baseline by day 28 in the control individuals. Our study reveals sex-dimorphic effects of previous mild COVID-19 and suggests that viral infections in humans can establish new immunological set-points that affect future immune responses in an antigen-agnostic manner.

Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children

Most studies of adaptive immunity to SARS-CoV-2 infection focus on peripheral blood, which may not fully reflect immune responses at the site of infection. Using samples from 110 children undergoing tonsillectomy and adenoidectomy during the COVID-19 pandemic, we identified 24 samples with evidence of previous SARS-CoV-2 infection, including neutralizing antibodies in serum and SARS-CoV-2-specific germinal center and memory B cells in the tonsils and adenoids. Single-cell B cell receptor (BCR) sequencing indicated virus-specific BCRs were class-switched and somatically hypermutated, with overlapping clones in the two tissues. Expanded T cell clonotypes were found in tonsils, adenoids and blood post-COVID-19, some with CDR3 sequences identical to previously reported SARS-CoV-2-reactive T cell receptors (TCRs). Pharyngeal tissues from COVID-19-convalescent children showed persistent expansion of germinal center and antiviral lymphocyte populations associated with interferon (IFN)-γ-type responses, particularly in the adenoids, and viral RNA in both tissues. Our results provide evidence for persistent tissue-specific immunity to SARS-CoV-2 in the upper respiratory tract of children after infection.

Influenza vaccination and single cell multiomics reveal sex dimorphic immune imprints of prior mild COVID-19

Viral infections can have profound and durable functional impacts on the immune system. There is an urgent need to characterize the long-term immune effects of SARS-CoV-2 infection given the persistence of symptoms in some individuals and the continued threat of novel variants. Here we use systems immunology, including longitudinal multimodal single cell analysis (surface proteins, transcriptome, and V(D)J sequences) from 33 previously healthy individuals after recovery from mild, non-hospitalized COVID-19 and 40 age- and sex-matched healthy controls with no history of COVID-19 to comparatively assess the post-infection immune status (mean: 151 days after diagnosis) and subsequent innate and adaptive responses to seasonal influenza vaccination. Identification of both sex-specific and -independent temporally stable changes, including signatures of T-cell activation and repression of innate defense/immune receptor genes (e.g., Toll-like receptors) in monocytes, suggest that mild COVID-19 can establish new post-recovery immunological set-points. COVID-19-recovered males had higher innate, influenza-specific plasmablast, and antibody responses after vaccination compared to healthy males and COVID-19-recovered females, partly attributable to elevated pre-vaccination frequencies of a GPR56 expressing CD8+ T-cell subset in male recoverees that are "poised" to produce higher levels of IFNγ upon inflammatory stimulation. Intriguingly, by day 1 post-vaccination in COVID-19-recovered subjects, the expression of the repressed genes in monocytes increased and moved towards the pre-vaccination baseline of healthy controls, suggesting that the acute inflammation induced by vaccination could partly reset the immune states established by mild COVID-19. Our study reveals sex-dimorphic immune imprints and in vivo functional impacts of mild COVID-19 in humans, suggesting that prior COVID-19, and possibly respiratory viral infections in general, could change future responses to vaccination and in turn, vaccines could help reset the immune system after COVID-19, both in an antigen-agnostic manner.

Normalizing and denoising protein expression data from droplet-based single cell profiling

Multimodal single-cell profiling methods that measure protein expression with oligo-conjugated antibodies hold promise for comprehensive dissection of cellular heterogeneity, yet the resulting protein counts have substantial technical noise that can mask biological variations. Here we integrate experiments and computational analyses to reveal two major noise sources and develop a method called "dsb" (denoised and scaled by background) to normalize and denoise droplet-based protein expression data. We discover that protein-specific noise originates from unbound antibodies encapsulated during droplet generation; this noise can thus be accurately estimated and corrected by utilizing protein levels in empty droplets. We also find that isotype control antibodies and the background protein population average in each cell exhibit significant correlations across single cells, we thus use their shared variance to correct for cell-to-cell technical noise in each cell. We validate these findings by analyzing the performance of dsb in eight independent datasets spanning multiple technologies, including CITE-seq, ASAP-seq, and TEA-seq. Compared to existing normalization methods, our approach improves downstream analyses by better unmasking biologically meaningful cell populations. Our method is available as an open-source R package that interfaces easily with existing single cell software platforms such as Seurat, Bioconductor, and Scanpy and can be accessed at "dsb [ https://cran.r-project.org/package=dsb ]".

