scholarly journals ‘Range’: A gain and dynamic range independent quantification of spread aiding in panel design

2020 ◽  
Author(s):  
Debajit Bhowmick ◽  
Frank van Diepen ◽  
Anita Pfauth ◽  
Renaud Tissier ◽  
Martijn van Baalen

AbstractIn flow cytometers, ideally each detector receives photons from one specific fluorochrome. However, photons usually end up in different detectors too (fluorescence spillover). ‘Compensation’ is a process that removes this extra signal from all detectors other than the primary detector dedicated to that fluorochrome. Post ‘compensation’, the measurement error of spillover signals become evident as spreading of the data. Spillover reduces the ability to resolve single positive from double positive cell populations. For successful multi-color panel design, it is important to know the expected spillover. The Spillover Spread Matrix (SSM) can be used to estimate the spillover spread, but the outcome is heavily influenced by detector sensitivity. In short, the same single stained control sample produces different spillover spread values when detector sensitivity are altered. Many researchers unknowingly use this artifact to “reduce” the spread by decreasing detector sensitivity. This can result in reduced sensitivity and diminished capacity to resolve cell populations. In this article, we introduce ‘Range’ as an alternative tool that can predict the spillover independent of detector sensitivity. ‘Range’ is also independent of dynamic range, that allows to compare spread values between different types of instruments, something not possible using SSM.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 251-251 ◽  
Author(s):  
Ariane Tormin ◽  
Ou Li ◽  
Stuart Walsh ◽  
Mats Ehinger ◽  
Jan Claas Brune ◽  
...  

Abstract Abstract 251 Primary MSC progenitor/stem cells (MSC-PC/SC) represent only a minute fraction of the bone marrow cells and they give rise to the well-known mesenchymal stromal cells (MSC) in culture. In vivo, MSC-PC/SC are probable constituents of the hematopoietic stem cell niche, thus playing an important role in supporting, maintaining and controlling hematopoiesis. Enrichment of primary MSC progenitors, i.e. CFU-F, has been recently reported based on expression of surface markers such as CD271, CD146, GD2, SSEA4, etc. Based on the expression of CD271 and CD146 on primary MSC (Quirici et al., Exp. Hematol. 2002; Sacchetti et al, Cell, 2007), we have recently identified two BM subpopulations (CD271+/CD146+/ CD45− and CD271+/CD146−/low/ CD45−) that highly enrich for primary MSC-PC/SC (Tormin et al, Blood 2008, 112[11]:843). These two populations contained all assayable CFU-F and both gave rise to typical cultured MSC (expression of standard surface markers, differentiation capacity into adipocytes, osteoblasts, chondrocytes). Interestingly, MSC derived from CD146−/low cells acquired CD146 expression in culture, and we therefore aimed to further investigate whether CD146 expression correlates to functional differences, e.g. stemness, or possibly differences in localization. CD271/CD146 subpopulations were FACS sorted from lineage-depleted BM-MNC. Single cell sorting of CD271/CD146/CD45− cells (n=6) confirmed the results of our prior CFU-F experiments, i.e. high enrichment of CFU-F and multipotency in the two putative stem cell populations. Six-color FACS analysis of primary BM cells showed that both populations coexpressed typical MSC markers (CD90, CD105, PDGFR-β, STRO-1), but not GD2, SSEA4, and endothelial markers. Single cell multiplex PCR on sorted primary MSC-PC/SC showed that both cell populations were negative for CD45, but did express “early” genes (Oct4, Sox2, Nanog), marker genes for the adipogenic lineage (CEBPA, LPIN1) and osteogenesis-related genes (ALPL, Runx2). Gene expression of CD146 correlated to its surface expression with some CD146 bands also detected among the CD146−/low sorted population. Next, we investigated possible differences in localization utilizing confocal microscopy of normal human BM sections. Reticular CD271/CD146 double positive and reticular CD271 single positive cells were identified. Double positive cells were mainly located adjacent to larger vessels and sinusoids but were also found in the marrow space. In contrast, CD271 single positive cells were primarily found in the endosteal space. These cells were furthermore negative for CD45 in contrast to CD45 coexpressing CD271+/low cells in the marrow space. As expected, CD146 single positive endothelial cells were found surrounding larger vessels. Thus, expression of CD146 in CD271+/CD45− cells correlated with localization (primarily endosteal versus primarily perivascular) and we therefore hypothesized that CD146 expression might be regulated by hypoxia levels. To test this, MSC were cultured under normoxic versus hypoxic conditions using deferoxamine mesylate (DFO) to mimic hypoxia. When sorted CD271+/CD146−/low/CD45− cells were cultured in normoxia, CD146 expression was lower compared with cultures initiated with CD271+/CD146+/CD45− cells in the beginning and up to the 1st passage. Thereafter, CD146 expression was comparable. However, when established MSC (CD146+) were cultured in the presence of DFO, CD146 expression was clearly downregulated, and after 7 days about 25% of cells became CD146 negative compared to 3% in normoxic controls. No changes were observed for CD90 and CD271 expression. Taken together, CD271+/CD146+/CD45– and CD271+/CD146–/low/CD45– bone marrow cells are putative primary MSC stem/progenitor populations. Both are highly enriched for primary MSC progenitors, they have comparable functional characteristics as well as comparable surface marker and gene expression profiles. Differences in CD146 expression correlated to localization and are likely to be caused by differences in oxygen levels. We therefore conclude that CD146 expression allows to distinguish the vary rare (0.19 ± 0.09%) primary endosteal niche MSC (CD271+/CD146−/low/CD45−) from vascular niche MSC (CD271+/CD146+/CD45−, 0.31 ± 0.13% of BM cells). Disclosures: No relevant conflicts of interest to declare.


