Resolving complex hierarchies in chemical mixtures: how chemometrics may serve in understanding the immune system

In this paper, we explore the ways in which manual sequential gating, machine learning and chemometrics compare, and show complementary strength in the analyses of the hierarchies of multicolour flow cytometry data, to resolve molecular and cell mixtures into insightful contributions to the immune system.

The Structural Basis of IKs Ion-Channel Activation: Mechanistic Insights from Molecular Simulations

ABSTRACTRelating ion-channel (iCh) structural dynamics to physiological function remains a challenge. Current experimental and computational techniques have limited ability to explore this relationship in atomistic detail over physiological timescales. A framework associating iCh structure to function is necessary for elucidating normal and disease mechanisms. We formulated a modeling schema that overcomes the limitations of current methods through applications of Artificial Intelligence Machine Learning (ML). Using this approach, we studied molecular processes that underlie human IKs voltage mediated gating. IKs malfunction underlies many debilitating and life-threatening diseases. Molecular components of IKs that underlie its electrophysiological function include KCNQ1 (pore forming tetramer) and KCNE1 (auxiliary subunit). Simulations, using the IKs structure-function model, reproduced experimentally recorded saturation of gating charge displacement at positive membrane voltages, two-step voltage sensor (VS) movement shown by fluorescence, iCh gating statistics, and current-voltage (I-V) relationship. New mechanistic insights include - (1) pore energy profile determines iCh subconductance (SC), (2) entire protein structure, not limited to the pore, contributes to pore energy and channel SC, (3) interactions with KCNE1 result in two distinct VS movements, causing gating charge saturation at positive membrane voltages and current activation delay, and (4) flexible coupling between VS and pore permits pore opening at lower VS positions, resulting in sequential gating. The new modeling approach is applicable to atomistic scale studies of other proteins on timescales of physiological function.

Relative frequency of immature CD34+/CD90+ subset in peripheral blood following mobilization correlates closely and inversely with the absolute count of harvested stem cells in multiple myeloma patients

Background/Aim. Stem cells (SCs) guarantee complete/longterm bone marrow (BM) repopulation after SC-transplants. The aim of the study was to evaluate absolute count of total SCs (determined by ISHAGE-sequential-gating protocol ? SCish) and relative frequency of immature CD34+/CD90+ (CD90+SCish) subset in peripheral blood (PB) as predictive factors of mobilization and apheresis product (AP) quality. Methods. Mobilization included chemotherapy and granulocytegrowth- factor (G-CSF). Harvesting was performed by Spectra- Optia-IDL-system. The SCsish were determined as a constitutional part of CD34+ cells in the ?stem-cell-region? using FC- 500 flow-cytometer. In this study, the original ISHAGEsequential- gating protocol was modified by introduction of anti-CD90-PE monoclonal-antibody into the analysis of CD90 expression on SCish (CD90+SCish). The results were presented as a percentage of SCish per nucleated-cell count, absolute SCish count in ?L of the PB or the AP, percentage of the CD90+SCish expressed to SCish and absolute CD90+SCish count in ?L of the PB or the AP. Results. The absolute count of total SCish and CD90+SCish was significantly higher (p = 0.0007 and p = 0.0266, respectively) in the AP than in the PB samples. The CD90+SCish/total SCish indexes from PB were higher than indexes from the AP (p = 0.039). The relative frequency of CD90+SCish showed a highly significant inverse correlation with the absolute count of total SCish in both, the PB and AP (p = 0.0003 and p = 0.0013 respectively). The relative frequency of CD90+SCish from the PB also showed a significant (p = 0.0002) inverse relationship with total SCish count in the AP. Patients with less than 10% CD90+SCish in the PB had evidently higher (p = 0.0025) total SCish count in the AP. Conclusion. We speculate that lower CD90+SCish yield in the AP is not a consequence of an inferior collection efficacy, but most likely a result of several still not fully resolved immature SC cytomorphological/ biophysical features. Therefore, following the mobilization by chemotherapy G-CSF, some logical questions appear ? whether we should follow the absolute count of total SCish, or, whether we should test for relative frequency of CD90+SCish prior to harvesting. To reach the final conclusions, it is essential to conduct further controlled and larger investigations concerning the correlation of circulating and harvested SCs with patients' hematopoietic recovery.

