Pitfalls in flow cytometric analyses of surfactant-exposed human leukocytes

deconvSeq: deconvolution of cell mixture distribution in sequencing data

MOTIVATION

Although single-cell sequencing is becoming more widely available, many tissue samples such as intracranial aneurysms are both fibrous and minute, and therefore not easily dissociated into single cells. To account for the cell type heterogeneity in such tissues therefore requires a computational method. We present a computational deconvolution method, deconvSeq, for sequencing data (RNA and bisulfite) obtained from bulk tissue. This method can also be applied to single-cell RNA sequencing data.

RESULTS

DeconvSeq utilizes a generalized linear model to model effects of tissue type on feature quantification, which is specific to the data structure of the sequencing type used. Estimated model coefficients can then be used to predict the cell type mixture within a tissue. Predicted cell type mixtures were validated against actual cell counts in whole blood samples. Using this method, we obtained a mean correlation of 0.998 (95% CI 0.995-0.999) from the RNA sequencing data of 35 whole blood samples and 0.95 (95% CI 0.91-0.98) from the reduced representation bisulfite sequencing data from 35 whole blood samples. Using symmetric balances to obtain the correlation between compositional parts, we found that the lowest correlation occurred for monocytes for both RNA and bisulfite sequencing. Comparison with other methods of decomposition such as deconRNAseq, CIBERSORT, MuSiC and EpiDISH showed that deconvSeq is able to achieve good prediction using mean correlation with far fewer genes or CpG sites in the signature set.

AVAILABILITY AND IMPLEMENTATION

Software implementing deconvSeq is available at https://github.com/rosedu1/deconvSeq.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Background autofluorescence induced by plant extracts in human lymphocytes: A flow cytometric analysis of a critical bias

The presence of background autofluorescence sources is considered as an important problem when performing fluorometric methods, due to the possible spectral overlap between it and the fluorescence emission of probes. Regarding that, we evaluated the presence of background autofluorescence in human lymphocytes after the treatment with extracts from three medicinal plants, including ethanolic extract from aerial parts of Ageratum fastigiatum, ethanolic extract from aerial parts of Eriosema campestre and the ethanolic extract from stem of Pseudobrickellia brasiliensis. Human peripheral blood mononuclear cells were treated with each extract in vitro during 24 h, followed by flow cytometric analysis. Additionally, the fluorescence emission of plant extracts was evaluated by fluorometry, using the same concentrations used in cell cultures. We identified that plant extracts treatment on lymphocytes induced background autofluorescence detectable in several wavelength ranges. Isolated extracts showed no expressive fluorescence emission in fluorometric analyses, suggesting that background autofluorescence was induced in lymphocytes by interactions between cellular components and extracts compounds. Here we discuss the importance to perform previous tests to evaluate a possible background autofluorescence induction after cell treatments with plant extracts or any other substance. In spite of being mandatory, background autofluorescence analysis of cells after treatments and stimulations is still underestimated on literature. In summary, following the precautions herein established should help to reduce the incidence of false positive results.

Anti-inflammatory effects of the new generation synthetic surfactant CHF5633 on Ureaplasma-induced cytokine responses in human monocytes

BACKGROUND

Synthetic surfactants represent a promising alternative to animal-derived preparations in the treatment of neonatal respiratory distress syndrome. The synthetic surfactant CHF5633 has proven biophysical effectiveness and, moreover, demonstrated anti-inflammatory effects in LPS-stimulated monocytes. With ureaplasmas being relevant pathogens in preterm lung inflammation, the present study addressed immunomodulatory features on Ureaplasma-induced monocyte cytokine responses.

METHODS

Ureaplasma parvum-stimulated monocytes were exposed to CHF5633. TNF-α, IL-1β, IL-8, IL-10, TLR2 and TLR4 expression were analyzed using qPCR and flow cytometry.

