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Chargin A, Morgan R, Sundram U, Shults K, Tsay EL, Ratti N, Patterson BK. Quantification of PD-L1 and PD-1 expression on tumor and immune cells in non-small cell lung cancer (NSCLC) using non-enzymatic tissue dissociation and flow cytometry. Cancer Immunol Immunother 2016; 65:1317-1323. [PMID: 27565980 PMCID: PMC11028699 DOI: 10.1007/s00262-016-1889-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 08/17/2016] [Indexed: 11/26/2022]
Abstract
OBJECTIVE We report a truly quantitative technology for PD-L1 expression in non-small cell lung cancer (NSCLC). In addition, we present a non-enzymatic technology that creates a cell suspension from fresh tumor tissue so that either fine-needle aspiration (FNA) or fresh tissue can be used in this assay. METHODS Non-enzymatic tissue homogenization (IncellPREP; IncellDx, Menlo Park, California) was performed on 4-mm punch biopsies. An FNA was taken from the same tumor to create matched sample sets. Cells were labeled with antibodies directed against CD45, PD-1, and PD-L1 and then stained with DAPI to identify intact, single cells, and to analyze cell cycle. RESULTS Comparing the IncellPREP homogenization and FNA demonstrated a strong correlation (r 2 - 0.8) for expression of PD-L1. We compared PD-L1 expression by flow cytometry using a 1 % cutoff for positivity in the tumor cell population and a 1 % cutoff of cells with at least 1+ intensity in immunohistochemically stained tissue sections as positive. Ten of 12 lung tumor samples were concordant while 2 were discordant. PD-L1 expression by flow cytometry varied widely (1.2-89.4 %) even in the positive concordant cases. In addition, PD-L1 expression in the aneuploid tumor population did not necessarily agree with the expression in the diploid tumor population. Fine, unequivocal quantification of PD-L1 on tumor and immune cells in NSCLC may allow for better prediction of response to therapies. The present study also offers a technology that can create a universal sample type from either FNA or fresh tissue.
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Affiliation(s)
- Amanda Chargin
- IncellDx, Inc., 1700 El Camino Real, Menlo Park, CA, 94027, USA
| | - Rian Morgan
- IncellDx, Inc., 1700 El Camino Real, Menlo Park, CA, 94027, USA
| | - Uma Sundram
- Department of Anatomic Pathology, William Beaumont Hospital, Royal Oak, MI, 48073, USA
| | - Keith Shults
- IncellDx, Inc., 1700 El Camino Real, Menlo Park, CA, 94027, USA
| | - Ellen L Tsay
- IncellDx, Inc., 1700 El Camino Real, Menlo Park, CA, 94027, USA
| | - Navneet Ratti
- Tissue Diagnostics Inc., 2829 Depot Road, Suite 4B, Hayward, CA, 94545, USA
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Tangri S, Vall H, Kaplan D, Hoffman B, Purvis N, Porwit A, Hunsberger B, Shankey TV. Validation of cell-based fluorescence assays: practice guidelines from the ICSH and ICCS - part III - analytical issues. CYTOMETRY PART B-CLINICAL CYTOMETRY 2014; 84:291-308. [PMID: 24022852 DOI: 10.1002/cyto.b.21106] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 05/20/2013] [Accepted: 06/14/2013] [Indexed: 11/07/2022]
Abstract
Clinical diagnostic assays, may be classified as quantitative, quasi-quantitative or qualitative. The assay's description should state what the assay needs to accomplish (intended use or purpose) and what it is not intended to achieve. The type(s) of samples (whole blood, peripheral blood mononuclear cells (PBMC), bone marrow, bone marrow mononuclear cells (BMMC), tissue, fine needle aspirate, fluid, etc.), instrument platform for use and anticoagulant restrictions should be fully validated for stability requirements and specified. When applicable, assay sensitivity and specificity should be fully validated and reported; these performance criteria will dictate the number and complexity of specimen samples required for validation. Assay processing and staining conditions (lyse/wash/fix/perm, stain pre or post, time and temperature, sample stability, etc.) should be described in detail and fully validated.