Robust, persistent adaptive immune responses to SARS-CoV-2 in the oropharyngeal lymphoid tissue of children

SARS-CoV-2 infection triggers adaptive immune responses from both T and B cells. However, most studies focus on peripheral blood, which may not fully reflect immune responses in lymphoid tissues at the site of infection. To evaluate both local and systemic adaptive immune responses to SARS-CoV-2, we collected peripheral blood, tonsils, and adenoids from 110 children undergoing tonsillectomy/adenoidectomy during the COVID-19 pandemic and found 24 with evidence of prior SARS-CoV-2 infection, including detectable neutralizing antibodies against multiple viral variants. We identified SARS-CoV-2-specific germinal center (GC) and memory B cells; single cell BCR sequencing showed that these virus-specific B cells were class-switched and somatically hypermutated, with overlapping clones in the adenoids and tonsils. Oropharyngeal tissues from COVID-19-convalescent children showed persistent expansion of GC and anti-viral lymphocyte populations associated with an IFN-γ-type response, with particularly prominent changes in the adenoids, as well as evidence of persistent viral RNA in both tonsil and adenoid tissues of many participants. Our results show robust, tissue-specific adaptive immune responses to SARS-CoV-2 in the upper respiratory tract of children weeks to months after acute infection, providing evidence of persistent localized immunity to this respiratory virus.

Pre-existing chromatin accessibility and gene expression differences among naive CD4+ T cells influence effector potential

CD4+ T cells have a remarkable potential to differentiate into diverse effector lineages following activation. Here, we probe the heterogeneity present among naive CD4+ T cells before encountering their cognate antigen to ask whether their effector potential is modulated by pre-existing transcriptional and chromatin landscape differences. Single-cell RNA sequencing shows that key drivers of variability are genes involved in T cell receptor (TCR) signaling. Using CD5 expression as a readout of the strength of tonic TCR interactions with self-peptide MHC, and sorting on the ends of this self-reactivity spectrum, we find that pre-existing transcriptional differences among naive CD4+ T cells impact follicular helper T (TFH) cell versus non-TFH effector lineage choice. Moreover, our data implicate TCR signal strength during thymic development in establishing differences in naive CD4+ T cell chromatin landscapes that ultimately shape their effector potential.

Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19

COVID-19 exhibits extensive patient-to-patient heterogeneity. To link immune response variation to disease severity and outcome over time, we longitudinally assessed circulating proteins as well as 188 surface protein markers, transcriptome, and T cell receptor sequence simultaneously in single peripheral immune cells from COVID-19 patients. Conditional-independence network analysis revealed primary correlates of disease severity, including gene expression signatures of apoptosis in plasmacytoid dendritic cells and attenuated inflammation but increased fatty acid metabolism in CD56^dimCD16^hi NK cells linked positively to circulating interleukin (IL)-15. CD8⁺ T cell activation was apparent without signs of exhaustion. Although cellular inflammation was depressed in severe patients early after hospitalization, it became elevated by days 17–23 post symptom onset, suggestive of a late wave of inflammatory responses. Furthermore, circulating protein trajectories at this time were divergent between and predictive of recovery versus fatal outcomes. Our findings stress the importance of timing in the analysis, clinical monitoring, and therapeutic intervention of COVID-19.

Cancer prognosis with shallow tumor RNA sequencing

Disrupted molecular pathways are often robustly associated with disease outcome in cancer^1-3. Although biologically informative transcriptional pathways can be revealed by RNA sequencing (RNA-seq) at up to hundreds of folds reduction in conventionally used coverage^4-6, it remains unknown how low-depth sequencing datasets perform in the challenging context of developing transcriptional signatures to predict clinical outcomes. Here we assessed the possibility of cancer prognosis with shallow tumor RNA-seq, which would potentially enable cost-effective assessment of much larger numbers of samples for deeper biological and predictive insights. By statistically modeling the relative risk of an adverse outcome for thousands of subjects in The Cancer Genome Atlas^7-13, we present evidence that subsampled tumor RNA-seq data with a few hundred thousand reads per sample provide sufficient information for outcome prediction in several types of cancer. Analysis of predictive models revealed robust contributions from pathways known to be associated with outcomes. Our findings indicate that predictive models of outcomes in cancer may be developed with dramatically increases in sample numbers at low cost, thus potentially enabling the development of more realistic predictive models that incorporate diverse variables and their interactions. This strategy could also be used, for example, in longitudinal analysis of multiple regions of a tumor alongside treatment for quantitative modeling and prediction of outcome in personalized oncology.

Differential Expression of the Transcription Factor GATA3 Specifies Lineage and Functions of Innate Lymphoid Cells

Lymphoid tissue inducer (LTi) cells are regarded as a subset of innate lymphoid cells (ILCs). However, these cells are not derived from the ILC common progenitor, which generates other ILC subsets and is defined by the expression of the transcription factor PLZF. Here, we examined transcription factor(s) determining the fate of LTi progenitors versus non-LTi ILC progenitors. Conditional deletion of Gata3 resulted in the loss of PLZF⁺ non-LTi progenitors but not the LTi progenitors that expressed the transcription factor RORγt. Consistently, PLZF⁺ non-LTi progenitors expressed high amounts of GATA3, whereas GATA3 expression was low in RORγt⁺ LTi progenitors. The generation of both progenitors required the transcriptional regulator Id2, which defines the common helper-like innate lymphoid progenitor (ChILP), but not cytokine signaling. Nevertheless, low GATA3 expression was necessary for the generation of functionally mature LTi cells. Thus, differential expression of GATA3 determines the fates and functions of distinct ILC progenitors.

