Approaching Mass Cytometry Translational Studies by Experimental and Data Curation Settings

Clinical studies are conducted to better understand the pathological mechanism of diseases and to find biomarkers associated with disease activity, drug response, or outcome prediction. Mass cytometry (MC) is a high-throughput single-cell technology that measures hundreds of cells per second with more than 40 markers per cell. Thus, it is a suitable tool for immune monitoring and biomarker discovery studies. Working in translational and clinical settings requires a careful experimental design to minimize, monitor, and correct the variations introduced during sample collection, preparation, acquisition, and analysis. In this review, we will focus on these important aspects of MC-related experiments and data curation in the context of translational clinical research projects.

Lack of strong innate immune reactivity renders macrophages alone unable to control productive Varicella-Zoster Virus infection in an isogenic human iPSC-derived neuronal co-culture model

With Varicella-Zoster Virus (VZV) being an exclusive human pathogen, human induced pluripotent stem cell (hiPSC)-derived neural cell culture models are an emerging tool to investigate VZV neuro-immune interactions. Using a compartmentalized hiPSC-derived neuronal model allowing axonal VZV infection, we previously demonstrated that paracrine interferon (IFN)-α2 signalling is required to activate a broad spectrum of interferon-stimulated genes able to counteract a productive VZV infection in hiPSC-neurons. In this new study, we now investigated whether innate immune signalling by VZV-challenged macrophages was able to orchestrate an antiviral immune response in VZV-infected hiPSC-neurons. In order to establish an isogenic hiPSC-neuron/hiPSC-macrophage co-culture model, hiPSC-macrophages were generated and characterised for phenotype, gene expression, cytokine production and phagocytic capacity. Even though immunological competence of hiPSC-macrophages was shown following stimulation with the poly(dA:dT) or treatment with IFN-α2, hiPSC-macrophages in co-culture with VZV-infected hiPSC-neurons were unable to mount an antiviral immune response capable of suppressing a productive neuronal VZV infection. Subsequently, a comprehensive RNA-Seq analysis confirmed the lack of strong immune responsiveness by hiPSC-neurons and hiPSC-macrophages upon, respectively, VZV infection or challenge. This may suggest the need of other cell types, like T-cells or other innate immune cells, to (co-)orchestrate an efficient antiviral immune response against VZV-infected neurons.

Single-cell immune profiling of Meniere Disease patients

BACKGROUND

Meniere Disease (MD) is an inner ear syndrome, characterized by episodes of vertigo, tinnitus and fluctuating sensorineural hearing loss. The pathological mechanism leading to sporadic MD is still poorly understood, however an allergic inflammatory response seems to be involved in some patients with MD.

OBJECTIVE

Decipher an immune signature associated with the syndrome.

METHODS

We performed mass cytometry immune profiling on peripheral blood from MD patients and controls. We analyzed differences in state and differences in abundance of the different cellular subsets. IgE levels were quantified through ELISA on supernatant of cultured whole blood.

RESULTS

We have identified two clusters of individuals according to the single cell cytokine profile. These clusters presented differences in IgE levels, immune cell population abundance, including a reduction of CD56^dim NK-cells, and changes in cytokine expression with a different response to bacterial and fungal antigens.

CONCLUSION

Our results support a systemic inflammatory response in some MD patients that show a type 2 response with allergic phenotype, which could benefit from personalized IL-4 blockers.

OP0231 MASS CYTOMETRY DATA RECLASSIFY SYSTEMIC AUTOIMMUNE DISEASE PATIENTS IN PHENOTYPICALLY DISTINCTIVE GROUPS

Background

Systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), systemic sclerosis (SSC), Sjögren’s syndrome (SJS), mixed connective tissue disease (MCTD), primary antiphospholipid syndrome (PAPS) and undifferentiated connective tissue disease (UCTD) are classified as systemic autoimmune diseases (SADs). They are diagnosed based on different clinical and laboratory criteria. Due to their high internal heterogeneity and overlapping symptoms, SADs are difficult to diagnose. Therefore, molecular and cellular-based studies need to be undertaken to precisely classify the patients. Mass cytometry is a single-cell proteomics technology that measures approximately 50 markers per cell, thus it is a suitable tool to perform deep-phenotyping studies in SADs.