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Cesano A, Spellmeyer D. Immune system functional pathway analysis using single cell network profiling (SCNP): a novel tool in cancer immunotherapy. Methods Mol Biol 2014; 1102:583-99. [PMID: 24259000 DOI: 10.1007/978-1-62703-727-3_31] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The development of cancer immunotherapies has been ongoing for many years and has shown limited success. Novel biomarkers are needed to identify patients most likely to respond to anticancer immune-therapeutic approaches. Moreover, a systems-level approach is required for comprehensive understanding of the interconnected components, pathways, and cell types associated with an immune response. In this chapter, we describe single cell network profiling (SCNP), a novel method for assessing and measuring immune function/dysfunction at a systems level. SCNP is a multiparametric flow-cytometry-based analysis that can simultaneously measure, at the single cell level, both extracellular surface markers and changes in intracellular signaling proteins in response to extracellular modulators. Measuring changes in signaling proteins following the application of an external modulation informs on the functional capacity of the signaling network which cannot be assessed by the measurement of basal signaling alone. In addition, the simultaneous analysis of multiple pathways in multiple cell subsets can provide insight into the connectivity of both cell signaling networks and immune cell subtypes. The experimental steps associated with an SCNP assay are (1) pre-analytical sample preparation; (2) modulation for functional analysis; (3) staining with antibody cocktail; (4) data acquisition on flow cytometer; and (5) data analysis and metrics. Important considerations for each step of the assay will be discussed, and data demonstrating the utility of SCNP for immune monitoring applications will be summarized.
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Zhu S, Panne U, Rurack K. A rapid method for the assessment of the surface group density of carboxylic acid-functionalized polystyrene microparticles. Analyst 2013; 138:2924-30. [PMID: 23531901 DOI: 10.1039/c3an36578f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Particle-based assays are becoming versatile analytical tools due to their cost-effectiveness, speed, straightforward and diverse functionalization chemistries, especially when polystyrene particles are used. The introduction of functional groups (-COOH, -NH2, etc.) to the surface of such polystyrene particles promotes their application in bioanalytics. However, the traditional method to determine the amount of surface carboxylate groups is conductivity titration, which is usually time- and resources-consuming and discontinuous. Here, we synthesized polystyrene microparticles with different contents of carboxylate groups, and then investigated a simpler and potentially continuous approach to determine the amount of surface carboxylate groups by Zeta potential measurements. The results were compared to the traditional titration method and to actual coupling efficiencies of the functionalized particles with a model oligonucleotide probe as determined by flow cytometry. All quantification methods revealed good agreement.
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Affiliation(s)
- Shengchao Zhu
- Abt. 1 Analytische Chemie, Referenzmaterialien, BAM Bundesanstalt für Materialforschung und -prüfung, Richard-Willstätter-Str. 11, D-12489 Berlin, Germany
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Kornblau SM, Cohen AC, Soper D, Huang YW, Cesano A. Age-related changes of healthy bone marrow cell signaling in response to growth factors provide insight into low risk MDS. CYTOMETRY PART B-CLINICAL CYTOMETRY 2013; 86:383-96. [PMID: 24106013 DOI: 10.1002/cyto.b.21125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/22/2013] [Accepted: 08/09/2013] [Indexed: 12/12/2022]
Abstract
BACKGROUND Single Cell Network Profiling (SCNP) is a multiparametric flow cytometry-based assay that quantifiably and simultaneously measures changes in intracellular signaling proteins in response to in vitro extracellular modulators at the single cell level. Myelodysplastic syndrome (MDS) is a heterogeneous clonal disorder of hematopoietic stem cells that occurs in elderly subjects and is characterized by dysplasia and ineffective hematopoiesis. The functional responsiveness of MDS bone marrow (BM) hematopoietic cells, including functionally distinct myeloid and erythroid precursor subsets, to hematopoietic growth factors (HGF) and the relationship of modulated signaling to disease characteristics is poorly understood. METHODS SCNP was used first to examine the effects of age on erythropoietin (EPO) and granulocyte colony stimulating factor (GCSF)-induced signaling in myeloid, nucleated red blood cells (nRBC), and CD34 expressing cell subsets in healthy BM (n = 15). SCNP was then used to map functional signaling profiles in low risk (LR) MDS (n = 7) for comparison to signaling in samples from healthy donors and to probe signaling associations within clinically defined subgroups. RESULTS In healthy BM samples, signaling responses to HGF were quite homogeneous (i.e., tightly regulated) with age-dependent effects observed in response to EPO but not to GCSF. Despite the relatively small number of samples assayed in the study, LR MDS could be classified into distinct subgroups based on both cell subset frequency and signaling profiles. CONCLUSIONS As a correlate of underlying genetic abnormalities, signal transduction analyses may provide a functional and potentially clinically relevant classification of MDS. Further evaluation in a larger cohort is warranted.