Overexpression of T-bet in HIV infection is associated with accumulation of B cells outside germinal centers and poor affinity maturation

Nearly all chronic human infections are associated with alterations in the memory B cell (MBC) compartment, including a large expansion of CD19hiT-bethi MBC in the peripheral blood of HIV-infected individuals with chronic viremia. Despite their prevalence, it is unclear how these B cells arise and whether they contribute to the inefficiency of antibody-mediated immunity in chronic infectious diseases. We addressed these questions by characterizing T-bet-expressing B cells in lymph nodes (LN) and identifying a strong T-bet signature among HIV-specific MBC associated with poor immunologic outcome. Confocal microscopy and quantitative imaging revealed that T-bethi B cells in LN of HIV-infected chronically viremic individuals distinctly accumulated outside germinal centers (GC), which are critical for optimal antibody responses. In single-cell analyses, LN T-bethi B cells of HIV-infected individuals were almost exclusively found among CD19hi MBC and expressed reduced GC-homing receptors. Furthermore, HIV-specific B cells of infected individuals were enriched among LN CD19hiT-bethi MBC and displayed a distinct transcriptome, with features similar to CD19hiT-bethi MBC in blood and LN GC B cells (GCBC). LN CD19hiT-bethi MBC were also related to GCBC by B cell receptor (BCR)-based phylogenetic linkage but had lower BCR mutation frequencies and reduced HIV-neutralizing capacity, consistent with diminished participation in GC-mediated affinity selection. Thus, in the setting of chronic immune activation associated with HIV viremia, failure of HIV-specific B cells to enter or remain in GC may help explain the rarity of high-affinity protective antibodies.

IFN-mediated negative feedback supports bacteria class-specific macrophage inflammatory responses

Despite existing evidence for tuning of innate immunity to different classes of bacteria, the molecular mechanisms used by macrophages to tailor inflammatory responses to specific pathogens remain incompletely defined. By stimulating mouse macrophages with a titration matrix of TLR ligand pairs, we identified distinct stimulus requirements for activating and inhibitory events that evoked diverse cytokine production dynamics. These regulatory events were linked to patterns of inflammatory responses that distinguished between Gram-positive and Gram-negative bacteria, both in vitro and after in vivo lung infection. Stimulation beyond a TLR4 threshold and Gram-negative bacteria-induced responses were characterized by a rapid type I IFN-dependent decline in inflammatory cytokine production, independent of IL-10, whereas inflammatory responses to Gram-positive species were more sustained due to the absence of this IFN-dependent regulation. Thus, disparate triggering of a cytokine negative feedback loop promotes tuning of macrophage responses in a bacteria class-specific manner and provides context-dependent regulation of inflammation dynamics.

Resident Macrophages Cloak Tissue Microlesions to Prevent Neutrophil-Driven Inflammatory Damage

Neutrophils are attracted to and generate dense swarms at sites of cell damage in diverse tissues, often extending the local disruption of organ architecture produced by the initial insult. Whether the inflammatory damage resulting from such neutrophil accumulation is an inescapable consequence of parenchymal cell death has not been explored. Using a combination of dynamic intravital imaging and confocal multiplex microscopy, we report here that tissue-resident macrophages rapidly sense the death of individual cells and extend membrane processes that sequester the damage, a process that prevents initiation of the feedforward chemoattractant signaling cascade that results in neutrophil swarms. Through this "cloaking" mechanism, the resident macrophages prevent neutrophil-mediated inflammatory damage, maintaining tissue homeostasis in the face of local cell injury that occurs on a regular basis in many organs because of mechanical and other stresses. VIDEO ABSTRACT.

Transcriptional Response of Respiratory Epithelium to Nontuberculous Mycobacteria

The incidence of pulmonary nontuberculous mycobacteria (NTM) disease is increasing, but host responses in respiratory epithelium infected with NTM are not fully understood. In this work, we aimed to identify infection-relevant gene expression signatures of NTM infection of the respiratory epithelium. We infected air-liquid interface (ALI) primary respiratory epithelial cell cultures with Mycobacterium avium subsp. avium (MAC) or Mycobacterium abscessus subsp. abscessus (MAB). We used cells from four different donors to obtain generalizable data. Differentiated respiratory epithelial cells at the ALI were infected with MAC or MAB at a multiplicity of infection of 100:1 or 1,000:1, and RNA sequencing was performed at Days 1 and 3 after infection. In response to infection, we found down-regulation of ciliary genes but upregulation of genes associated with cytokines/chemokines, such as IL-32, and cholesterol biosynthesis. Inflammatory response genes tended to be more upregulated by MAB than by MAC infection. Primary respiratory epithelial cell infection with NTM at the ALI identified ciliary function, cholesterol biosynthesis, and cytokine/chemokine production as major host responses to infection. Some of these pathways may be amenable to therapeutic manipulation.

Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism

The mammalian gut is colonized by numerous microorganisms collectively termed the microbiota, which have a mutually beneficial relationship with their host. Normally, the gut microbiota matures during ontogeny to a state of balanced commensalism marked by the absence of adverse inflammation. Subsets of innate lymphoid cells (ILCs) and conventional T cells are considered to have redundant functions in containment and clearance of microbial pathogens, but how these two major lymphoid-cell populations each contribute to shaping the mature commensal microbiome and help to maintain tissue homeostasis has not been determined. Here we identify, using advanced multiplex quantitative imaging methods, an extensive and persistent phosphorylated-STAT3 signature in group 3 ILCs and intestinal epithelial cells that is induced by interleukin (IL)-23 and IL-22 in mice that lack CD4+ T cells. By contrast, in immune-competent mice, phosphorylated-STAT3 activation is induced only transiently by microbial colonization at weaning. This early signature is extinguished as CD4+ T cell immunity develops in response to the expanding commensal burden. Physiologically, the persistent IL-22 production from group 3 ILCs that occurs in the absence of adaptive CD4+ T-cell activity results in impaired host lipid metabolism by decreasing lipid transporter expression in the small bowel. These findings provide new insights into how innate and adaptive lymphocytes operate sequentially and in distinct ways during normal development to establish steady-state commensalism and tissue metabolic homeostasis.

Insecticide resistance, associated mechanisms and fitness aspects in two Brazilian Stegomyia aegypti (= Aedes aegypti) populations

In Brazil, insecticide resistance in Stegomyia aegypti (= Aedes aegypti) (Diptera: Culicidae) populations to pyrethroids and to the organophosphate (OP) temephos is disseminated. Currently, insect growth regulators (IGRs) and the OP malathion are employed against larvae and adults, respectively. Bioassays with mosquitoes from two northeast municipalities, Crato and Aracaju, revealed, in both populations, susceptibility to IGRs and malathion (RR₉₅  ≤ 2.0), confirming the effectiveness of these compounds. By contrast, temephos and deltamethrin (pyrethroid) resistance levels were high (RR₉₅  > 10), which is consistent with the use of intense chemical control. In Crato, RR₉₅ values were > 50 for both compounds. Knock-down-resistant (kdr) mutants in the voltage-gated sodium channel, the pyrethroid target site, were found in 43 and 32%, respectively, of Aracaju and Crato mosquitoes. Biochemical assays revealed higher metabolic resistance activity (esterases, mixed function oxidases and glutathione-S-transferases) at Aracaju. With respect to fitness aspects, mating effectiveness was equivalently impaired in both populations, but Aracaju mosquitoes showed more damaging effects in terms of longer larval development, decreased bloodmeal acceptance, reduced engorgement and lower numbers of eggs laid per female. Compared with mosquitoes in Crato, Aracaju mosquitoes exhibited lower OP and pyrethroid RR₉₅ , increased activity of detoxifying enzymes and greater effect on fitness. The potential relationship between insecticide resistance mechanisms and mosquito viability is discussed.

Combining gene expression data from inflamed tissue and machine learning for blood biomarker discovery

Inflammation is common in virtually all diseases. Since immune cells travel through the blood to inflamed tissues, peripheral blood reflects inflammation at distant sites. However, blood biomarkers are hard to detect in global gene expression data since blood is not the site of perturbation and statistical corrections for multiple testing reduce sensitivity. We hypothesized that combining transcriptional signatures from inflamed tissue and machine learning would be useful to derive blood biomarkers. We first tested this in the mouse model of influenza infection. We identified a set of early genes in the lungs associated with lethality after infection. We then tested their differential abundance early in the blood of mice infected with a range of influenza doses. We applied elastic net to build a biomarker able to predict disease outcome (4 classes: early lethal, late lethal, non-lethal vs. non-infected; accuracy on training and validation sets: 91% and 79%). We next confirmed our hypothesis in lung cancer and breast cancer in humans. We identified sets of genes associated with tumors but not with tumor-free tissues and tested their differential abundance in the blood of patients compared to healthy controls. Using elastic net, we built two blood biomarkers to classify subjects according to disease status (case vs. control; accuracy on training and validation sets in breast cancer: 92% and 67%; in lung cancer: 89% and 78%). In conclusion, combining inflamed tissue signatures and machine learning, we were able to derive blood biomarkers for three different diseases in two different species. We expect that this novel strategy can be applied in other diseases as well.

This work was supported by the Intramural Research Program of NIAID, NIH.

Induced negative regulation decodes PAMP quality and quantity to generate bacteria-specific inflammatory responses

Toll-like receptors (TLRs) expressed on macrophages are ligated in various combinations by diverse pathogen-associated molecular patterns (PAMPs), but how mixtures of signals through these receptors are integrated to mediate distinct biological responses to different pathogens remains unknown. By stimulating macrophages using a wide matrix of TLR2/TLR4 concentration combinations, we identified conditions resulting in non-linear responses. Transcriptomic and RNAi analyses identified negative regulators induced in a TLR-specific manner that regulated cytokine production dynamics and chemokine milieus across the combinatorial matrix. TLR4 ligand concentration explained much of the variation in production of many chemokines. However, combinations of sub-maximal amounts of either single ligand produced a zone of non-linear responses with sustained production of select inflammatory mediators, due to lack of negative regulation induced only at higher individual ligand concentrations. A similar sustained response was observed for Gram-positive bacteria, as compared to a panel of Gram-negative species, which express high amounts of the TLR4 ligand LPS. The novel TLR4-specific negative regulators we describe thus aid the innate immune system in discriminating Gram-negative from Gram-positive species, supporting qualitatively distinct inflammatory responses to these classes of bacteria.

