BUSCADOR RECOLECTA

Chronic lymphocytic leukemia (CLL) is a lymphoid neoplasm characterized by the accumulation of mature B cells. The diagnosis is established by the detection of monoclonal B lymphocytes in peripheral blood, even in early stages [monoclonal B-cell lymphocytosis (MBLhi)], and its clinical course is highly heterogeneous. In fact, there are well-characterized multiple prognostic factors that are also related to the observed genetic heterogenicity, such as immunoglobulin heavy chain variable region (IGHV) mutational status, del17p, and TP53 mutations, among others. Moreover, a dysregulation of the immune system (innate and adaptive immunity) has been observed in CLL patients, with strong impact on immune surveillance and consequently on the onset, evolution, and therapy response. In addition, the tumor microenvironment is highly complex and heterogeneous (i.e., matrix, fibroblast, endothelial cells, and immune cells), playing a critical role in the evolution of CLL. In this study, a quantitative profile of 103 proteins (cytokines, chemokines, growth/regulatory factors, immune checkpoints, and soluble receptors) in 67 serum samples (57 CLL and 10 MBLhi) has been systematically evaluated. Also, differential profiles of soluble immune factors that discriminate between MBLhi and CLL (sCD47, sCD27, sTIMD-4, sIL-2R, and sULBP-1), disease progression (sCD48, sCD27, sArginase-1, sLAG-3, IL-4, and sIL-2R), or among profiles correlated with other prognostic factors, such as IGHV mutational status (CXCL11/I-TAC, CXCL10/IP-10, sHEVM, and sLAG-3), were deciphered. These results pave the way to explore the role of soluble immune checkpoints as a promising source of biomarkers in CLL, to provide novel insights into the immune suppression process and/or dysfunction, mostly on T cells, in combination with cellular balance disruption and microenvironment polarization leading to tumor escape., Peer reviewed

Data from figures 1 and 3, and a juypter notebook for plotting this data., Peer reviewed

Chronic lymphocytic leukemia (CLL) is a lymphoid neoplasm characterized by the accumulation of mature B cells. The diagnosis is established by the detection of monoclonal B lymphocytes in peripheral blood, even in early stages [monoclonal B-cell lymphocytosis (MBLhi)], and its clinical course is highly heterogeneous. In fact, there are well-characterized multiple prognostic factors that are also related to the observed genetic heterogenicity, such as immunoglobulin heavy chain variable region (IGHV) mutational status, del17p, and TP53 mutations, among others. Moreover, a dysregulation of the immune system (innate and adaptive immunity) has been observed in CLL patients, with strong impact on immune surveillance and consequently on the onset, evolution, and therapy response. In addition, the tumor microenvironment is highly complex and heterogeneous (i.e., matrix, fibroblast, endothelial cells, and immune cells), playing a critical role in the evolution of CLL. In this study, a quantitative profile of 103 proteins (cytokines, chemokines, growth/regulatory factors, immune checkpoints, and soluble receptors) in 67 serum samples (57 CLL and 10 MBLhi) has been systematically evaluated. Also, differential profiles of soluble immune factors that discriminate between MBLhi and CLL (sCD47, sCD27, sTIMD-4, sIL-2R, and sULBP-1), disease progression (sCD48, sCD27, sArginase-1, sLAG-3, IL-4, and sIL-2R), or among profiles correlated with other prognostic factors, such as IGHV mutational status (CXCL11/I-TAC, CXCL10/IP-10, sHEVM, and sLAG-3), were deciphered. These results pave the way to explore the role of soluble immune checkpoints as a promising source of biomarkers in CLL, to provide novel insights into the immune suppression process and/or dysfunction, mostly on T cells, in combination with cellular balance disruption and microenvironment polarization leading to tumor escape., Peer reviewed