2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A586-A586
Author(s):  
Sara Schad ◽  
Andrew Chow ◽  
Heng Pan ◽  
Levi Mangarin ◽  
Roberta Zappasodi ◽  
...  

BackgroundCD4 and CD8 T cells are genetically and functionally distinct cell subsets of the adaptive immune system that play pivotal roles in immune surveillance and disease control. During development in the thymus, transcription factors ThPOK and Runx3 regulate the differentiation and maturation of these two lineages into single positive T cells that enter the periphery with mutually exclusive expression of either the CD4 or CD8 co-receptor.1–2 Despite our expectation that these two cell fates are fixed, mature CD4+CD8+ double positive (DP) T cells have been described in the context of numerous immunological responses, including cancer, but their molecular and functional properties and therapeutic relevance remain controversial and largely unknown.3–5MethodsOur lab has identified and characterized a heterogenous DP T cell population in murine and human melanoma tumors comprised of CD4 and CD8 T cells re-expressing the opposite co-receptor and a parallel uptake in the opposite cell type’s phenotype and function. Using CD4 (Trp1) and CD8 (Pmel) transgenic TCR T cells specific to B16 melanoma antigens gp75 and gp100 respectively, we demonstrate the re-expression of the opposite co-receptor following adoptive T cell transfer in B16 melanoma tumor bearing mice.ResultsSpecifically, up to 50% of transferred CD4 Trp1 T cells will re-express CD8 to become a DP T cell in the tumor microenvironment. Further, these CD4 derived DP T cells upregulate CD8 lineage regulator Runx3 and cytolytic genes Gzmb, Gzmk, and Prf1 to become potent cytotoxic T cells. Alternatively, a subset of CD8 Pmel T cells differentiate into DP T cells characterized by the increased expression of CD4, ThPOK, and regulatory marker FoxP3 (figure 1). In addition, we utilized 10x single cell and ATAC sequencing to further characterize these divergent DP T cell populations among open repertoire T cells isolated from murine and human melanoma tumors.ConclusionsOur findings highlight the capability of single positive T cells to differentiate in response to antigen and local stimuli into novel T cell subsets with polyfunctional characteristics. The resulting cell subsets will potentially affect the tumor microenvironment in distinct ways. Our studies may inform therapeutic approaches to identify antigen specific T cells as well as innovative signaling pathways to target when genetically engineering T cells to optimize cytotoxic function in the setting of adoptive cell therapy.Ethics ApprovalThe human biospecimen analyses were approved by Memorial Sloan Kettering Cancer Center IRB #06-107ReferencesEllmeier W, Haust L & Tschismarov R. Transcriptional control of CD4 and CD8 coreceptor expression during T cell development. Cell Mol Life Sci 2013;70:4537–4553.Luckey MA, et al. The transcription factor ThPOK suppresses Runx3 and imposes CD4+ lineage fate by inducing the SOCS suppressors of cytokine signaling. Nature Immunology 2014; 15, 638–645.Bohner P, et al. Double positive CD4(+)CD8(+) T Cells are enriched in urological cancers and favor T Helper-2 polarization. Front Immunol 2019; 10, 622.Nascimbeni M, Shin E-C, Chiriboga L, Kleiner DE & Rehermann B. Peripheral CD4(+)CD8(+) T cells are differentiated effector memory cells with antiviral functions. Blood 2004;104:478–486.Nishida K, et al. Clinical importance of the expression of CD4+CD8+ T cells in renal cell carcinoma. Int Immunol 2020;32:347–357.