This research was supported by the Intramural Research Program of the NIH, NIAID

Sequential activity of innate and adaptive lymphocytes supports non-inflammatory gut microbial commensalism

The mammalian gut is colonized by trillions of microorganisms termed the “microbiota”, which have a mutually beneficial relationship with their host. In normal individuals, the gut microbiota matures after birth to a state of balanced commensalism that is marked by the absence of adverse inflammation. Both innate lymphoid cells (ILCs) and antigen-specific conventional T cells contribute to containment and clearance of microbial pathogens. But how these two major lymphoid cell populations help shape the mature commensal (non-pathogenic) microbiome and maintain tissue homeostasis has not been determined. Using advanced multiplex quantitative imaging methods, here we show that in the absence of adaptive lymphocytes, IL-23 induced by specific commensal bacteria such as Segmented Filamentous Bacteria (SFB) persistently activates RORgt+ group 3 innate lymphoid cells (ILC3s) in the ileum to produce IL-22, which induces STAT3 activation in virtually all epithelial cells, contributing to production of molecules such as anti-microbial peptides that protect the tissue from microbial damage. The distinct roles of ILCs in handling gut microbes play out in normal mice during development. The pSTAT3 signature is absent after birth, which is followed by microbial colonization and strong ILC3 activation and an extensive epithelial pSTAT3 signature upon weaning. This innate immune activity is subsequently extinguished as adaptive CD4+ T cell immunity develops in response to the expanding commensal burden. Our findings provide new insights into how innate and adaptive lymphocytes sequentially operate during normal development to establish steady state commensalism.

Mapping the chromatin and RNA expression landscapes of human macrophages to interrogate the function of disease-associated genetic polymorphisms

Macrophages are known to show highly dynamic responses to diverse stimuli, and have been implicated in metabolic syndrome and related diseases. Genome-wide association studies have identified many single-nucleotide polymorphisms (SNPs) associated with these common conditions, largely in non-coding regions; how these SNPs influence disease processes remains largely unknown. We hypothesized that examining RNA expression and chromatin state in macrophages across diverse activation conditions would elucidate the roles of macrophages in mediating the effects of disease-linked SNPs on the development of disease. We measured gene expression via RNAseq and histone 3 lysine 27 acetylation via ChIPseq as an indicator of promoter/enhancer activity in human blood monocyte-derived macrophages stimulated in vitro with a range of inflammatory and disease-relevant stimuli. Over 11,000 genes and 43,000 regulatory elements show condition-dependent activity in this dataset. Functional enrichment in modules of co-expressed transcripts confirmed expected stimuli-specific biology and reveal potentially novel relationships between distinct stimulation states. Correlation of regulatory element activity with module gene expression shows broad inflammatory/anti-inflammatory separation, and metabolic-trait associated SNPs tend to be embedded within regulatory elements whose activity is associated with both non-inflammatory and, surprisingly, some anti-viral macrophage gene modules. Ongoing work includes using these data to infer the transcriptional networks underlying these states. This study was supported by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases, NIH.

Environment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network

Cell-to-cell variation in gene expression and the propagation of such variation (PoV or "noise propagation") from one gene to another in the gene network, as reflected by gene-gene correlation across single cells, are commonly observed in single-cell transcriptomic studies and can shape the phenotypic diversity of cell populations. While gene network "rewiring" is known to accompany cellular adaptation to different environments, how PoV changes between environments and its underlying regulatory mechanisms are less understood. Here, we systematically explored context-dependent PoV among genes in human macrophages, utilizing different cytokines as natural perturbations of multiple molecular parameters that may influence PoV. Our single-cell, epigenomic, computational, and stochastic simulation analyses reveal that environmental adaptation can tune PoV to potentially shape cellular heterogeneity by changing parameters such as the degree of phosphorylation and transcription factor-chromatin interactions. This quantitative tuning of PoV may be a widespread, yet underexplored, property of cellular adaptation to distinct environments.

Detection and Distribution of V1016Ikdr Mutation in the Voltage-Gated Sodium Channel Gene in Aedes aegypti (Diptera: Culicidae) Populations From Sergipe State, Northeast Brazil

Aedes aegypti (L.) resistance to pyrethroids was recorded in Brazil few years after its introduction as the adulticide in the National Dengue Control Program campaigns. Altered susceptibility to pyrethroids had been reported in the state of Sergipe, northeast Brazil, through biological assays, even before its use against Ae. aegypti in the state. Metabolic and target-site resistance mechanisms were also revealed in samples from Aracaju, the capital of Sergipe. Herein, we investigated the presence and distribution of the kdr mutation V1016I^kdr in Ae. aegypti populations from different municipalities of the state. Aedes aegypti eggs were collected from seven municipalities located in areas showing different climatic types and infestation levels. Approximately 20 Ae. aegypti females from each municipality (total of 135 subjects) were individually submitted to allele-specific polymerase chain reaction (AS-PCR) for the 1016 site of the voltage-gated sodium channel (Na_V). The V1016I^kdr mutation was found in subjects from all the municipalities under study with a high frequency of heterozygotes in several locations. Homozygous recessive subjects (resistant kdr genotype) were found only in one municipality. The results suggest a wide distribution of the V1016I^kdr mutation in the northeast Brazil, which indicates urgent need for monitoring the effectiveness of the pyrethroids currently used for vector control.