RESULTS

CHF5633 did not induce pro-inflammation, and did not aggravate Ureaplasma-induced pro-inflammatory cytokine responses. It suppressed U. parvum-induced intracellular TNF-α (p < 0.05) and IL-1β (p < 0.05) in neonatal monocytes and inhibited Ureaplasma-induced TNF-α mRNA (p < 0.05), TNF-α protein (p < 0.001), and IL-1β (p = 0.05) in adult monocytes. Ureaplasma-modulated IL-8, IL-10, TLR2 and TLR4 were unaffected.

CONCLUSION

CHF5633 does neither act pro-apoptotic nor pro-inflammatory in native and Ureaplasma-infected monocytes. Suppression of Ureaplasma-induced TNF-α and IL-1β underlines anti-inflammatory features of CHF5633.

The new generation synthetic reconstituted surfactant CHF5633 suppresses LPS-induced cytokine responses in human neonatal monocytes

BACKGROUND

New generation synthetic surfactants represent a promising alternative in the treatment of respiratory distress syndrome in preterm infants. CHF5633, a new generation reconstituted agent, has demonstrated biophysical effectiveness in vitro and in vivo. In accordance to several well-known surfactant preparations, we recently demonstrated anti-inflammatory effects on LPS-induced cytokine responses in human adult monocytes. The present study addressed pro- and anti-inflammatory effects of CHF5633 in human cord blood monocytes.

METHODS

Purified neonatal CD14(+) cells, either native or simultaneously stimulated with E. coli LPS, were exposed to CHF5633. TNF-α, IL-1β, IL-8 and IL-10 as well as TLR2 and TLR4 expression were analyzed by means of real-time quantitative PCR and flow cytometry.

RESULTS

CHF5633 did not induce pro-inflammation in native human neonatal monocytes and did not aggravate LPS-induced cytokine responses. Exposure to CHF5633 led to a significant decrease in LPS-induced intracellular TNF-α protein expression, and significantly suppressed LPS-induced mRNA and intracellular protein expression of IL-1β. CHF5633 incubation did not affect cell viability, indicating that the suppressive activity was not due to toxic effects on neonatal monocytes. LPS-induced IL-8, IL-10, TLR2 and TLR4 expression were unaffected.

CONCLUSION

Our data confirm that CHF5633 does not exert unintended pro-apoptotic and pro-inflammatory effects in human neonatal monocytes. CHF5633 rather suppressed LPS-induced TNF-α and IL-1β cytokine responses. Our data add to previous work and may indicate anti-inflammatory features of CHF5633 on LPS-induced monocyte cytokine responses.

Impact of the New Generation Reconstituted Surfactant CHF5633 on Human CD4+ Lymphocytes

Background

Natural surfactant preparations, commonly isolated from porcine or bovine lungs, are used to treat respiratory distress syndrome in preterm infants. Besides biophysical effectiveness, several studies have documented additional immunomodulatory properties. Within the near future, synthetic surfactant preparations may be a promising alternative. CHF5633 is a new generation reconstituted synthetic surfactant preparation with defined composition, containing dipalmitoyl-phosphatidylcholine, palmitoyl-oleoyl-phosphatidylglycerol and synthetic analogs of surfactant protein (SP-) B and SP-C. While its biophysical effectiveness has been demonstrated in vitro and in vivo, possible immunomodulatory abilities are currently unknown.

Aim

The aim of the current study was to define a potential impact of CHF5633 and its single components on pro- and anti-inflammatory cytokine responses in human CD4⁺ lymphocytes.

Methods

Purified human CD4⁺ T cells were activated using anti CD3/CD28 antibodies and exposed to CHF5633, its components, or to the well-known animal-derived surfactant Poractant alfa (Curosurf^®). Proliferative response and cell viability were assessed using flow cytometry and a methylthiazolyldiphenyltetrazolium bromide colorimetric assay. The mRNA expression of IFNγ, IL-2, IL-17A, IL-22, IL-4, and IL-10 was measured by quantitative PCR, while intracellular protein expression was assessed by means of flow cytometry.