Contribution of different Ca2+ channels to the acrosome reaction-mediated initiation of sperm motility in the newt Cynops pyrrhogaster

SummaryInitiation of sperm motility in urodeles, which is induced by a sperm motility-initiating substance (SMIS) in the sequestered granules on the surface of egg jelly, is mediated by the acrosome reaction (AR), which is triggered by an AR-inducing substance (ARIS) on a sheet-like structure. Details of the unique process of the interaction between egg jelly and sperm in these species is still unclear. The current study showed the fine structure of egg jelly in the newt Cynops pyrrhogaster, a urodele species, revealing that its outer surface was covered by a sheet-like structure of approximately 0.29 μm in thickness. Granules of approximately 2 μm in diameter with small particles of approximately 54 nm were attached to its surface and distributed inhomogeneously just beneath the sheet-like structure. Emission spectrometry revealed that the Ca2+ concentration was maintained at a high level compared with that of the blood plasma and the vas deferens fluid, suggesting that egg jelly is a reliable source of Ca2+ for the sperm–egg interaction. Blockers of the T-type voltage-dependent Ca2+ channel (VDCC), but not the L-type VDCC, inhibited both AR and initiation of sperm motility. Conversely, Ni+, which affects the α1 H subunit of T-type VDCC, only inhibited the initiation of sperm motility. These data suggest that, in response to ARIS and SMIS, sequential gating of distinct Ca2+ channels occurs in the AR, followed by the initiation of sperm motility on the surface of the egg jelly in C. pyrrhogaster at fertilization.

Combined ROR1 and CD160 Detection For Improved Minimal Residual Disease In Patients With Chronic Lymphocytic Leukemia (CLL)

Introduction Over the past decade, treatments for patients with chronic lymphocytic leukemia (CLL) have produced complete remissions (CR) without evidence for minimal residual disease (MRD), particularly for younger and/or fitter patients. In this setting, achieving an MRD-negative CR has prognostic implications, yielding longer progression free survival (PFS) and overall survival (OS) than for patients who achieve a CR with persistent MRD. Complicating efforts to incorporate testing for MRD in clinical practice has been the lack of a defined consensus on the methods of MRD detection. In this study, we report on a novel combination of mAbs for MRD detection by flow cytometry based on two antigens: the NK-cell receptor and tumor specific antigen, CD160; and the tumor associated antigen, receptor tyrosine kinase-like orphan receptor 1 (ROR-1). Objective To compare a novel single-tube, tumor-specific (CD160+ROR1) targeted approach to MRD detection against the previously published CD160 flow cytometric assay (CD160FCA) (Farren et al, 2011) and the new, single-tube 8-color ERIC assay. Methods Between October 2012 and July 2013, prospective assessment of MRD was performed on peripheral blood in 56 patients (86 samples). We developed a flow cytometric assay using mAbs specific for CD160 or ROR1 (Fukuda et al, 2008). For this we used the following mAb from BD Biosciences: CD2 FITC, CD5 Pe-Cy7, CD19 PerCP5.5, CD45V500, CD160PE, ROR-1 AF647 (“ROR-160FCA”) and a sequential gating strategy. This was compared with CD160FCA and the 8-color ERIC consortium protocol (unpublished). Light chain analysis (LCR) was performed in all cases and reported where detectable. A proof of concept spiking experiment simulating MRD was prepared by mixing CLL and normal peripheral blood leukocytes in a serial dilution to a level of 10-5(n=3). Statistical analysis was performed using Spearman Rank correlation coefficients, Mann-Whitney t-test, and Bland-Altman method comparison. Significance was set at <0.05%. Results To establish the proof of principle, MRD levels ranging from 0.001% to 100% (Neat CLL) were prepared by serial dilutions, in which MRD levels could be established by the ROR-160FCA to 10-5 (n=3). Assessment of the observed incidence against expected incidence of CLL MRD demonstrated a highly significant correlation (R2=0.96, p=0.01). In the study, the range of detectable disease went from <0.01% to 38.59%, of which 37% of samples had levels below <0.01%. Analyzing all flow cytometric methods, a highly significant correlation was observed between all three: CD160FCA vs ERIC: Spearman R=0.96 (95%CI: 0.93 - 0.97, p<0.001); CD160FCA vs ROR-160FCA: Spearman R=0.97 (95%CI: 0.96 – 0.99, p<0.001); ROR-160FCA vsERIC: Spearman R=0.97 (95%CI: 0.94 – 0.98, p<0.001). 54 samples had levels of disease <1%. Bland-Altman assay comparison in these patients again demonstrated significant associations between the assays (CD160FCA vs ERIC: mean 0.08 ±0.15; CD160FCA vs ROR-160FCA: mean 0.04 ±0.19; ROR-160FCA vs ERIC: mean 0.03 ±0.25). Light chain restriction was detectable in 24 patients (size of the restricted population ranged from 0.2% to 47% of all cellular events). This sub-group of patients also demonstrated excellent correlation between level of LCR and detectable disease by CD160FCA (Spearman R=0.96, 95%CI: 0.92-0.98, p<0.001), ERIC (R=0.95, 95%CI: 0.92-0.98, p<0.01) and ROR-160FCA (R=0.97, 95%CI 0.93-0.98, p<0.001). Conclusion Monitoring minimal residual disease in CLL is a key focus for clinical trials, as MRD is an important prognostic marker in CLL in terms of PFS and OS. Here we provide a single tube assay, ROR-160FCA, which is unique by targeting two antigens restricted to malignant B-cells, CD160 and ROR1. ROR-160FCA is equivalent in MRD detection compared to both CD160FCA and the current ERIC assay under development. The two tumor-specific antigens give ROR-160FCA the potential for improved sensitivity, particularly where limited sample is available. Furthermore, it only requires a simple sequential gating strategy, is rapid, and appears more cost effective than other Methods. References Farren TW, Giustiniani J, Liu FT et al. Blood. 2011;118 (8):2174-2183. Fukuda T, Chen L, Endo T et al. Proc Natl Acad Sci U S A. 2008;105 (8):3047-3052. Disclosures: Farren: BD Biosciences: Research Funding. Warner:BD Biosciences: Employment, Research Funding. Agrawal:BD Biosciences: Research Funding.