Protective role of G-CSF in dextran sulfate sodium-induced acute colitis through generating gut-homing macrophages

Granulocyte colony-stimulating factor (G-CSF) is a pleiotropic cytokine best known for its role in promoting the generation and function of neutrophils. G-CSF is also found to be involved in macrophage generation and immune regulation; however, its in vivo role in immune homeostasis is largely unknown. Here, we examined the role of G-CSF in dextran sulfate sodium (DSS)-induced acute colitis using G-CSF receptor-deficient (G-CSFR(-/-)) mice. Mice were administered with 1.5% DSS in drinking water for 5days, and the severity of colitis was measured for the next 5days. GCSFR(-/-) mice were more susceptible to DSS-induced colitis than G-CSFR(+/+) or G-CSFR(-/+) mice. G-CSFR(-/-) mice harbored less F4/80(+) macrophages, but a similar number of neutrophils, in the intestine. In vitro, bone marrow-derived macrophages prepared in the presence of both G-CSF and macrophage colony-stimulating factor (M-CSF) (G-BMDM) expressed higher levels of regulatory macrophage markers such as programmed death ligand 2 (PDL2), CD71 and CD206, but not in arginase I, transforming growth factor (TGF)-β, Ym1 (chitinase-like 3) and FIZZ1 (found in inflammatory zone 1), and lower levels of inducible nitric oxide synthase (iNOS), CD80 and CD86 than bone marrow-derived macrophages prepared in the presence of M-CSF alone (BMDM), in response to interleukin (IL)-4/IL-13 and lipopolysaccharide (LPS)/interferon (IFN)-γ, respectively. Adoptive transfer of G-BMDM, but not BMDM, protected G-CSFR(-/-) mice from DSS-induced colitis, and suppressed expression of tumor necrosis factor (TNF)-α, IL-1β and iNOS in the intestine. These results suggest that G-CSF plays an important role in preventing colitis, likely through populating immune regulatory macrophages in the intestine.

Random yet deterministic: convergent immunoglobulin responses to influenza

B cell clonal expansion is a hallmark of host-defense and vaccination responses. Given the vast immunoglobulin repertoire, individuals may expand B cells carrying largely distinct immunoglobulin genes following antigenic challenge. Using immunoglobulin-repertoire sequencing to dynamically track responses to influenza vaccination, Jackson et al. find evidence of convergent immunoglobulin responses across individuals.

Recent progress using systems biology approaches to better understand molecular mechanisms of immunity

The immune system is composed of multiple dynamic molecular and cellular networks, the complexity of which has been revealed by decades of exacting reductionist research. However, understanding of the immune system sufficient to anticipate its response to novel perturbations requires a more integrative or systems approach to immunology. While methods for unbiased high-throughput data acquisition and computational integration of the resulting datasets are still relatively new, they have begun to substantially enhance our understanding of immunological phenomena. Such approaches have expanded our view of interconnected signaling and transcriptional networks and have highlighted the function of non-linear processes such as spatial regulation and feedback loops. In addition, advances in single cell measurement technology have demonstrated potential sources and functions of response heterogeneity in system behavior. The success of the studies reviewed here often depended upon integration of one or more systems biology approaches with more traditional methods. We hope these examples will inspire a broader range of immunologists to probe questions in a quantitative and integrated manner, advancing collective efforts to understand the immune "system".

The anti-inflammatory role of granulocyte colony-stimulating factor in macrophage–dendritic cell crosstalk afterLactobacillus rhamnosusGR-1 exposure

MΦs are important sensory cells of the innate immune system and regulate immune responses through releasing different combinations of cytokines. In this study, we examined whether cytokines released by MΦs in response to the probiotic bacterial strain GR-1 modulate the responses of DCs. The cytokine profile released by GR-1-treated MΦs was characterized by low levels of TNF-α, GM-CSF, IL-6, and IL-12 but very high levels of G-CSF. GR-1 CM did not induce expression of the shared p40 subunit of IL-12 and IL-23 and costimulatory molecules CD80 or CD86 or increase T cell stimulatory capacity in DCs. However, in G-CSFR-deficient DCs or after antibody-mediated neutralization of G-CSF, GR-1 CM induced IL-12/23 p40 production significantly, indicating that G-CSF within the GR-1 CM inhibits IL-12/23 p40 production induced by other CM components. GR-1 CM and rG-CSF also inhibited LPS-induced IL-12 production at the mRNA and protein levels. The inhibition of IL-12 production by G-CSF was at least in part mediated through inhibition of JNK activation. Finally, splenic DCs of GR-1-injected mice produced less IL-12/23 p40 than those of PBS-injected mice in response to LPS ex vivo, and this was at least partially dependent on exposure to GR-1-induced G-CSF in vivo. Altogether, these results suggest that G-CSF modulates the IL-12/23 p40 response of DCs in the context of the probiotic GR-1 through MΦ–DC crosstalk.