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Affiliation(s)
- Steven M Kornblau
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
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Davis BH, McLaren CE, Carcio AJ, Wong L, Hedley BD, Keeney M, Curtis A, Culp NB. Determination of optimal replicate number for validation of imprecision using fluorescence cell-based assays: Proposed practical method. CYTOMETRY PART B-CLINICAL CYTOMETRY 2013; 84:329-37. [DOI: 10.1002/cyto.b.21116] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 05/25/2013] [Accepted: 07/10/2013] [Indexed: 11/09/2022]
Affiliation(s)
| | - Christine E. McLaren
- Department of Epidemiology; University of California Irvine; Irvine; California; 92697-7550
| | | | - Linda Wong
- Trillium Diagnostics, LLC; Bangor; Maine; 04401
| | - Benjamin D. Hedley
- London Laboratory Services Group; London Health Sciences Centre; London; Ontario; N6A 5W9; Canada
| | - Mike Keeney
- London Laboratory Services Group; London Health Sciences Centre; London; Ontario; N6A 5W9; Canada
| | - Adam Curtis
- Trillium Diagnostics, LLC; Bangor; Maine; 04401
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Cesano A, Putta S, Rosen DB, Cohen AC, Gayko U, Mathi K, Woronicz J, Hawtin RE, Cripe L, Sun Z, Tallman MS, Paietta E. Functional pathway analysis using SCNP of FLT3 receptor pathway deregulation in AML provides prognostic information independent from mutational status. PLoS One 2013; 8:e56714. [PMID: 23431389 PMCID: PMC3576376 DOI: 10.1371/journal.pone.0056714] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 01/14/2013] [Indexed: 11/21/2022] Open
Abstract
FMS-like tyrosine kinase 3 receptor (FLT3) internal tandem duplication (ITD) mutations result in constitutive activation of this receptor and have been shown to increase the risk of relapse in patients with acute myeloid leukemia (AML); however, substantial heterogeneity in clinical outcomes still exists within both the ITD mutated and unmutated AML subgroups, suggesting alternative mechanisms of disease relapse not accounted by FLT3 mutational status. Single cell network profiling (SCNP) is a multiparametric flow cytometry based assay that simultaneously measures, in a quantitative fashion and at the single cell level, both extracellular surface marker levels and changes in intracellular signaling proteins in response to extracellular modulators. We previously reported an initial characterization of FLT3 ITD-mediated signaling using SCNP. Herein SCNP was applied sequentially to two separate cohorts of samples collected from elderly AML patients at diagnosis. In the first (training) study, AML samples carrying unmutated, wild-type FLT3 (FLT3 WT) displayed a wide range of induced signaling, with a fraction having signaling profiles comparable to FLT3 ITD AML samples. Conversely, the FLT3 ITD AML samples displayed more homogeneous induced signaling, with the exception of patients with low (<40%) mutational load, which had profiles comparable to FLT3 WT AML samples. This observation was then confirmed in an independent (verification) cohort. Data from the second cohort were also used to assess the association between SCNP data and disease-free survival (DFS) in the context of FLT3 and nucleophosmin (NPM1) mutational status among patients who achieved complete remission (CR) to induction chemotherapy. The combination of SCNP read outs together with FLT3 and NPM1 molecular status improved the DFS prediction accuracy of the latter. Taken together, these results emphasize the value of comprehensive functional assessment of biologically relevant signaling pathways in AML as a basis for the development of highly predictive tests for guidance of post-remission therapy.
