Implementation of flow cytometry testing on rare matrix samples: Special considerations and best practices when the sample is unique or difficult to obtain.

The publication of Clinical and Laboratory Standards Institute's guideline H62 has provided the flow cytometry community with much-needed guidance on development and validation of flow cytometric assays (CLSI, 2021). It has also paved the way for additional exploration of certain topics requiring additional guidance. Flow cytometric analysis of rare matrices, or unique and/or less frequently encountered specimen types, is one such topic and is the focus of this manuscript. This document is the result of a collaboration subject matter experts from a diverse range of backgrounds and seeks to provide best practice consensus guidance regarding these types of specimens. Herein, we define rare matrix samples in the setting of flow cytometric analysis, address validation implications and challenges with these samples, and describe important considerations of using these samples in both clinical and research settings.

Flow cytometry assay modifications: Recommendations for method validation based on CLSI H62 guidelines.

The Clinical and Laboratory Standards Institute (CLSI) H62-Validation of Assays Performed by Flow Cytometry guideline, released in 2021, provides recommendations for platform workflow and quality system essentials, instrument setup and standardization, assay development and optimization and fit-for-purpose analytical method validation. In addition, CLSI H62 includes some recommendations for the validation strategies after a validated flow cytometric method has been modified. This manuscript builds on those recommendations and discusses the impact of different types of assay modifications on assay performance. Recommendations regarding which validation parameters to evaluate depending on the type of modification are provided. The impact of assay modification on the assay's intended use is discussed. When recommending minor deviations from the CLSI H62 process for a laboratory-initiated assay revision (e.g., specimen numbers for sensitivity, specificity, or precision studies), a rationale based on expert opinion is provided with the understanding that not every laboratory, assay type, and circumstance can be comprehensively addressed in this paper. These recommendations are meant as a practical recommendation and are not intended to be restrictive, prescriptive, or understood as necessarily sufficient to meet every specific requirement from regulatory bodies (e.g., FDA or New York State Department of Health).

A flow cytometric assay for HLA-DR expression on monocytes validated as a biomarker for enrollment in sepsis clinical trials.

PURPOSE: Decreased expression of HLA-DR on monocytes (mHLA-DR) is a reliable indicator of immunosuppression in patients with sepsis and is correlated with increased risk of secondary infection and mortality. A flow cytometry-based laboratory developed test for the measurement of mHLA-DR in whole blood was validated for clinical trial enrollment, which is considered medical decision-making, for patients with severe sepsis or septic shock. METHODS: The BD Quantibrite™ anti-HLA-DR/anti-monocyte reagent measures antibodies bound per cell of HLA-DR on CD14+ monocytes. The mHLA-DR assay was planned to support inclusion/exclusion of patients for a clinical trial and was validated according to New York State Department of Health (NYSDOH) requirements for a new non-malignant leukocyte immunophenotyping assay. RESULTS: Normal, healthy donor and sepsis patient samples were stable up to 72 h post-collection in Cyto-Chex BCT phlebotomy tubes. Pre-determined acceptance criteria were met for precision parameters (average %CV ≤ 20%) and global laboratory-to-laboratory comparisons (average %Δ ≤ 20%). The approaches taken to evaluate and report accuracy, analytical specificity and sensitivity, reportable range, reference interval, and the proposed multi-level quality control were accepted by NYSDOH. CONCLUSIONS: In this study, the validation strategy necessary when the intended use of assay results changes from exploratory to medical decision making (patient enrollment), which successfully resulted in regulatory approval, is described.

High-sensitivity flow cytometric assays: Considerations for design control and analytical validation for identification of Rare events.

