11 research outputs found

    Multidimensional Single-Cell Analysis of BCR Signaling Reveals Proximal Activation Defect As a Hallmark of Chronic Lymphocytic Leukemia B Cells

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    <div><p>Purpose</p><p>Chronic Lymphocytic Leukemia (CLL) is defined by a perturbed B-cell receptor-mediated signaling machinery. We aimed to model differential signaling behavior between B cells from CLL and healthy individuals to pinpoint modes of dysregulation.</p><p>Experimental Design</p><p>We developed an experimental methodology combining immunophenotyping, multiplexed phosphospecific flow cytometry, and multifactorial statistical modeling. Utilizing patterns of signaling network covariance, we modeled BCR signaling in 67 CLL patients using Partial Least Squares Regression (PLSR). Results from multidimensional modeling were validated using an independent test cohort of 38 patients.</p><p>Results</p><p>We identified a dynamic and variable imbalance between proximal (pSYK, pBTK) and distal (pPLCÎł2, pBLNK, ppERK) phosphoresponses. PLSR identified the relationship between upstream tyrosine kinase SYK and its target, PLCÎł2, as maximally predictive and sufficient to distinguish CLL from healthy samples, pointing to this juncture in the signaling pathway as a hallmark of CLL B cells. Specific BCR pathway signaling signatures that correlate with the disease and its degree of aggressiveness were identified. Heterogeneity in the PLSR response variable within the B cell population is both a characteristic mark of healthy samples and predictive of disease aggressiveness.</p><p>Conclusion</p><p>Single-cell multidimensional analysis of BCR signaling permitted focused analysis of the variability and heterogeneity of signaling behavior from patient-to-patient, and from cell-to-cell. Disruption of the pSYK/pPLCÎł2 relationship is uncovered as a robust hallmark of CLL B cell signaling behavior. Together, these observations implicate novel elements of the BCR signal transduction as potential therapeutic targets.</p></div

    Statistical Analysis of CLL B-cell Phosphoprofile using Partial Least Squares Regression (PLSR) against disease status.

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    <p>This figure details our method for analyzing phosphoflow data by Partial Least Squares Regression (PLSR) against disease status: A Training: 1 CLL B cells or healthy B cells were isolated using the gating described in the methods section. 2 Phosphospecific antibodies allowed detection of the phosphoresponse for pPLCÎł2, pSYK, pBTK, pBLNK and ppERK. The percentage of cells positive for each phosphospecific antibody was calculated based on the unstimulated histograms. These %pX<sup>+</sup> provide the raw data for Partial Least Squares Regression analysis, PLSR. 3 PLSR was applied to best correlate a linear combination of these phosphoprofiles for each patient (all healthy controls and all CLL samples pooled together) with a variable defining disease status (arbitrarily set to 0 for healthy individuals and 1 for CLL patients). This step of the analysis is referred to as “Training” as the PLSR algorithm uses a subset of CLL B cells and Healthy B cells to model the covariance of each phosphoresponse. 4 The output of PLSR analysis is a linear combination V<sub>PLSR</sub> with weights (ÎČ<i><sub>i</sub></i>) to each observed “predictor” variable (%pX<i><sub>i</sub></i><sup>+</sup>). The PLSR algorithm output attempts to find weights that best match the differences between healthy and CLL patient phosphoprofiles with disease status. B Test: Using the model (V<sub>PLSR</sub>) defined during the training phase, we tested the power of our model by its ability to correctly predict the disease status of independently-acquired CLL patients and healthy individuals. Phosphoresponses are measured and linearly-combined into a V<sub>PLSR</sub> variable as specified by the training step. C BCR signaling diagram highlighting pathway-based understanding of the V<sub>PLSR</sub> score and weights. D Example of V<sub>PLSR</sub> predictive power: two samples (one CLL and one healthy control) were tested side-by-side. As predicted, V<sub>PLSR</sub> helps discriminate their differences in phosphoresponses. As illustrated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079987#pone-0079987-g003" target="_blank">Fig. 3A</a>, %pX<sup>+</sup> values over an unstimulated control are calculated and linearly combined to yield V<sub>PLSR</sub> for the sample under consideration. Sample 1119, yields V<sub>PLSR</sub> = 0.02, while Sample 1062, yields V<sub>PLSR</sub> = 0.84, consistently with disease status (healthy and CLL, respectively).</p

    Variability in the Signaling Profile Allows Partioning of CLL Patients Into Distinct Prognostic Groups.