Table_1_Enhancing control systems of higher plant culture chambers via multilevel structural mechanistic modelling. Table_2_Enhancing control systems of higher plant culture chambers via multilevel structural mechanistic modelling. Table_3_Enhancing control systems of higher plant culture chambers via multilevel structural mechanistic modelling. Table_4_Enhancing control systems of higher plant culture chambers via multilevel structural mechanistic modelling. Table_5_Enhancing control systems of higher plant culture chambers via multilevel structural mechanistic modelling. Table_6_Enhancing control systems of higher plant culture chambers via multilevel structural mechanistic modelling., Peer reviewed

Additional file 6: Fig. S6. RIPK3 inhibition does not alter Aβo-induced microgliosis in wild-type mice. (A, B) Representative micrographs and quantitative analysis of brain sections from wild-type mice treated as indicated in the images, immunostained with anti-Iba1 antibody (scale bar, 200 μm). The data are presented as mean ± S.E.M. and were analyzed by one-way ANOVA followed by Bonferroni post-test. *p < 0.05; **p < 0.01., Fondecyt FONDAP ISCIII CIBERNED Junta de Andalucia Consejería de Economía y Conocimiento MICIN Ramon y Cajal Program National Institutes of Health., Peer reviewed

Additional file 7: Fig. S7. Aβo neurotoxicity is worsened when microglial cells are present. (A) To characterize Aβo, a negative stain with 1% uranyl acetate was performed followed by electron microscopy analysis. Arrows indicate small oligomeric structures (scale bar, 200 nm). (B, C) Representative images and quantitative analysis of neurons treated as indicated, immunostained with anti-acetylated tubulin antibody (scale bar, 100 μm). (D, E) Representative micrographs and quantitative measurement of neurons and neuron/microglia cocultures treated as indicated, immunolabeled with anti-acetylated tubulin and anti-Iba1 antibodies as specified in the images (scale bar, 100 μm in the middle panel; 50 μm in the right panel). Each experiment was performed at least three independent times, with three replicates per condition each time. The data are presented as mean ± S.E.M. and were analyzed by one-way ANOVA followed by Bonferroni post-test. *p < 0.05; **p < 0.01; ****p < 0.0001., Fondecyt FONDAP ISCIII CIBERNED Junta de Andalucia Consejería de Economía y Conocimiento MICIN Ramon y Cajal Program National Institutes of Health., Peer reviewed

Additional file 8: Fig. S8. Full blots of pMLKL and RIPK3 western blots. (A) The membrane was first probed with an anti-hsp90 antibody and then incubated with anti-RIPK3. (B) The membrane was cut, and each piece was incubated with the indicated antibody. Left panel: colorimetric image showing protein ladder. (C) The membrane was cut and incubated with an anti-pMLKL antibody. Following stripping, and after confirming that no bands could be visualized with ECL, membranes were blocked, and detection of the IgG was done. Left panel: colorimetric image showing protein ladder. (D) The membrane was cut, and each piece was incubated with the indicated antibody. Left panel: colorimetric image showing protein ladder., Fondecyt FONDAP ISCIII CIBERNED Junta de Andalucia Consejería de Economía y Conocimiento MICIN Ramon y Cajal Program National Institutes of Health., Peer reviewed

Additional file 9: Fig. S9. TNF-α alone is not sufficient to trigger neuronal necroptosis. (G, H) Representative micrographs and quantitative measurements of neurons treated for 72 h with CMctrl, CMAβ, TNF-α, and with CMctrl/TNF-α, immunolabeled with anti-acetylated tubulin antibody (scale bar, 200 μm). The data are presented as mean ± S.E.M. and were analyzed by one-way ANOVA followed by Bonferroni post-test. *p < 0.05; **p < 0.01., Fondecyt FONDAP ISCIII CIBERNED Junta de Andalucia Consejería de Economía y Conocimiento MICIN Ramon y Cajal Program National Institutes of Health., Peer reviewed

