Deep genomic analysis of malignant peripheral nerve sheath tumor cell lines challenges current malignant peripheral nerve sheath tumor diagnosis

Malignant peripheral nerve sheath tumors (MPNSTs) are soft-tissue sarcomas of the peripheral nervous system that develop either sporadically or in the context of neurofibromatosis type 1 (NF1). MPNST diagnosis can be challenging and treatment outcomes are poor. We present here a resource consisting of the genomic characterization of 9 widely used human MPNST cell lines for their use in translational research. NF1-related cell lines recapitulated primary MPNST copy number profiles, exhibited NF1 , CDKN2A , and SUZ12/EED tumor suppres-sor gene (TSG) inactivation, and presented no gain-of-function mutations. In contrast, sporadic cell lines collectively displayed different TSG inactivation patterns and presented kinase-activating mutations, fusion genes, altered muta-tional frequencies and COSMIC signatures, and different methylome-based clas-sifications. Cell lines re-classified as melanomas and other sarcomas exhibited a different drug-treatment response. Deep genomic analysis, methylome-based classification, and cell-identity marker expression, challenged the identity of common MPNST cell lines, opening an opportunity to revise MPNST differential diagnosis

Adhesion Molecules Associated with Female Genital Tract Infection

Altres ajuts: Marie Curie Career Integration Grant i una beca Fundació Dexeus Salut de la DonaEfforts to develop vaccines that can elicit mucosal immune responses in the female genital tract against sexually transmitted infections have been hampered by an inability to measure immune responses in these tissues. The differential expression of adhesion molecules is known to confer site-dependent homing of circulating effector T cells to mucosal tissues. Specific homing molecules have been defined that can be measured in blood as surrogate markers of local immunity (e.g. α4β7 for gut). Here we analyzed the expression pattern of adhesion molecules by circulating effector T cells following mucosal infection of the female genital tract in mice and during a symptomatic episode of vaginosis in women. While CCR2, CCR5, CXCR6 and CD11c were preferentially expressed in a mouse model of Chlamydia infection, only CCR5 and CD11c were clearly expressed by effector T cells during bacterial vaginosis in women. Other homing molecules previously suggested as required for homing to the genital mucosa such as α4β1 and α4β7 were also differentially expressed in these patients. However, CD11c expression, an integrin chain rarely analyzed in the context of T cell immunity, was the most consistently elevated in all activated effector CD8+ T cell subsets analyzed. This molecule was also induced after systemic infection in mice, suggesting that CD11c is not exclusive of genital tract infection. Still, its increase in response to genital tract disorders may represent a novel surrogate marker of mucosal immunity in women, and warrants further exploration for diagnostic and therapeutic purposes

Analysis of protein carbonylation - pitfalls and promise in commonly used methods

Abstract Oxidation of proteins has received a lot of attention in the last decades due to the fact that they have been shown to accumulate and to be implicated in the progression and the patho-physiology of several diseases such as Alzheimer, coronary heart diseases, etc. This has also resulted in the fact that research scientist became more eager to be able to measure accurately the level of oxidized protein in biological materials, and to determine the precise site of the oxidative attack on the protein, in order to get insights into the molecular mechanisms involved in the progression of diseases. Several methods for measuring protein carbonylation have been implemented in different laboratories around the world. However, to date no methods prevail as the most accurate, reliable and robust. The present paper aims at giving an overview of the common methods used to determine protein carbonylation in biological material as well as to highlight the limitations and the potential. The ultimate goal is to give quick tips for a rapid decision making when a method has to be selected and taking into consideration the advantage and drawback of the methods

Adhesion Molecules Associated with Female Genital Tract Infection

Altres ajuts: Marie Curie Career Integration Grant i una beca Fundació Dexeus Salut de la DonaEfforts to develop vaccines that can elicit mucosal immune responses in the female genital tract against sexually transmitted infections have been hampered by an inability to measure immune responses in these tissues. The differential expression of adhesion molecules is known to confer site-dependent homing of circulating effector T cells to mucosal tissues. Specific homing molecules have been defined that can be measured in blood as surrogate markers of local immunity (e.g. α4β7 for gut). Here we analyzed the expression pattern of adhesion molecules by circulating effector T cells following mucosal infection of the female genital tract in mice and during a symptomatic episode of vaginosis in women. While CCR2, CCR5, CXCR6 and CD11c were preferentially expressed in a mouse model of Chlamydia infection, only CCR5 and CD11c were clearly expressed by effector T cells during bacterial vaginosis in women. Other homing molecules previously suggested as required for homing to the genital mucosa such as α4β1 and α4β7 were also differentially expressed in these patients. However, CD11c expression, an integrin chain rarely analyzed in the context of T cell immunity, was the most consistently elevated in all activated effector CD8+ T cell subsets analyzed. This molecule was also induced after systemic infection in mice, suggesting that CD11c is not exclusive of genital tract infection. Still, its increase in response to genital tract disorders may represent a novel surrogate marker of mucosal immunity in women, and warrants further exploration for diagnostic and therapeutic purposes

Frequency of adhesion molecules in CD38⁺ HLA-DR⁺ T_EM cells from different conditions affecting women.