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    <p>A Graphic representation of all five phosphoresponses for CLL patients (blue, n = 110) as compared to the healthy controls (red, n = 11). A pentagon was created for each sample by connecting the percent of responding cells (over unstimulated control) recorded on the axes. A wide variability in extent of response was observed in the CLL group, encompassing all possible level of responsiveness. Three distinct groups of CLL could be defined based on the responsiveness (inset): patients with uniformly low response (left, at least 4 of the 5 pX<sup>+</sup><40%), patients with uniformly high response (right, at least 4 pX<sup>+</sup>>75%), and patients with intermediate, healthy-like response (middle, at least 4 pX<sup>+</sup> within the range of healthy samples). This groups of patients yielded n = 28 among low-responders, n = 36 among intermediate (healthy-like) responders and n = 17 among high-responders. B Kaplan-Meyer curves showing time from diagnosis to first treatment (TTFT) was plotted for the three distinct CLL subgroups described in D. Patients whose phosphoprofile consists of uniformly high phosphoresponses had a statistically significant (p<0.01) shorter time to first treatment (TTFT). Furthermore, high responders had a larger fraction that had required treatment (p<0.04). Those patients whose %pX<sup>+</sup> values were uniformly low or similar to healthy individuals across the 5 responses studied had a significantly longer time to first treatment, and fewer patients within this cohort have required treatment at the time of this analysis. C Distinct IGHV status (% deviation from germline sequence) is also observed between these three subgroups. The dashed line indicates the 2% cutoff for mutational status, mutated vs. unmutated. Mean ± Std. Error % Mutated: Healthy-like = 2.02±0.43; High = 0.73±.21; Low = 3.9±.86. D Three-dimensional visualization of three phosphoresponses ([%pPLCÎł2<sup>+</sup>, %pBLNK<sup>+</sup> and %pSYK<sup>+</sup>], or ([%pPLCÎł2<sup>+</sup>, %pSYK<sup>+</sup> and %ppERK<sup>+</sup>]) for (blue) all CLL and (red) healthy samples. Each panel demonstrates the clear separation of the healthy patient samples from the CLL patient samples solely by virtue of the combined %pX<sup>+</sup> values for the three phosphoresponses.</p

    Phosphoprofiling of the Proximal BCR Signaling Pathway Uncovers High Variability in BCR Signaling Pathway Behavior in CLL B cells.

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    <p>A. Simplified diagram of the BCR signaling pathway components investigated in this study. B. Representative histograms of phosphoresponses of B- cells for two CLL patients (a high and a low responder) and one healthy individual. CLL and healthy B cells were gated as described in the methods section. Stimulated samples (anti-IgM+H<sub>2</sub>O<sub>2</sub>) are indicated by a black line, unstimulated samples are shaded grey. C. Contour maps of the average B cell population: For each cohort, CLL and healthy, the cellular phosphoresponse fluorescence intensity values are averaged and viewed two dimensionally. Bimodality in the phosphoresponse of CLL B cells can be seen for the pairwise pPLCÎł2 vs. pSYK) (see also Supp. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079987#pone.0079987.s003" target="_blank">Fig. S2</a> for other combinations of phosphoresponses). Healthy B cells show modest variability within the B-cell population, while the CLL B cells can be distinguished by their all-or-none response. D. Following IgM crosslinking, phosphoresponses are shown as the percentage of responding cells for each patient over an unstimulated matched control. This view of the wide, continuous range of each CLL patients' phosphoprofile highlights the high variability in the behavior of the BCR signaling pathway. Only the pPLCÎł2 response showed statistical significance when comparing healthy to CLL cells (***p<0.0001).</p

    Cell-to-cell variability analysis for V<sub>PLSR</sub> as a function of CD20 and CD5 abundance.

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    <p>A V<sub>PLSR</sub> analysis of high responder, low responder, and healthy-like responder groups. Three representative patient samples are shown for each responder type. All CLL B-cell samples have a majority of their cellular population exhibiting a V<sub>PLSR</sub>>0.695 consistent with the CLL range (blue, as shown in the scale bar). Histograms represent the mean and spread of the V<sub>PLSR</sub> values within each sample's B-cell population for low, high, and healthy-like responders. While low and high responders have a V<sub>PLSR</sub> score centered around 1, the width of this peak is highly variable, but much more so in the healthy-like CLL. Healthy samples uniformly have a large variance of V<sub>PLSR</sub> scores. B Evaluation of the heterogeneity within the samples as a measure of the variance of V<sub>PLSR</sub> within the B cell population. Healthy-like responders exhibited a significantly larger variance compared to high or how responders (healthy-like vs. high: p = 0.0005; healthy-like vs. low: p = 0.0008; high vs. low: p = 0.23). The variance of V<sub>PLSR</sub> within the B cell population of healthy samples is also shown.</p
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