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MESH Headings
- Aged
- Aged, 80 and over
- Apoptosis
- Cells, Cultured
- Disease-Free Survival
- Female
- Humans
- Induction Chemotherapy
- Kaplan-Meier Estimate
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Male
- Middle Aged
- Multivariate Analysis
- Mutagenesis
- Mutation
- Nucleophosmin
- Principal Component Analysis
- Prognosis
- Signal Transduction
- Single-Cell Analysis
- fms-Like Tyrosine Kinase 3/genetics
- fms-Like Tyrosine Kinase 3/metabolism
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Affiliation(s)
- Alessandra Cesano
- Nodality, Inc., South San Francisco, California, United States of America
- * E-mail:
| | - Santosh Putta
- Nodality, Inc., South San Francisco, California, United States of America
| | - David B. Rosen
- Nodality, Inc., South San Francisco, California, United States of America
| | - Aileen C. Cohen
- Nodality, Inc., South San Francisco, California, United States of America
| | - Urte Gayko
- Nodality, Inc., South San Francisco, California, United States of America
| | - Kavita Mathi
- Nodality, Inc., South San Francisco, California, United States of America
| | - John Woronicz
- Nodality, Inc., South San Francisco, California, United States of America
| | - Rachael E. Hawtin
- Nodality, Inc., South San Francisco, California, United States of America
| | - Larry Cripe
- Eastern Cooperative Oncology Group (ECOG), Boston, Massachusetts, United States of America
- Indiana University Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Zhuoxin Sun
- Eastern Cooperative Oncology Group (ECOG), Boston, Massachusetts, United States of America
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Martin S. Tallman
- Eastern Cooperative Oncology Group (ECOG), Boston, Massachusetts, United States of America
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Elisabeth Paietta
- Eastern Cooperative Oncology Group (ECOG), Boston, Massachusetts, United States of America
- Montefiore Medical Center North Division, Bronx, New York, United States of America
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Cesano A, Rosen DB, O'Meara P, Putta S, Gayko U, Spellmeyer DC, Cripe LD, Sun Z, Uno H, Litzow MR, Tallman MS, Paietta E. Functional pathway analysis in acute myeloid leukemia using single cell network profiling assay: effect of specimen source (bone marrow or peripheral blood) on assay readouts. CYTOMETRY PART B-CLINICAL CYTOMETRY 2012; 82:158-72. [PMID: 22334473 DOI: 10.1002/cyto.b.21007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 12/06/2011] [Accepted: 12/17/2011] [Indexed: 11/05/2022]
Abstract
BACKGROUND Single cell network profiling (SCNP) is used to simultaneously measure the effects of modulators on signaling networks at the single cell level. SCNP-based biomarker assays predictive of response to induction therapy and relapse risk in acute myeloid leukemia (AML) patients are being developed. Such assays have typically used bone marrow (BM) as the sample source of blasts. Because circulating peripheral blasts are detectable in ∼65% of AML patients and peripheral blood (PB) sampling is less invasive than BM sampling, this study was performed to assess the effect of sample source on AML blasts signaling as measured in SCNP assay. METHODS SCNP using multiparametric flow cytometry was used to evaluate the activation state of intracellular signaling molecules in leukemic blasts under basal conditions and after treatment with modulators in 46 pairs of BM mononuclear cells/PB mononuclear cells. The relationship between readouts of modulated intracellular proteins ("nodes") was measured using linear regression, Bland-Altman method, and Lin's concordance correlation coefficient. RESULTS The majority (156/161) of signaling nodes show strong correlations between paired PB and BM samples independently from the statistical method used. Notable exceptions were two PB samples with almost undetectable levels of circulating blasts compared with paired BM samples. CONCLUSIONS Our results demonstrate that specimen source (BM or PB) does not significantly affect proteomic signaling in patients with AML and circulating blasts. The ability to use PB as a sample source will facilitate the monitoring of cellular signaling effects following administration of targeted therapies and at time points when BM aspirates are not clinically justifiable.