The current consensus recommendation papers dealing with the unique requirements for the analytical validation of assays performed by flow cytometry address the validation of sensitivity (both analytical and functional) only in general terms. In this paper, a detailed approach for designing and validating the sensitivity of rare event methods is described. The impact of panel design and optimization on the lower limit of quantification (LLOQ) and suggestions for reporting data near, or below, the LLOQ are addressed. This paper serves to provide best practices for the development, optimization, and analytical validation of flow cytometric assays designed to assess rare events. Note that this paper does not discuss clinical sensitivity validation, which addresses the positive and negative predictive value of the test result.

Best practices for optimization and validation of flow cytometry-based receptor occupancy assays.

In the development of therapeutic compounds that bind cell surface molecules, it is critical to demonstrate the extent to which the drug engages its target. For cell-associated targets, flow cytometry is well-suited to monitor drug-to-target engagement through receptor occupancy assays (ROA). The technology allows for the identification of specific cell subsets within heterogeneous populations and the detection of nonabundant cellular antigens. There are numerous challenges in the design, development, and implementation of robust ROA. Among the most difficult challenges are situations where there is receptor modulation or when the target-antigen is expressed at low levels. When the therapeutic molecules are bi-specific and bind multiple targets, these challenges are increased. This manuscript discusses the challenges and proposes best practices for designing, optimizing, and validating ROA.

Role of receptor occupancy assays by flow cytometry in drug development.

The measurement of the binding of a biotherapeutic to its cellular target, receptor occupancy (RO), is increasingly important in development of biologically-based therapeutic agents. Receptor occupancy (RO) assays by flow cytometry describe the qualitative and/or quantitative assessment of the binding of a therapeutic agent to its cell surface target. Such RO assays can be as simple as measuring the number of cell surface receptors bound by an antireceptor therapeutic agent or can be designed to address more complicated scenarios such as internalization or shedding events once a receptor engages the administered therapeutic agent. Data generated from RO assays can also be used to model whether given doses of an experimental therapeutic agent and their administration schedules lead to predicted levels of receptor occupancy and whether the receptor is modulated (up or down) on cells engaged by the therapeutic agent. There are a variety of approaches that can be used when undertaking RO assays and with the ability to measure distinct subsets in heterogeneous populations, flow cytometry is ideally suited to RO measurements. This article highlights the importance of RO assays on the flow cytometric platform in the development of biotherapeutic agents.

Aggregates of oxidized proteins (lipofuscin) induce apoptosis through proteasome inhibition and dysregulation of proapoptotic proteins.

Cellular senescence may be accompanied by accumulation of large aggregates of oxidized proteins, also known as lipofuscin. The hypothesis that cellular accumulation of lipofuscin-like materials (LIP) results in cell death as a result of proteasome inhibition was examined. Rat neonatal cardiomyocytes were incubated with synthetic LIP for up to 48 h. This was accompanied by increases in cellular autofluorescence (207% by 48 h; p < 0.05) and electron microscopic evidence of internalization of LIP particles. LIP incubation resulted in loss of viability (-46% by 48 h; p < 0.05) through apoptotic cell death. Although 20S-proteasome activity was increased by 74% after 6 h, both 20S- and 26S-proteasome activities were decreased after 48 h of incubation (-54% (p < 0.05) and -50%, respectively), accompanied by large increases in ubiquitinated proteins. Several proteasome-regulated proapoptotic proteins, including c-Jun (2.9-fold; p < 0.05), Bax (1.8-fold; p < 0.05), and p27(kip1) (3.2-fold; p < 0.05), were observed to be increased by 48 h. Observation of ubiquitinated homologues of Bax and p27(kip1) suggested that part of the increase was due to decreased proteasomal degradation of these proteins. The results of this study are consistent with the conclusion that accumulation of LIP results in inhibition of the proteasome, which initiates an apoptotic cascade as a result of dysregulation of several proapoptotic proteins.

T cell receptor V beta repertoire of the antigen specific CD8 T lymphocyte subset of HIV infected children.

