Automated prediction of the clinical impact of structural copy number variations.

Copy number variants (CNVs) play an important role in many biological processes, including the development of genetic diseases, making them attractive targets for genetic analyses. The interpretation of the effect of these structural variants is a challenging problem due to highly variable numbers of gene, regulatory, or other genomic elements affected by the CNV. This led to the demand for the interpretation tools that would relieve researchers, laboratory diagnosticians, genetic counselors, and clinical geneticists from the laborious process of annotation and classification of CNVs. We designed and validated a prediction method (ISV; Interpretation of Structural Variants) that is based on boosted trees which takes into account annotations of CNVs from several publicly available databases. The presented approach achieved more than 98% prediction accuracy on both copy number loss and copy number gain variants while also allowing CNVs being assigned "uncertain" significance in predictions. We believe that ISV's prediction capability and explainability have a great potential to guide users to more precise interpretations and classifications of CNVs.

Retinoic acid enhances histamine content and H1 receptor expression in human neuroblastoma cell line Paju.

BACKGROUND: A human neuroblastoma cell line (Paju) was induced by retinoic acid (RA) to differentiate into neuron-like cells. MATERIALS AND METHODS: We studied the expression and the possible role of histamine receptors H1 and H2 in retinoic-acid mediated differentiation by semiquantitative RT-PCR. We studied the effect of exogeneously added RA on the morphological change of the human neuroblastoma cell line and the differentiation was followed by vimentine, glial fibrillary acidic protein (GFAP) and neurofilament (NF) immunostaining. We monitored the change of the histidine decarboxylase (HDC) expression and the histamine content during the RA treatment by immunoblot and flow cytometry methods. RESULTS: Our data showed that H1 and H2 histamine receptors are present on Paju cells. Ten nM RA markedly increased the H1 receptor expression of these cells, while the H2 expression was unchanged. CONCLUSION: In the RA-treated Paju cells, the histamine content increased compared to the untreated cells, suggesting that neuroblastoma-derived histamine is involved in the regulation of RA-induced in vitro differentiation by H1 receptors.

Different patterns of the L-histidine decarboxylase (HDC) gene expression in mice resistant and susceptible to experimental cutaneous leishmaniasis.

OBJECTIVE AND DESIGN: In the present study the experimental murine Leishmania major ( L. major) infection model was used to investigate the role of histamine biosynthesis in cutaneous leishmaniasis. SUBJECTS, TREATMENT AND METHODS: A novel RNase Protection Assay (RPA) was developed and applied for the assessment of L-histidine decarboxylase (HDC) gene expression in organs of resistant C57BL/6 and susceptible BALB/c mice after infection with L. major. RESULTS: In the acute phase of infection a rapid but transient induction of HDC expression was observed in the infected lymph nodes of both strains correlating both temporally and spatially with parasite spread. The signal was present in the draining popliteal lymph nodes of both hosts, however, only susceptible mice known to be unable to control parasite dissemination showed induction of HDC in their distant periaortic lymph nodes as well. During the chronic phase of infection only the heavily parasitized organs of BALB/c mice showed high HDC gene expression. CONCLUSIONS: These data suggest that expression of the histamine-producing enzyme HDC in the decisive acute phase of leishmaniasis is not coupled with development of either appropriate Th1 or inadequate Th2 responses to L. major. We hypothesize, however, that during the chronic phase of infection elevated HDC levels, possibly of mast cell origin, are associated with Th2-dominated responses and serious disease development.

Inhibition of effects of endogenously synthesized histamine disturbs in vitro human dendritic cell differentiation.

Histamine, a principal mediator in various physiological and pathological cell functions is synthesized from L-histidine exclusively by histidine decarboxylase, an enzyme, which is expressed in many tissues of mammalian organism. Histamine plays a role in various cellular functions, including cell differentiation. The aim of this study was to determine the presence and to characterize the role of the endogenously produced histamine during in vitro dendritic cell (DC) differentiation induced by interleukin-4 (IL-4) and granulocyte-monocyte colony stimulating factor (GM-CSF). The changes in intracellular histamine content, biosynthesis and gene expression of histidine decarboxylase were investigated during this process. One also studied how histamine receptor antagonists and a histamine synthesis blocker influence the expression of differentiation antigens on the DC during in vitro maturation. During in vitro differentiation parallel culture incubations were performed by adding H1 receptor antagonist triprolidine, H2 receptor antagonist tiotidine, the tamoxifene derivate DPPE which blocks the intracellular binding of histamine, and an irreversible blocker of histidine decarboxylase, alpha-fluoromethyl histamine (alpha-FMH). The results show simultaneous increase in both histidine decarboxylase level and histamine content during differentiation of elutriated monocytes toward DC. Both blockade of de novo histamine production (by alpha-FMH) and inhibition of histamine binding (by H1 and H2 receptor antagonists, triprolidine and tiotidine, respectively) markedly decreased CD40 expression and that of CD45 from the 3rd day of treatment. DPPE by disturbing intracellular interaction of histamine with cytochrome P-450 moieties was able to decrease the expression of CD45, CD86, HLA-DR, CD33, CD40 and CD11c. Based on the data it is suggested that endogenous histamine is actively synthesized during cytokine-induced in vitro DC differentiation. The functional relevance and autocrine and paracrine action of endogenously produced histamine is supported by the data showing that inhibition of histamine synthesis by HDC, blocking of histamine binding by both 'extracellular' histamine receptors (by specific antagonists, triprolidine and tiotidine) and 'intracellular' antagonists (DPPE) disturb the differentiation of DC. This conclusion is supported by the fact, that by the inhibition of histamine acting in an autocrine/paracrine way, the expression pattern of differentiation markers on DC is markedly changed.

Both interferon (IFN)alpha and IFNgamma inhibit histidine decarboxylase expression in the HT168 human melanoma cell line.

OBJECTIVE: Histamine plays an important role in a series of processes including inflammation, allergy, gastric acid secretion, neurotransmission, embryogenesis and in various tumours. Histidine decarboxylase (HDC), the enzyme solely responsible for generation of histamine is expressed in many cells including regenerating and tumour cells. HDC expression is regulated by multiple tissue factors, e.g. various cytokines and growth hormones. In this study the effect of interferon alpha and interferon gamma on the expression of HDC and on cell proliferation in vitro on melanoma cell line. METHODS: We used recombinant human interferon alpha, interferon gamma and human melanoma cell line HT168. RESULTS: Our data show that both IFNalpha and IFNgamma decreased the HDC mRNA and protein expression, though with dissimilar kinetics. IFNgamma strongly suppresses the proliferation at 72 h, while IFNalpha has a more moderate effect. CONCLUSIONS: Since previously the inhibitory effect of histamine on gene expression of interferon gamma was detected, a reciprocal inhibition between histamine and IFNgamma is proposed.