Author(s):  
Aris I. Giotakis ◽  
Jozsef Dudas ◽  
Rudolf Glueckert ◽  
Daniel Dejaco ◽  
Julia Ingruber ◽  
...  

AbstractEpithelial, connective tissue and immune cells contribute in various ways to the pathophysiology of chronic rhinosinusitis (CRS). However, data of their distribution in upper airway mucosa are sparse. We aimed to provide quantitative, purely informative data on the distribution of these cell lineages and their coexpression patterns, which might help identifying, e.g., cells in the epithelium undergoing through epithelial–mesenchymal transition (EMT). For this purpose, we used immunofluorescence multichannel image cytometry (IMIC). We examined fixed paraffin-embedded tissue samples (FFPE) of six patients with chronic rhinosinusitis (CRS) and of three patients without CRS (controls). The direct-conjugated antibodies pancytokeratin, vimentin and CD45/CD18 were used for coexpression analysis in epithelial layer and lamina propria. Image acquisition and analysis were performed with TissueFAXS and StrataQuest, respectively. To distinguish positive from negative expression, a ratio between cell-specific immunostaining intensity and background was developed. Isotype controls were used as negative controls. Per patient, a 4.5-mm2 tissue area was scanned and a median of 14,875 cells was recognized. The most common cell types were cytokeratin-single-positive (26%), vimentin-single-positive (13%) and CD45/CD18-single-positive with CD45/CD18–vimentin-double-positive cells (29%). In the patients with CRS, CD45/CD18-single-positive cells were 3–6 times higher compared to the control patients. In the epithelial layer, cytokeratin–vimentin-double-positive EMT cells were observed 3–5 times higher in the patients with CRS than in the control patients. This study provided quantitative data for the distribution of crucial cell types in CRS. Future studies may focus on the distribution and coexpression patterns of different immune cells in CRS or even cancer tissue.


2018 ◽  
Vol 46 (4) ◽  
pp. 441-449
Author(s):  
Sowmya Angusamy ◽  
Tamer Mansour ◽  
Mohammed Abdulmageed ◽  
Rachel Han ◽  
Brian C. Schutte ◽  
...  

Abstract Background: The adaptive immune system of neonates is relatively underdeveloped. The thymus is an essential organ for adaptive T cell development and might be affected during the natural course of oxygen induced lung injury. The effect of prolonged hyperoxia on the thymus, thymocyte and T cell development, and its proliferation has not been studied extensively. Methods: Neonatal mice were exposed to 85% oxygen (hyperoxia) or room air (normoxia) up to 28 days. Flow cytometry using surface markers were used to assay for thymocyte development and proliferation. Results: Mice exposed to prolonged hyperoxia had evidence of lung injury associated alveolar simplification, a significantly lower mean weight, smaller thymic size, lower mean thymocyte count and higher percentage of apoptotic thymocytes. T cells subpopulation in the thymus showed a significant reduction in the count and proliferation of double positive and double negative T cells. There was a significant reduction in the count and proliferation of single positive CD4+ and CD8+ T cells. Conclusions: Prolonged hyperoxia in neonatal mice adversely affected thymic size, thymocyte count and altered the distribution of T cells sub-populations. These results are consistent with the hypothesis that prolonged hyperoxia causes defective development of T cells in the thymus.


2021 ◽  
Author(s):  
Thomas J. Kucharski ◽  
Rufus Hards ◽  
Kristina M. Godek ◽  
Scott A. Gerber ◽  
Duane A. Compton

SummaryKinetochore protein phosphorylation promotes the correction of erroneous microtubule attachments to ensure faithful chromosome segregation during cell division. Determining how phosphorylation executes error correction requires an understanding of whether kinetochore substrates are completely (i.e. all-or-none) or only fractionally phosphorylated. Using quantitative mass spectrometry (MS), we measured phospho-occupancy on the conserved kinetochore protein Hec1 (NDC80) that directly binds microtubules. None of the positions measured exceeded ∼50% phospho-occupancy, and the cumulative phospho-occupancy changed by only ∼20% in response to changes in microtubule attachment status. The narrow dynamic range of phospho-occupancy is maintained by ongoing phosphatase activity. Further, both Cdk1-Cyclin B1 and Aurora kinases phosphorylate Hec1 to enhance error correction in response to different types of microtubule attachment errors. Thus, networks of kinases and phosphatases maintain low inherent phospho-occupancy to promote microtubule attachment to kinetochores while providing for high sensitivity of kinetochore-microtubule attachments to very small changes in phospho-occupancy to ensure high mitotic fidelity.