<p>Percentages of the expression of chemokine receptors in CD38⁺ HLA-DR⁺ (<b>a</b>) CD4⁺ effector memory T (T_EM) cells and (<b>b</b>) CD8⁺ T_EM cells determined by flow cytometry are shown for normal donors (ND) and the different groups of patients. Percentages of the expression of integrins and other adhesion molecules in CD38⁺ HLA-DR⁺ (<b>c</b>) CD4⁺ T_EM and (<b>d</b>) CD8⁺ T_EM cells determined by flow cytometry are shown for ND and the different groups of patients. General gating strategy is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156605#pone.0156605.g003" target="_blank">Fig 3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156605#pone.0156605.s002" target="_blank">S2 Fig</a>. Each bar represents the median ± interquartile range of healthy young women (ND; white bars, n = 13), women with psoriasis (PS; grey bars, n = 5), ulcerative colitis (UC; checkered bars, n = 4) and bacterial vaginosis (BV; dark bars, n = 5). P values indicate: *<0.05; **<0.01.</p

CD11c expression in T cells from blood and genital tract after vaginal or systemic <i>Chlamydia</i> infection.

<p>The frequency of CD11c in CD3⁺ T cells was determined by flow cytometry 7 days after vaginal (VAG) or intravenous (IV) infection with <i>C</i>. <i>muridarum</i> in blood or genital tract from mice. Each time point represents the median ± interquartile range of controls (n = 6), VAG-infected animals (n = 8) and IV-infected animals (n = 4).</p

CD11c expression in activated CD4 /CD8 cells from different tissues after vaginal <i>Chlamydia</i> infection in mice.

<p>The frequency of CD44⁺ CD11c⁺ in CD4⁺ (left panels) and CD8⁺ cells (right panels) was determined by flow cytometry 14 days after vaginal (VAG) infection with <i>C</i>. <i>muridarum</i> in spleen, draining lymph nodes (dLNs), blood and genital tract (GT) from mice. Examples from one infected and one control animal are shown.</p

Functions enriched among the top up-regulated genes in activated effector T cells from <i>Chlamydia</i>-infected vs. uninfected mouse samples with Canonical pathways.

<p>Functions enriched among the top up-regulated genes in activated effector T cells from <i>Chlamydia</i>-infected vs. uninfected mouse samples with Canonical pathways.</p

Gating strategy and representative plots of adhesion molecule analysis in circulating T_EM cells from women.

<p>The overall gating strategy for a representative single normal donor is shown. (<b>a</b>) General gating strategy for effector memory T (T_EM) cells consist of the following consecutive gates: lymphocytes, singlets and live CD3⁺ T cells (top row); CD4⁺ and CD4^- (putative CD8⁺) T cells, and the effector CCR7^- fraction for each of these subsets (bottom row). (<b>b</b>) Representative plots of molecules analyzed in T_EM cells in one of the panels are shown: activated CD38 and/or HLA-DR T_EM cells, expression of CCR5 and CCR2, expression of CXCR6, and expression of CXCR3 and CD11c for CD4⁺ T_EM cells (top row) and CD8⁺ T_EM cells (bottom row). Isotype controls are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156605#pone.0156605.s003" target="_blank">S3 Fig</a>.</p

Kinetics of CCR2, CCR5, CXCR6 and CD11c frequency after vaginal <i>Chlamydia</i> infection in mice.

<p>The frequency of CCR5 (<b>a, b</b>), CCR2 (<b>c, d</b>), CXCR6 (<b>e, f</b>) and CD11c (<b>g, h</b>) was determined in activated CD44⁺ (left graphs) and CD44^- (right graphs) effector memory T (T_EM) cells from blood by flow cytometry at 7, 10 and 14 days after vaginal infection with <i>C</i>. <i>muridarum</i> in mice. After gating on live CD3⁺ cells and CD4⁺ or CD4^- (putative CD8⁺) T cells, the frequency of CCR5, CCR2, CXCR6 and CD11c was quantified in the CD62L^- CD44⁺/CD44^- T cell subsets. Each time point represents the median ± interquartile range of three or seven infected animals and all controls (n = 12).</p