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Affiliation(s)
- Alessandra Cesano
- Clinical Affairs, Nodality Inc., South San Francisco, California 94080, USA.
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Green CL, Brown L, Stewart JJ, Xu Y, Litwin V, Mc Closkey TW. Recommendations for the validation of flow cytometric testing during drug development: I instrumentation. J Immunol Methods 2011; 363:104-19. [DOI: 10.1016/j.jim.2010.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 07/12/2010] [Accepted: 07/12/2010] [Indexed: 10/25/2022]
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Preobrazhensky SN, Bahler DW. Optimization of flow cytometric measurement of ZAP-70 in chronic lymphocytic leukemia. CYTOMETRY PART B-CLINICAL CYTOMETRY 2008; 74:118-27. [PMID: 17948236 DOI: 10.1002/cyto.b.20378] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND The goal of this study was to optimize a cell staining procedure for flow cytometric detection of zeta-chain associated protein-70 (ZAP-70). Our specific objectives were to improve antibody selection criteria, identify a cell permeabilization procedure better tailored to ZAP-70 analysis, as well as to establish objective criteria to control antigen stability. METHODS Sequentially titrated 2F3.2-FITC, 1E7.2-FITC, and 1E7.2-Alexa Fluor 488 anti-ZAP-70 antibodies were used to stain normal B and T cells and Scatchard analysis was applied to calculate K(d) and B(max) values from saturation curves of specific binding. ZAP-70 staining was compared in cells permeabilized with two commercially available kits, Triton X-100, and a custom saponin procedure. RESULTS Normal B-cells were found to provide an excellent measure of nonspecific staining while varying ZAP-70 antibodies and concentrations. Comparing Scatchard analyses of specific T-cell binding revealed that 1E7.2-Alexa Fluor 488 had the highest binding affinity of the tested anti-ZAP-70 antibodies and was the best choice. The highest levels of ZAP-70 fluorescence occurred when cells were permeabilized using a noncommercial saponin procedure. Decrease of chronic lymphocytic leukemia cell viability correlated with diminished ZAP-70 expression; when viability was lower than 95% the percentage of bright positive samples was significantly decreased, indicating a possibility of false-negative results. CONCLUSIONS The efficiency and reliability of flow cytometric detection of ZAP-70 can be optimized by using Scatchard analysis to help select the most effective antibodies and antibody concentrations that maximize specific to nonspecific binding, by using a "custom" ZAP-70 permeabilization procedure, and by better controlling antigen stability by measuring cell viability.
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Marti G, Orfao A, Goolsby C. ZAP-70 in CLL: towards standardization of a biomarker for patient management: history of clinical cytometry special issue. CYTOMETRY PART B-CLINICAL CYTOMETRY 2007; 70:197-200. [PMID: 16906575 DOI: 10.1002/cyto.b.20137] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
Rai and Binet staging of chronic lymphocytic leukaemia (CLL) is being superseded by new prognostic markers. The mutational status of the immunoglobulin variable region heavy-chain genes segregates the disease into more benign and more malignant versions, and has been confirmed as an important prognostic marker in prospective clinical trials. A search for surrogate markers for this difficult-to-perform assay has led to flow cytometric assays for CD38 and ZAP-70 expression, although in both cases there are problems with standardization and interpretation of the assays. A separate pathway of research has revealed two chromosomal aberrations--deletions of 11q and 17p--as important prognostic markers. Fluorescent in-situ hybridization has made their detection readily available. These five markers are in different stages of evaluation, but some of them are ready to be used for risk-adapted therapy in clinical trials. Other assays are in earlier stages of assessment.
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Affiliation(s)
- Terry J Hamblin
- University of Southampton, c/o Department of Haematology, Royal Bournemouth Hospital, Castle Lane East, Bournemouth BH7 7DW, UK.
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