Objectives

Explore differences and similarities between SADs and build reclassification framework using high-dimensional cytometry data.

Methods

The whole blood samples collected from 129 individuals, including patients and controls were stained with a 39-plex antibody panel and acquired in 9 batches on a CyTOF (HELIOS) instrument. Data were cleaned, and normalized for batch effects using semi-automated cytof analysis pipeline. Cell frequencies and median signal intensities (MSI) for each population were extracted using FlowSOM for mononuclear cells (PBMC) and Phenograph for granulocytes. Secretion of 44 cytokines and chemokines were analyzed using a multiplexed luminex assay. Diseases were compared by Kruskal-Wallis analysis and hierarchical clustering and reclassification was done using unsupervised k-means clustering. Cytokine analysis across clusters was performed using Kruskal-Wallis test.

Results

Differently expressed features were observed between patient groups, regarding frequency of classical monocytes, B and T cells subpopulations, mature and immature granulocytes and intensities of CD38, HLA-DR and CD95 across various populations. However, none of them were disease specific. K-means clustering identified four patient clusters, which were composed by a mixture of different diagnosis. Cluster C1 was characterized by increased levels of circulating cells from PBMC compartment, and lower activation of different populations of the T cell compartment. It presented lower frequency in multiple granulocyte populations and the highest expression of CD95 and CD38. This cluster was also associated with antimalarial and steroid treatment. Clusters C1 and C2 were exactly opposite to each other, cluster C3 was characterized by intermediate features between C1 and C2 and cluster C4 could be considered as undifferentiated, mixed group. Higher production of TNFα, IL-10 and IP-10 were found in patients from C1 compared to C2, suggesting more active phenotype in C1 and physiological one in C2. The cytokine levels were independent of the treatment.

Conclusion

We constructed a patient reclassification framework using cell frequencies and expression levels of functional markers. To our knowledge this is the first time when 7 different SADs were compared using mass cytometry. In agreement with other reports we did not detect any disease-specific cellular markers. Distribution of diagnosis across different clusters confirms diseases heterogeneity. Patients can be classified into phenotypically similar groups, that could potentially benefit from the same line of treatment.

Acknowledgements

This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 831434 (3TR) and The JU receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. Also from No 115565 PRECISESADS.

Disclosure of Interests

None declared

PeacoQC: Peak-based selection of high quality cytometry data

In cytometry analysis, a large number of markers is measured for thousands or millions of cells, resulting in high-dimensional datasets. During the measurement of these samples, erroneous events can occur such as clogs, speed changes, slow uptake of the sample etc., which can influence the downstream analysis and can even lead to false discoveries. As these issues can be difficult to detect manually, an automated approach is recommended. In order to filter these erroneous events out, we created a novel quality control algorithm, Peak Extraction And Cleaning Oriented Quality Control (PeacoQC), that allows for automated cleaning of cytometry data. The algorithm will determine density peaks per channel on which it will remove low quality events based on their position in the isolation tree and on their mean absolute deviation distance to these density peaks. To evaluate PeacoQC's cleaning capability, it was compared to three other existing quality control algorithms (flowAI, flowClean and flowCut) on a wide variety of datasets. In comparison to the other algorithms, PeacoQC was able to filter out all different types of anomalies in flow, mass and spectral cytometry data, while the other methods struggled with at least one type. In the quantitative comparison, PeacoQC obtained the highest median balanced accuracy and a similar running time compared to the other algorithms while having a better scalability for large files. To ensure that the parameters chosen in the PeacoQC algorithm are robust, the cleaning tool was run on 16 public datasets. After inspection, only one sample was found where the parameters should be further optimized. The other 15 datasets were analyzed correctly indicating a robust parameter choice. Overall, we present a fast and accurate quality control algorithm that outperforms existing tools and ensures high-quality data that can be used for further downstream analysis. An R implementation is available.