Reguatory T-Cell Subsets Demonstrate Quantitative Differences but Not Functional Abnormalities in Patients with Multiple Myeloma (MM) Compared with Healthy Controls.

The immunologically hostile microenvironment of MM contributes to the limited success of immunotherapy strategies. In addition to direct tumour-induced immunosuppression, tumour cells may generate suppressor cells such as Treg cells which can profoundly suppress immune responses and induce tolerance. This study aimed to determine if Treg subsets are increased in the peripheral blood (PB) and bone marrow (BM) of patients with MGUS/MM and how this correlates with increasing disease burden. PB samples from 166 patients with MGUS/MM (Newly diagnosed (ND), n=34; Plateau/low disease burden (LD), n=63; Relapsed/refractory (R/R), n=27 and MGUS, n=42) with a median age of 69 years (range 39–89 yrs) were analysed by FACS and compared to PB from 32 age/sex matched controls. Using a sequential gating strategy, naturally occurring Treg cells (nTregs) were identified as CD4+/CD25+/FoxP3+ T-cells and expressed as a percentage of the CD4+ T-cells. Double negative T cells (DN Tregs) were identified as CD3+/CD4−/CD8−/alphabeta-TCR+/gammadelta−TCR− and expressed as a percentage of the CD3+ cells. Sera were analysed by ELISA for IL10 and TGF-beta. nTReg cells were significantly increased in patients with MGUS/MM compared with controls (Controls 1.6% ± 0.2, MGUS 2.3% ± 0.3, ND 2.4% ± 0.2, LD 4.2% ± 0.7 & R/R 3.8% ± 0.5; p=0.003). There was a positive correlation of nTRegs number with paraprotein level (R=0.3, p=0.005). Patients on Thalidomide at the time of sample collection had significantly higher numbers of nTRegs of 6% in comparison to patients who never received Thalidomide (3%) and patients who previously received the drug (3.5%, p=0.005). Analysis of BM (n=12) demonstrated a significantly reduced number of nTRegs in comparison to PB (1.6% vs 3.0%, p=0.025), which is higher than the number of nTRegs in the BM of controls (0.7%). Functionally, nTRegs from patients demonstrated suppressive activity of both autologous and allogeneic T-cells similar to nTRegs cells from control PB (p=NS). In contrast, DN TRegs were significantly reduced in patients with myeloma (ND 1.0% ± 0.2, LD 1.1% ± 0.1, R/R 1.3% ± 0.2) compared with MGUS and controls (2.1% ± 0.9 & 3.3% ± 0.7, respectively; p=0.02). Serum IL10 levels were significantly lower in ND (17 ± 38 pg/ml) and LD (29 ± 36 pg/ml) than in Controls (55 ± 89 pg/ml), MGUS (72 ± 151 pg/ml) and R/R (90 ±182 pg/ml, p=0.02). TGF-b levels differed significantly between groups (Controls 3765 ± 1593 pg/ml, MGUS 3506 ± 1504 pg/ml, ND 4774 ± 9879 pg/ml, LD 1915 ± 1324 pg/ml, R/R 2802 ± 2011 pg/ml, p=0.025). These results provide further evidence of immune dysregulation in MM. The association with advanced disease stage suggests a causal association.

Attentional Gating in Primary Visual Cortex: A Physiological Basis for Dyslexia

The visual magnocellular pathway is known to play a central part in visuospatial attention and in directing attention to specific parts of the visual world in serial search. It is proposed that, in the case of reading, this mechanism is trained to perform a sequential gating of visual information coming into the primary visual cortex to enable further orderly processing by the ventral stream. This scheme, taken together with the potential for plasticity between the different afferent channels in the case of a relative impairment of the magnocellular system, can provide some limited rationale for the beneficial effects that have been claimed for the use of coloured overlays and glasses.