Nanocomposite metal amorphous-carbon thin films deposited by hybrid PVD and PECVD technique

Carbon based films can combine the properties of solid lubricating graphite structure and hard diamond crystal structure, i.e., high hardness, chemical inertness, high thermal conductivity and optical transparency without the crystalline structure of diamond. Issues of fundamental importance associated with nanocarbon coatings are reducing stress, improving adhesion and compatibility with substrates. In this work new nanocomposite coatings with improved toughness based in nanocrystalline phases of metals and ceramics embedded in amorphous carbon matrix are being developed within the frame of a research project: nc-MeNxCy/a-C(Me) with Me = Mo, Si, Al, Ti, etc. Carbide forming metal/carbon (Me/C) composite films with Me = Mo, W or Ti possess appropriate properties to overcome the limitation of pure DLC films. These novel coating architectures will be adopted with the objective to decrease residual stress, improve adherence and fracture toughness, obtain low friction coefficient and high wear-resistance. Nanocomposite DLC's films were deposited by hybrid technique using a PVD-Physically Vapor Deposition (magnetron sputtering) and Plasma Enhanced Chemical Vapor Deposition (PECVD), by the use of CH4 gas. The parameters varied were: deposition time, substrate temperature (180 degrees C) and dopant (Si + Mo) of the amorphous carbon matrix. All the depositions were made on silicon wafers and steel substrates precoated with a silicon inter-layer. The characterisation of the film's physico-mechanical properties will be presented in order to understand the influence of the deposition parameters and metal content used within the a-C matrix in the thin film properties. Film microstructure and film hybridization state was characterized by Raman Spectroscopy. In order to characterize morphology SEM and AFM will be used. Film composition was measured by Energy-Dispersive X-ray analysis (EDS) and by X-ray photoelectron spectroscopy (XPS). The contact angle for the produced DLC's on silicon substrates were also measured. Thin film adherence was studied by micro-scratch test. Residual stresses in the produced coatings will be analysed by bending technique.

Novel nanocomposite coatings with dispersed organic nanoparticles for solar absorbers

A natural pigment (Anthocyanin extracted from Sambucus nigra L. fruit) was incorporated by dipping sputtered titanium oxide films into a pigment solution. The pigment solution has red colour and an absorption peak located in the wavelength range of 520 to 540 nm. Titanium oxide thin films were prepared by reactive DC magnetron sputtering and reactive pulsing DC magnetron sputtering from a Titanium target in O2 + Ar atmosphere onto glass slides. Pigment incorporation in thin films was found dependent of both morphology and composition, which depends on deposition parameters, like pulsing frequency and oxygen flow rate. The incorporation of this pigment in TiOx thin films increases the final solar absorption and decreases the final average roughness of these films. The effect in solar absorption is higher in films prepared by DC and pulsed DC at pulsing frequency of 200 kHz.

Reduced expression of basal and probiotic-inducible G-CSF in intestinal mononuclear cells is associated with inflammatory bowel disease

BACKGROUND

Granulocyte-colony stimulating factor (G-CSF) is a pleiotropic cytokine involved in the hematopoiesis of granulocytes, neuroprotection, and immunomodulation. Previously, we have shown that probiotic Lactobacillus rhamnosus GR-1 induces G-CSF production from bone marrow-derived macrophages. Whether this probiotic also induces G-CSF in intestinal mononuclear cells is unknown.

METHODS

G-CSF release in response to L. rhamnosus GR-1 was analyzed in isolated intestinal lamina propria mononuclear cells from inflammatory bowel disease (IBD) and non-IBD patients. The effects of G-CSF on proinflammatory cytokine production in human peripheral blood mononuclear cells and intestinal tissue from C57BL/6 wildtype and G-CSF receptor knockout mice was examined.

RESULTS

Normal mouse or human intestinal lamina propria cells constitutively express high levels of G-CSF, of which production was further enhanced by exogenous L. rhamnosus GR-1. However, cells obtained from IBD patients showed reduced G-CSF production under basal conditions and also lower production after exogenous GR-1 treatments. Intestinal tissue samples isolated from G-CSF receptor-deficient mice constitutively expressed higher levels of TNFalpha, IL-23, and IL-12 than those from wildtype mice, and pretreatment of G-CSF suppressed lipopolysaccharide (LPS)-induced IL-23 in human peripheral blood mononuclear cells.

CONCLUSIONS

These results suggest that high G-CSF production induced by commensals such as L. rhamnosus is important in maintaining normal immunological homeostasis in the intestine and defects in the production of G-CSF are associated with IBD.