Data processing workflow for large-scale immune monitoring studies by mass cytometry

Mass cytometry is a powerful tool for deep immune monitoring studies. To ensure maximal data quality, a careful experimental and analytical design is required. However even in well-controlled experiments variability caused by either operator or instrument can introduce artifacts that need to be corrected or removed from the data. Here we present a data processing pipeline which ensures the minimization of experimental artifacts and batch effects, while improving data quality. Data preprocessing and quality controls are carried out using an R pipeline and packages like CATALYST for bead-normalization and debarcoding, flowAI and flowCut for signal anomaly cleaning, AOF for files quality control, flowClean and flowDensity for gating, CytoNorm for batch normalization and FlowSOM and UMAP for data exploration. As proper experimental design is key in obtaining good quality events, we also include the sample processing protocol used to generate the data. Both, analysis and experimental pipelines are easy to scale-up, thus the workflow presented here is particularly suitable for large-scale, multicenter, multibatch and retrospective studies.

Stabilization of Human Whole Blood Samples for Multicenter and Retrospective Immunophenotyping Studies

Whole blood is often collected for large-scale immune monitoring studies to track changes in cell frequencies and responses using flow (FC) or mass cytometry (MC). In order to preserve sample composition and phenotype, blood samples should be analyzed within 24 h after bleeding, restricting the recruitment, analysis protocols, as well as biobanking. Herein, we have evaluated two whole blood preservation protocols that allow rapid sample processing and long-term stability. Two fixation buffers were used, Phosphoflow Fix and Lyse (BD) and Proteomic Stabilizer (PROT) to fix and freeze whole blood samples for up to 6 months. After analysis by an 8-plex panel by FC and a 26-plex panel by MC, manual gating of circulating leukocyte populations and cytokines was performed. Additionally, we tested the stability of a single sample over a 13-months period using 45 consecutive aliquots and a 34-plex panel by MC. We observed high correlation and low bias toward any cell population when comparing fresh and 6 months frozen blood with FC and MC. This correlation was confirmed by hierarchical clustering. Low coefficients of variation (CV) across studied time points indicate good sample preservation for up to 6 months. Cytokine detection stability was confirmed by low CVs, with some differences between fresh and fixed conditions. Thirteen months regular follow-up of PROT samples showed remarkable sample stability. Whole blood can be preserved for phenotyping and cytokine-response studies provided the careful selection of a compatible antibody panel. However, possible changes in cell morphology, differences in antibody affinity, and changes in cytokine-positive cell frequencies when compared to fresh blood should be considered. Our setting constitutes a valuable tool for multicentric and retrospective studies. © 2020 International Society for Advancement of Cytometry.

Key steps and methods in the experimental design and data analysis of highly multi-parametric flow and mass cytometry

High-dimensional, single-cell cell technologies revolutionized the way to study biological systems, and polychromatic flow cytometry (FC) and mass cytometry (MC) are two of the drivers of this revolution. As up to 30-50 dimensions respectively can be measured per single-cell, they allow deep phenotyping combined with cellular functions studies, like cytokine production or protein phosphorylation. In parallel, the bioinformatics field develops algorithms that are able to process incoming data and extract the most useful and meaningful biological information. However, the success of automated analysis tools depends on the generation of high-quality data. In this review we present the most recent FC and MC computational approaches that are used to prepare, process and interpret high-content cytometry data. We also underscore proper experimental design as a key step for obtaining good quality data.

Periodontal pathogen exposure facilitates disease activity in Systemic Lupus Erythematosus

This study was undertaken to evaluate whether exposure to subgingival plaque bacteria and periodontal dysbiosis influences disease parameters in systemic lupus erythematosus (SLE).