OBJECTIVE: Analysis of the T cell receptor V beta repertoire during HIV infection reveals expansions in multiple V beta families of CD8 T cells, but their antigenic specificity is ill-defined. We sought to determine the TCR V beta repertoire of HIV specific CD8 T lymphocytes in infected children. DESIGN/METHODS: We performed flow cytometry to examine TCR V beta families as identified by specific monoclonal antibodies and binding of HIV peptide loaded tetrameric MHC complexes in peripheral blood samples from a group of HIV infected children. RESULTS: Simultaneous assessment of 12 selected expanded V beta families amongst nine HIV infected patients for tetramer binding revealed only one child in whom the expanded V beta population bound HIV Gag or Pol tetramers. In four HIV infected children, percentage tetramer binding cells was determined in 21 TCR V beta families. The tetramer binding cells of three children exhibited a widely distributed TCR V beta repertoire while in the fourth patient they were preferentially localized within two TCR V beta families. Repeat analysis revealed that the TCR V beta repertoire of tetramer binding cells was stable. CONCLUSIONS: These data provide evidence that the HIV-specific CD8 T cell response in children is usually distributed widely among many different TCR V beta families. The heterogeneity of the TCR V beta repertoire usage by the antigen specific CD8 T cells may reflect the dynamic interaction between host and pathogen during the course of HIV infection and may be influenced by the rate of viral mutation, CD4 T cell helper activity, or other factors.

Discordant expression of perforin and granzyme A in total and HIV-specific CD8 T lymphocytes of HIV infected children and adolescents.

OBJECTIVE: Perforin and granzyme are cytotoxic effector molecules that are believed to play essential roles in cytotoxic T cell (CTL) activity. We tested the hypothesis that dysregulation of these effector molecules contributes to defects of CD8 antiviral immune responses in pediatric subjects in chronic stages of perinatal HIV infection. DESIGN/METHOD: Studies of CD8 T cells were conducted in 33 treatment experienced HIV+ patients (median age, 10.6 years) and in 14 age-matched healthy controls. CD8 T cells specific for HIV Gag and Pol peptides were identified in HLA-A2+ patients by tetramer binding assays. HIV-specific and total CD8 T cells were examined for perforin, granzyme and expression of CD27, a marker that is lost in terminally differentiated cells. RESULTS: Three populations of CD8 T cells were identified: granzyme+ perforin+; granzyme+ perforin- and cells negative for both perforin and granzyme. In HIV infected patients, granzyme+ cells were increased in total CD8 T cells (39% versus 13% in controls) and were highest in HIV Gag-specific CD8 cells (42%). Perforin+ CD8 T cells were approximately fivefold fewer than granzyme+ CD8 T cells and were enriched in CD27 negative cells. Most HIV-specific CD8 cells were CD27+. Granzyme expression in CD8 T cells correlated negatively with CD4 percentage and positively with virus load. CONCLUSION: A disproportionate and generalized increase in CD27+, granzyme+, CD8 T cells is a hallmark of established pediatric HIV infection. These findings support the concept of skewed maturation, with failure of CD8 T cells to mature into perforin-enriched, CD27-negative, effector cells.

CD8+ T cells in HIV disease exhibit cytokine receptor perturbation and poor T cell receptor activation but are responsive to gamma-chain cytokine-driven proliferation.