2021 ◽  
Vol 7 ◽  
Author(s):  
Ethan J. Kilmister ◽  
Lauren Hansen ◽  
Paul F. Davis ◽  
Sean R. R. Hall ◽  
Swee T. Tan

Treatment of vascular anomalies (VAs) is mostly empirical and, in many instances unsatisfactory, as the pathogeneses of these heterogeneous conditions remain largely unknown. There is emerging evidence of the presence of cell populations expressing stemness-associated markers within many types of vascular tumors and vascular malformations. The presence of these populations in VAs is supported, in part, by the observed clinical effect of the mTOR inhibitor, sirolimus, that regulates differentiation of embryonic stem cells (ESCs). The discovery of the central role of the renin-angiotensin system (RAS) in regulating stem cells in infantile hemangioma (IH) provides a plausible explanation for its spontaneous and accelerated involution induced by β-blockers and ACE inhibitors. Recent work on targeting IH stem cells by inhibiting the transcription factor SOX18 using the stereoisomer R(+) propranolol, independent of β-adrenergic blockade, opens up exciting opportunities for novel treatment of IH without the β-adrenergic blockade-related side effects. Gene mutations have been identified in several VAs, involving mainly the PI3K/AKT/mTOR and/or the Ras/RAF/MEK/ERK pathways. Existing cancer therapies that target these pathways engenders the exciting possibility of repurposing these agents for challenging VAs, with early results demonstrating clinical efficacy. However, there are several shortcomings with this approach, including the treatment cost, side effects, emergence of treatment resistance and unknown long-term effects in young patients. The presence of populations expressing stemness-associated markers, including transcription factors involved in the generation of induced pluripotent stem cells (iPSCs), in different types of VAs, suggests the possible role of stem cell pathways in their pathogenesis. Components of the RAS are expressed by cell populations expressing stemness-associated markers in different types of VAs. The gene mutations affecting the PI3K/AKT/mTOR and/or the Ras/RAF/MEK/ERK pathways interact with different components of the RAS, which may influence cell populations expressing stemness-associated markers within VAs. The potential of targeting these populations by manipulating the RAS using repurposed, low-cost and commonly available oral medications, warrants further investigation. This review presents the accumulating evidence demonstrating the presence of stemness-associated markers in VAs, their expression of the RAS, and their interaction with gene mutations affecting the PI3K/AKT/mTOR and/or the Ras/RAF/MEK/ERK pathways, in the pathogenesis of VAs.


2021 ◽  
Vol 11 (23) ◽  
pp. 11347
Author(s):  
Elisha Munsu ◽  
Hana Mohd Zaini ◽  
Patricia Matanjun ◽  
Noorakmar Ab Wahab ◽  
Nurul Shaeera Sulaiman ◽  
...  

The effect of the addition of three types of tropical edible seaweeds, Kappaphycus alvarezii (KA), Sargassum polycystum (SP), and Caulerpa lentilifira (CL), on sausages were studied. Nine sausage formulations with three levels of inclusion (2%, 4%, and 6%) of each seaweed were prepared, analysed, and compared with the control sample (without seaweed) in terms of their physicochemical properties, total phenolic content, and lipid oxidation. The modified sausages had low moisture and fat content (p < 0.05) but high ash and dietary fiber content (p < 0.05) compared to the control sausage. The addition of seaweed powder changed the texture of the sausages, mainly its hardness and chewiness (p < 0.05), but no significant difference in cohesiveness and springiness was found (p < 0.05). The modified sausages were shown to have high water holding capacities and cooking yields. The different types of seaweed modified the colour of the chicken sausages differently. In general, the L* (brightness) and b* (yellowness) values was low for all sausage samples containing seaweed powder (p < 0.05), while the a* (redness) value increased with the addition of the KA and SP seaweed powder but decreased for the sausage sample with added CL seaweed powder (p < 0.05). Moreover, the modified sausages have higher total phenolic contents and high antioxidant capacities, which contributed to slowing the oxidation of lipid in sausages during storage (p < 0.05). Sensory evaluation showed that the panellists found up to 4% of KA and 2% of SP to be acceptable. Overall, the seaweeds, especially KA and SP, could potentially be developed as excellent additives for the manufacture of highly technological high-quality meat products.