Circulating antibodies to periodontal bacteria are surrogate markers to determine an ongoing bacterial burden, or are indicators of past exposure. SLE patient sera in the Oklahoma Lupus Cohort (n=303) were used to measure antibody titers against periodontal pathogens (A. actinomycetemcomitans, P. gingivalis, and T. denticola) and commensals (C. ochracea and S. gordonii) by ELISA. Correlations between anti-bacterial antibodies and clinical parameters of SLE including autoantibodies, complement, and disease activity (SLEDAI and BILAG) were studied. The effect of oral infection with A. actinomycetemcomitans on SLE in NZM2328 lupus mice was evaluated.

SLE patients had varying amounts of antibodies to different oral bacteria. The antibody titers against A. actinomycetemcomitans, P. gingivalis, T. denticola, and C. ochracea were higher in patients positive for anti-dsDNA, and in patients with low complement. Only antibodies to A. actinomycetemcomitans and P. gingivalis, but not T. denticola, were associated with higher disease activity. A. actinomycetemcomitans infected NZM2328 mice developed an increase in histone reactive T cells and an accelerated onset of proteinuria, and lupus nephritis.

Our results indicate that exposure to only specific pathogenic periodontal bacteria influences disease activity in SLE patients. The results from lupus mice suggest that this may be due to the amplification of local autoimmunity in response to infection. These findings provide a rationale for assessing and improving periodontal health in SLE patients.

Brief Report: Patients With Primary Sjögren's Syndrome Who Are Positive for Autoantibodies to Tripartite Motif-Containing Protein 38 Show Greater Disease Severity

OBJECTIVE

Autoantibodies reactive with Ro52 (tripartite motif-containing protein 21 [TRIM21]) are detected in 70% of patients with primary Sjögren's syndrome (SS). TRIM21 belongs to a 34-member C-IV family of TRIM proteins. Although autoantibodies against other TRIM proteins within the C-IV family have been detected in the sera of patients with primary SS, their clinical relevance remains unclear. This study was undertaken to investigate the frequency of anti-TRIM38 in patients with primary SS and evaluate its association with various clinical measures of the disease.

METHODS

Serum samples from patients with primary SS (n = 235) and controls (n = 50) were analyzed for reactivity with in vitro-transcribed and -translated (35) S-methionine-labeled TRIM38 protein. The associations of anti-TRIM38 with various laboratory and clinical measures of primary SS were evaluated. Reactivity of anti-TRIM38 with different structural domains of TRIM38 was analyzed. Affinity-purified anti-TRIM38 antibodies were used to immunoprecipitate TRIM21.

RESULTS

TRIM38-reactive autoantibodies were detected in the sera of 24 of the 235 patients with primary SS and 2 of the 50 controls. Anti-TRIM38 positivity was significantly associated with the presence of anti-Ro60, anti-Ro52, anti-La, rheumatoid factor, and hypergammaglobulinemia. Clinically, anti-TRIM38 was associated with significantly higher ocular surface staining scores, lower Schirmer's test scores, and minor labial salivary gland biopsy focus scores of ≥3.0. Anti-TRIM38 antibodies mainly recognized the cortactin-binding protein 2 (CortBP-2; amino acids 128-238) and the B30.2/SPRY (amino acids 268-465) domains on TRIM38. Affinity-purified antibodies to TRIM38-CortBP-2 and TRIM38-B30.2/SPRY domains reacted with TRIM21.

CONCLUSION

Our data demonstrate that anti-TRIM38 specificity arising in a subset of patients with primary SS is associated with increased severity of the disease.

A potential link between immune response to a periodontal bacterium, Aggregatibacter actinomycetemcomintans and Systemic Lupus Erythematosus

Infections are a significant cause of morbidity in Systemic Lupus Erythematosus (SLE). Although oral health is considerably compromised in SLE patients, the role of oral pathogens in influencing lupus pathogenesis is not known. In the present study, antibody responses to a periodontogenic, facultative anaerobic bacterium, Aggregatibacter actinomycetemcomitans (Aa), (which serve as an indicator of past or ongoing infection with Aa), were measured in SLE patients (n=587) and healthy controls (n=75). The associations between anti-Aa antibody titers and clinical measures of SLE were evaluated. The effect of Aa infection on development of lupus was investigated in the NZM2328 mice. The ability of Aa to induce neutrophil extracellular traps (NETs) was studied in vitro.