BACKGROUND: Cytokines are important for inducing T cell maturation, proliferation, and survival. Despite the known dysregulation of cytokines in human immunodeficiency virus (HIV) infection, cytokine receptor expression is relatively unexplored. METHODS: We examined maturation markers (naive, central memory, effector memory, and effector); the cytokine receptors interleukin (IL)-2R beta , common gamma (C gamma ) chain, IL-7R alpha , IL-15R alpha; and proliferative responses of T cells in a cohort of HIV-infected pediatric patients (median age, 14.82 years) receiving antiretroviral therapy, arbitrarily designated as immunologic responders (group I) and nonresponders (group II) on the basis of a CD4+ T cell count cutoff of 25%. RESULTS: Patients had increased percentages of effector memory CD8+ T cells, in comparison with those in healthy control subjects, with reduced expression of IL-7R alpha in the central memory and effector memory subsets and of the C gamma chain in all maturation subsets of CD8+ T cells. IL-7R alpha +CD8+ T cell percentages were directly correlated with CD4+ T cell percentages. In immunologic nonresponders, anti-CD3+ or HIV Gag antigen-induced CD8+ T cell proliferation was impaired, but proliferation in response to the homeostatic cytokines IL-2 and IL-15 was preserved.Conclusions. Cytokine receptor deficiencies may contribute to immune deficiency in HIV-infected patients, and gamma -chain-utilizing cytokines may play an important role in vivo in maintaining the memory subsets of T cells in patients with CD4+ T cell deficiency.

Response to superantigen stimulation in peripheral blood mononuclear cells from children perinatally infected with human immunodeficiency virus and receiving highly active antiretroviral therapy.

Our understanding of the pathogenesis of perinatal human immunodeficiency virus (HIV) infection is still evolving. We sought to characterize the response to the bacterial superantigen Staphylococcus enterotoxin B (SEB) of lymphocytes from HIV-infected children receiving treatment with highly active antiretroviral therapy (HAART). Using the flow cytometric methodology, we quantified apoptosis, proliferation, cytokine production, and activation antigen upregulation in CD4 and CD8 T lymphocytes following in vitro stimulation of peripheral blood mononuclear cells (PBMCs) with SEB. The levels of proliferation, CD4 interleukin-2 (IL-2) production, CD8 gamma interferon (IFN-gamma) production, and upregulation of CD69 expression by cells from HIV-infected children were indistinguishable from those by cells from controls. However, stimulation with SEB dramatically decreased the ratio of resting apoptotic cells to cycling apoptotic cells in the controls but not in the patients. In addition, unstimulated spontaneous apoptosis of CD4 T cells remained greater in the patients than in the controls. The percentages of IL-2-positive CD8 T cells and IFN-gamma-positive CD4 T cells following SEB stimulation were significantly lower in the patients than in the controls. Our multiparameter approach was able to demonstrate differences in lymphocyte superantigen responsiveness in HIV-infected children receiving HAART in comparison to that in uninfected controls, notably, an apoptotic versus a proliferative response to stimulation.

Alterations in T-cell receptor Vbeta repertoire of CD4 and CD8 T lymphocytes in human immunodeficiency virus-infected children.

Perturbations in the T-cell receptor (TCR) Vbeta repertoire were assessed in the CD4 and CD8 T lymphocytes of human immunodeficiency virus (HIV)-infected children who were receiving therapy during the chronic phase of infection by flow cytometry (FC) and PCR analysis. By FC, representation of 21 TCR Vbeta subfamilies was assessed for an increased or decreased percentage in CD4 and CD8 T cells, and by PCR, 22 TCR Vbeta subfamilies of CD4 and CD8 T cells were analyzed by CDR3 spectratyping for perturbations and reduction in the number of peaks, loss of Gaussian distribution, or clonal dominance. The majority of the TCR Vbeta subfamilies were examined by both methods and assessed for deviation from the norm by comparison with cord blood samples. The CD8-T-lymphocyte population exhibited more perturbations than the CD4 subset, and clonal dominance was present exclusively in CD8 T cells. Of the 55 total CD8-TCR Vbeta families classified with clonal dominance by CDR3 spectratyping, only 18 of these exhibited increased expression by FC. Patients with high numbers of CD8-TCR Vbeta families with decreased percentages had reduced percentages of total CD4 T cells. Increases in the number of CD4-TCR Vbeta families with increased percentages showed a positive correlation with skewing. Overall, changes from normal were often discordant between the two methods. This study suggests that the assessment of HIV-induced alterations in TCR Vbeta families at cellular and molecular levels yields different information and that our understanding of the immune response to HIV is still evolving.