Assessment of pulmonary function in patients before and after laparoscopic and open esophagogastric surgery

BACKGROUND

Laparoscopy is a technique used in various surgical procedures. Few studies in the literature compare stress between laparoscopic and open surgery used for esophagogastric surgical procedures. Pulmonary function is known to be significantly affected in open surgeries, increasing postoperative morbidity and mortality. The current study aimed to assess pulmonary function in patients before and after open and laparoscopic esophagogastric surgery.

METHODS

For this study, 75 patients were divided into two groups: 50 patients undergoing laparoscopy and 25 patients undergoing open surgery. The following parameters were determined by spirometry before and after surgery: forced expiratory volume in the first second (FEV(1)), forced vital capacity (FVC), and forced expiratory flow in the midexpiratory phase (FEF(25-75%)).

RESULTS

A decrease in FEV(1,) FVC, and FEF((25-75%)) was observed in the two groups on postoperative days 2, 3, and 4, as compared with the preoperative period. Likewise, FEV(1) and FVC showed a significant reduction on postoperative days 2, 3, and 4 in the patients who underwent to open surgery, but only on the day 2 in those who underwent to laparoscopic surgery. A significant decrease in FEF((25-75%)) was observed only on postoperative day 2 in the group that underwent open surgery. Significant differences in FEV(1) between the groups were observed on postoperative days 2, 3, and 4. No significant difference in FVC was noted between the groups, and a difference in FEF((25-75%)) was observed only on postoperative day 4.

CONCLUSIONS

Postoperative pulmonary dysfunction was more important for the patients undergoing open surgery than for those undergoing laparoscopic surgery.

The effect of expectations on slow oculomotor control--IV. Anticipatory smooth eye movements depend on prior target motions

Prior work had shown that smooth eye movements depend both on the motion of the target on the retina and on the subject's expectations about future target motion (Kowler and Steinman, 1979a,b). Effects of expectation cannot be eliminated by making target motions unpredictable (Kowler and Steinman, 1981). The experiment reported here shows that effects of expectations on smooth eye movement depend in a lawful way on the history of prior target motions. Anticipatory smooth eye movements (involuntary drifts in the direction of future target motion) were measured while subjects fixated a stationary target that was expected to step in an unpredictable direction (right or left). Anticipatory smooth eye movement velocity depended on the sequence of steps in prior trials, e.g. velocity was faster to the right when the prior steps were to the right. The influence of prior steps diminished the further back into the past the step occurred. Sequential dependencies were also observed for the saccades used to track the target steps. Anticipatory smooth eye movement velocity was predicted by a two-state Markov model developed by Falmagne et al. (1975) for similar sequential dependencies observed in a manual reaction-time task (button-pressing). The model uses the prior sequence of target motions to predict the subject's expectation, and assumes that the expectation determines anticipatory smooth eye movement velocity. The fit of the model to the data was good which shows that taking expectations into account is both necessary and feasible. Taking expectations into account, quantitatively, allows accurate predictions about smooth eye movement velocity when target motions are unpredictable.

Compensatory eye movements during active and passive head movements: fast adaptation to changes in visual magnification

Rotational eye and head movements were recorded with great precision with scleral and cranial search coils in a rotating magnetic field. Compensatory eye movements were recorded in light and darkness during active as well as passive head movements in the frequency range 0.33-1.33 Hz. From the recorded, nominal gaze movements the effective gaze was reconstructed taking into account magnification or reduction factors of corrective spectacles. Effective gain was calculated as the ratio between the velocities of the effective corrective eye movements and the head movements. In the light, effective gain of compensatory eye movements during active head motion was mostly between 0.97 and 1.03. It was never precisely unity and differed systematically between subjects and between the two eyes of each subject. During passive head motion in the light, gain was lower by about 3% than during active motion. During active head movement in the dark, gain was mostly between 0.92 and 1.00; values were about 5% lower than during active motion in the light. During passive head movement in the dark, gain was about 13% lower than during active motion, and the variability of the oculomotor response increased. Adaptation of these base-line conditions was induced by fitting the subjects with magnifying or reducing spectacles for periods of 40 min to 24 h. The largest required change in amplitude of eye movements was 36%. When active head movements were made, the amplitude of compensatory eye movements in the light as well as in the dark adjusted rapidly. Most of the adaptation of the vestibulo-ocular reflex in the dark was completed in about 30 min. This rate is much faster than that found in previous experiments requiring larger adaptive changes. Differential adaptation to unequal demands for the two eyes proved to be very hard or impossible. In a mild conflict situation the system adjusted to an intermediate level, distributing the error symmetrically between the eyes. When the discrepancy was large, the adaptive process of both eyes was controlled by the one eye which provided the most meaningful information. It is concluded that the system generating compensatory eye movements performs best during active rather than passive head movements, and that adaptation to moderate changes in optimal gain are made very rapidly.

Eye movements of preschool children

Accurate recordings of eye movements of children 4 and 5 years old show that their eye movements differed from those of adults. During maintained fixation, saccades were large (1 degree to 2 degrees) and smooth eye movement speeds were high (45 minutes of arc per second). Saccade latencies were highly variable during target step tracking. Smooth pursuit latencies were longer than those of adults. These hitherto unknown characteristics limit a child's ability to use eye movements to acquire visual information.