Results

Neither CHF5633 nor any of its phospholipid components with or without SP-B or SP-C analogs had any influence on proliferative ability and viability of CD4⁺ lymphocytes under the given conditions. IFNγ, IL-2, IL-17A, IL-22, IL-4, and IL-10 mRNA as well as IFNγ, IL-2, IL-4 and IL-10 protein levels were unaffected in both non-activated and activated CD4⁺ lymphocytes after exposure to CHF5633 or its constituents compared to non-exposed controls. However, in comparison to Curosurf^®, expression levels of anti-inflammatory IL-4 and IL-10 mRNA were significantly increased in CHF5633 exposed CD4⁺ lymphocytes.

Conclusion

For the first time, the immunomodulatory capacity of CHF5633 on CD4⁺ lymphocytes was evaluated. CHF5633 did not show any cytotoxicity on CD4⁺ cells. Moreover, our in vitro data indicate that CHF5633 does not exert unintended pro-inflammatory effects on non-activated and activated CD4⁺ T cells. As far as anti-inflammatory cytokines are concerned, it might lack an overall reductive ability in comparison to animal-derived surfactants, potentially leaving pro- and anti-inflammatory cytokine response in balance.

Effects of the New Generation Synthetic Reconstituted Surfactant CHF5633 on Pro- and Anti-Inflammatory Cytokine Expression in Native and LPS-Stimulated Adult CD14+ Monocytes

Background

Surfactant replacement therapy is the standard of care for the prevention and treatment of neonatal respiratory distress syndrome. New generation synthetic surfactants represent a promising alternative to animal-derived surfactants. CHF5633, a new generation reconstituted synthetic surfactant containing SP-B and SP-C analogs and two synthetic phospholipids has demonstrated biophysical effectiveness in vitro and in vivo. While several surfactant preparations have previously been ascribed immunomodulatory capacities, in vitro data on immunomodulation by CHF5633 are limited, so far. Our study aimed to investigate pro- and anti-inflammatory effects of CHF5633 on native and LPS-stimulated human adult monocytes.

Methods

Highly purified adult CD14⁺ cells, either native or simultaneously stimulated with LPS, were exposed to CHF5633, its components, or poractant alfa (Curosurf^®). Subsequent expression of TNF-α, IL-1β, IL-8 and IL-10 mRNA was quantified by real-time quantitative PCR, corresponding intracellular cytokine synthesis was analyzed by flow cytometry. Potential effects on TLR2 and TLR4 mRNA and protein expression were monitored by qPCR and flow cytometry.

Results

Neither CHF5633 nor any of its components induced inflammation or apoptosis in native adult CD14⁺ monocytes. Moreover, LPS-induced pro-inflammatory responses were not aggravated by simultaneous exposure of monocytes to CHF5633 or its components. In LPS-stimulated monocytes, exposure to CHF5633 led to a significant decrease in TNF-α mRNA (0.57 ± 0.23-fold, p = 0.043 at 4h; 0.56 ± 0.27-fold, p = 0.042 at 14h). Reduction of LPS-induced IL-1β mRNA expression was not significant (0.73 ± 0.16, p = 0.17 at 4h). LPS-induced IL-8 and IL-10 mRNA and protein expression were unaffected by CHF5633. For all cytokines, the observed CHF5633 effects paralleled a Curosurf®-induced modulation of cytokine response. TLR2 and TLR4 mRNA and protein expression were not affected by CHF5633 and Curosurf®, neither in native nor in LPS-stimulated adult monocytes.

Conclusion

The new generation reconstituted synthetic surfactant CHF5633 was tested for potential immunomodulation on native and LPS-activated adult human monocytes. Our data confirm that CHF5633 does not exert unintended pro-inflammatory effects in both settings. On the contrary, CHF5633 significantly suppressed TNF-α mRNA expression in LPS-stimulated adult monocytes, indicating potential anti-inflammatory effects.