2014 ◽  
Vol 115 (suppl_1) ◽  
Author(s):  
Karen Maass ◽  
Jia Lu ◽  
Fiona See ◽  
Guoxin Kang ◽  
Camila Delgado ◽  
...  

We have previously demonstrated that contactin2 (Cntn2) protein is enriched in Purkinje cells of the adult cardiac conduction system (CCS). Here we present a mouse embryonic stem cell (mESC) reporter line to identify Purkinje-like cardiomyocytes in vitro. Methods and Results: Dual reporter Purkinje cell mESC were generated from Cntn2-eGFP blastocysts, transduced with αMHC-mCherry lentivirus. The mESC expressed markers of pluripotency (Oct3/4; Sox2, Nanog) and differentiated into all three germ layers (Nestin, a-fetoprotein, Brachyury). Cultures differentiated under serum-free, cardiogenic conditions were enriched in cardiomyocytes (n=5), consisting of single positive aMHC-mCherry [57.76±3.7%] and double positive αMHC-mCherry/Cntn2-eGFP cells [1.9±0.9%]. Compared with eGFP negative cardiomyocytes (n=15), double positive cells (n=11) revealed electrophysiological characteristics consistent with Purkinje-like derivatives, including increased peak sodium currents (180.3±20.5 pA/pF vs. =-118.0±21.2pA/pF), faster upstroke velocities (133.7±12.3 V/s vs.60.0±13.2V/s) and elongated action potential duration (APD90=170.2±17.5ms vs. APD90=120.6±17.3ms). Calcium imaging demonstrated chronotrop regulation and spontaneous Ca2+ oscillations in mCherry+eGFP+ cells. Immunofluorecence analysis demonstrated endogenous expression of Purkinje cell markers, including Cntn2, Cx40 and Troponin-T, in double positive cells. Quantitative real-time PCR analysis of double positive cells verified cardiomyocyte-specific transcript expression [Mlc2v: 3.8x106-fold (p<0.05); Nkx2.5: 178-fold (p<0.05) compared to double negative cells]. Moreover, double positive cells expressed significantly elevated levels of CCS-specific transcripts compared to mCherry-single positive cells [Cntn2: 31-fold (p<0.001); Cx40: 878 -fold (p<0.01); Cav3.1: 11-fold (p<0.05); HCN4: 7-fold (p<0.001)]. Conclusion: The dual reporter Purkinje cell mESC reporter line permits identification and enrichment of ventricular CCS derivatives. [Supported by NYSTEM contracts #C024327 and #C028115 to GIF].


Blood ◽  
1998 ◽  
Vol 91 (12) ◽  
pp. 4434-4443 ◽  
Author(s):  
Chang H. Kim ◽  
Louis M. Pelus ◽  
John R. White ◽  
Hal E. Broxmeyer

Abstract Differentiation-dependent thymocyte migration in the thymus may be important for T lymphopoiesis and might be regulated by thymic chemoattractants. We examined modulation of chemotactic responsiveness of thymocyte subsets during their early to late stages of development in response to 2 thymus-expressed chemokines, SDF-1 and CKβ-11/MIP-3β/ELC. SDF-1 shows chemotactic preference for immature thymocytes (subsets of triple negative thymocytes and double positive [DP] subset) over mature single positive (SP) thymocytes. CKβ-11/MIP-3β/ELC shows low chemotactic activity on the immature thymocytes, but it strongly attracts mature SP thymocytes, effects opposite to that of SDF-1. SDF-1–dependent chemoattraction of immature thymocytes is not significantly desensitized by a negative concentration gradient of CKβ-11/MIP-3β/ELC, and chemoattraction of mature SP thymocytes to CKβ-11/MIP-3β/ELC is not antagonized by SDF-1, demonstrating that these two chemokines have different chemoattractant preferences for thymocyte subsets and would probably not inhibit each other's chemotaxis in the event of microenvironmental coexpression. The chemotactic responsiveness of thymocytes and mature T cells to the 2 chemokines is respectively enhanced after selection process and migration to the spleen. These studies demonstrate the presence of thymocyte chemoattractants with differential chemotactic preference for thymocytes, a possible mechanism for thymocyte migration in the thymus.


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