Both SLE patients and controls showed the presence of anti-Aa. In SLE patients, the anti-Aa titers correlated strongly with anti-dsDNA, anti-chromatin, anti-RNP, and anti-Sm; but not with anti-Ro52, anti-Ro60, and anti-La antibodies. NZM2328 mice developed a robust immune response to Aa, and the Aa infection caused an accelerated onset of autoantibody and renal disease. In addition, Aa readily induced NETosis in NZM2328 neutrophils.

Our data suggest for the first time that SLE patients are exposed to oral pathogen Aa, and this exposure significantly influences immune responses against a subset of lupus-associated autoantigens, possibly through NETosis. Furthermore, our studies suggest that management of oral health in SLE patients might prove to be beneficial for controlling lupus.

Multiple TRIM proteins are targets of autoimmune response in lupus and Sjogren's syndrome. (HUM7P.308)

TRIM21 belongs to the large family of tripartite motif containing proteins, and is often targeted by autoantibodies in lupus and Sjogren’s syndrome. Considering the significant protein domain homology between different TRIM proteins, we hypothesized that additional TRIM proteins are targets of autoimmunity. Based on the literature, in this study we investigated autoantibody responses to TRIM38. While 9% of lupus patients (n=149) had anti-TRIM38 antibodies, the incidence in Sjogren’s syndrome patients (n=150) was 12%, and in controls (n=50) it was 4%. With respect to TRIM21, the incidence was 62%, 68%, and 4% respectively. In Sjogren’s syndrome patients, the presence of anti-TRIM38 antibodies was closely associated with the increased severity of dry eye parameters. Epitope mapping studies showed that anti-TRIM21 antibodies reacted with the RING, Coiled coil and PRY-SPRY domains of TRIM21, whereas anti-TRIM38 antibodies reacted only with the Coiled coil and PRY-SPRY domains of TRIM38. All anti-TRIM38 positive patients also had anti-TRIM21 antibodies. Affinity purified anti-TRIM21 antibodies from lupus patients did not immunoprecipitate TRIM38, indicating lack of cross-reactivity at B cell level. However, we observed T cell cross-reactivity between TRIM21298-312 and TRIM38302-316. Our study suggests that immune responses to TRIM proteins can evolve through epitope spreading and contribute towards exacerbating the pathogenesis in autoimmune disorders.

Anti-TRIM21 autoantibody and inflammasome interaction in pathogenesis of Sjogren's syndrome (BA3P.200)

Sjögren’s syndrome is a chronic autoimmune disorder mainly affecting the exocrine glands and is commonly associated with autoantibodies to TRIM21. This study was undertaken to determine the role of TRIM21-reactive antibodies in pathogenesis of Sjögren’s syndrome. NZM mouse strains (2758, 2328, 2410) were immunized with recombinant TRIM21 protein adsorbed on to alum. Mice were monitored for autoantibodies, serum cytokines and pilocarpine induced salivation. Although all NZM mouse strains generated a robust anti-TRIM21 antibody response, salivary gland dysfunction only occurred in the NZM2758 mice. Moreover, alum immunized NZM2758 mice also displayed some loss of glandular function. Serum levels of IL-1α and CXCL1 were upregulated in alum and alum-TRIM21 treated groups of NZM2758 mice. In contrast, levels of IL-2, IL-5, IL-6 and IL-17 were upregulated, only in the alum-TRIM21 treated mice. Antibodies from TRIM21 immunized mice penetrated live cells in vitro, and showed cytoplasmic staining. Passive transfer of sera from TRIM21 immunized mice induced salivary gland dysfunction in recipient mice, only if the recipients were pre primed with alum. Our study shows that in a genetically susceptible mouse strain, anti-TRIM21 antibodies directly affected salivary gland function and this phenomenon was dependent on the activation of inflammasome pathway. Thus, interaction between innate and adaptive immunity is critical for pathogenesis of Sjögren’s syndrome.