FIGURES. Figure 1. Workflow of the SNVs for the AF-2018 and MEGASTROKE-CES datasets. NaN: Not a number. SNV: Single Nucleotide Variant. Figure 2. Manhattan plot of MTAG-CES. The X axis represents chromosome location, and the Y axis represents the minus logarithm on base 10 of p-value. Figure 3. Polygenic risk score (PRS) performance. Panel A is a bar plot of the r2 for the PRS models of eight different thresholds in the training set. Panel B represents the p-value variation along the full range of thresholds evaluated in the training set. Panel C shows ROC curves and panel D Precision-Recall curves for the PRS performance in the independent test set. SUPPLEMENTARY FIGURES. Supplementary Figure 1. GO Biological processes enriched in CES prioritized gene set. Supplementary Figure 2. GO Biological processes enriched exclusively in analysis of AF associated genes independently of CES risk. Supplementary Figure 3. Polygenic risk score (PRS) performance for the individual predictors. Panel A shows ROC curves and panel B Precision-Recall curves for the PRS performance in the independent test set., [Background] Occult atrial fibrillation (AF) is one of the major causes of embolic stroke of undetermined source (ESUS). Knowing the underlying etiology of an ESUS will reduce stroke recurrence and/or unnecessary use of anticoagulants. Understanding cardioembolic strokes (CES), whose main cause is AF, will provide tools to select patients who would benefit from anticoagulants among those with ESUS or AF. We aimed to discover novel loci associated with CES and create a polygenetic risk score (PRS) for a more efficient CES risk stratification., [Methods] Multitrait analysis of GWAS (MTAG) was performed with MEGASTROKE-CES cohort (n = 362,661) and AF cohort (n = 1,030,836). We considered significant variants and replicated those variants with MTAG p-value < 5 × 10−8 influencing both traits (GWAS-pairwise) with a p-value < 0.05 in the original GWAS and in an independent cohort (n = 9,105). The PRS was created with PRSice-2 and evaluated in the independent cohort., [Results] We found and replicated eleven loci associated with CES. Eight were novel loci. Seven of them had been previously associated with AF, namely, CAV1, ESR2, GORAB, IGF1R, NEURL1, WIPF1, and ZEB2. KIAA1755 locus had never been associated with CES/AF, leading its index variant to a missense change (R1045W). The PRS generated has been significantly associated with CES improving discrimination and patient reclassification of a model with age, sex, and hypertension., [Conclusion] The loci found significantly associated with CES in the MTAG, together with the creation of a PRS that improves the predictive clinical models of CES, might help guide future clinical trials of anticoagulant therapy in patients with ESUS or AF., Peer reviewed

Supplementary Table 2. Detailed number of participants (IS and controls) included from each project. IS: ischemic strokes patients., [Background] Occult atrial fibrillation (AF) is one of the major causes of embolic stroke of undetermined source (ESUS). Knowing the underlying etiology of an ESUS will reduce stroke recurrence and/or unnecessary use of anticoagulants. Understanding cardioembolic strokes (CES), whose main cause is AF, will provide tools to select patients who would benefit from anticoagulants among those with ESUS or AF. We aimed to discover novel loci associated with CES and create a polygenetic risk score (PRS) for a more efficient CES risk stratification., [Methods] Multitrait analysis of GWAS (MTAG) was performed with MEGASTROKE-CES cohort (n = 362,661) and AF cohort (n = 1,030,836). We considered significant variants and replicated those variants with MTAG p-value < 5 × 10−8 influencing both traits (GWAS-pairwise) with a p-value < 0.05 in the original GWAS and in an independent cohort (n = 9,105). The PRS was created with PRSice-2 and evaluated in the independent cohort., [Results] We found and replicated eleven loci associated with CES. Eight were novel loci. Seven of them had been previously associated with AF, namely, CAV1, ESR2, GORAB, IGF1R, NEURL1, WIPF1, and ZEB2. KIAA1755 locus had never been associated with CES/AF, leading its index variant to a missense change (R1045W). The PRS generated has been significantly associated with CES improving discrimination and patient reclassification of a model with age, sex, and hypertension., [Conclusion] The loci found significantly associated with CES in the MTAG, together with the creation of a PRS that improves the predictive clinical models of CES, might help guide future clinical trials of anticoagulant therapy in patients with ESUS or AF., Peer reviewed