RNA content in human lymphocyte subpopulations

Integrated analysis of multimodal single-cell data

The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we introduce "weighted-nearest neighbor" analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of 211,000 human peripheral blood mononuclear cells (PBMCs) with panels extending to 228 antibodies to construct a multimodal reference atlas of the circulating immune system. Multimodal analysis substantially improves our ability to resolve cell states, allowing us to identify and validate previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets and to interpret immune responses to vaccination and coronavirus disease 2019 (COVID-19). Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets and to look beyond the transcriptome toward a unified and multimodal definition of cellular identity.

Increased levels of inosine in a mouse model of inflammation

One possible mechanism linking inflammation with cancer involves the generation of reactive oxygen, nitrogen, and halogen species by activated macrophages and neutrophils infiltrating sites of infection or tissue damage, with these chemical mediators causing damage that ultimately leads to cell death and mutation. To determine the most biologically deleterious chemistries of inflammation, we previously assessed products across the spectrum of DNA damage arising in inflamed tissues in the SJL mouse model nitric oxide overproduction ( Pang et al. ( 2007 ) Carcinogenesis 28 , 1807 - 1813 ). Among the anticipated DNA damage chemistries, we observed significant changes only in lipid peroxidation-derived etheno adducts. We have now developed an isotope-dilution, liquid chromatography-coupled, tandem quadrupole mass spectrometric method to quantify representative species across the spectrum of RNA damage products predicted to arise at sites of inflammation, including nucleobase deamination (xanthosine and inosine), oxidation (8-oxoguanosine), and alkylation (1,N(6)-ethenoadenosine). Application of the method to the liver, spleen, and kidney from the SJL mouse model revealed generally higher levels of oxidative background RNA damage than was observed in DNA in control mice. However, compared to control mice, RcsX treatment to induce nitric oxide overproduction resulted in significant increases only in inosine and only in the spleen. Further, the nitric oxide synthase inhibitor, N-methylarginine, did not significantly affect the levels of inosine in control and RcsX-treated mice. The differences between DNA and RNA damage in the same animal model of inflammation point to possible influences from DNA repair, RcsX-induced alterations in adenosine deaminase activity, and differential accessibility of DNA and RNA to reactive oxygen and nitrogen species as determinants of nucleic acid damage during inflammation.

Optimized lymphocyte protein extraction performed simultaneously with DNA and RNA isolation: application to the study of factors affecting DNA, RNA, and protein recovery from lymphocytes of the oldest individuals

We describe an optimized procedure for protein extraction performed simultaneously with that of DNA and RNA from a single tissue sample that is, unlike the original protocol, suitable for quantitative studies. This optimized protocol is particularly well adapted to studies where gene regulation at DNA, RNA, and protein levels must be examined simultaneously, and when the amount of starting biological material is limited. We applied this procedure to the study of factors affecting both qualitatively and quantitatively the extraction of DNA, RNA, and proteins from lymphocytes of very old individuals, since we observed variability in the recovery of these molecular species with advanced age. Therefore, we investigated the combined effects of age and time delay between blood collection and lymphocyte isolation on the recovery of DNA, RNA, and proteins simultaneously extracted from Danish nonagenarians and centenarians versus younger adult samples. Our results suggest that neither RNA nor DNA nor protein contents of lymphocytes are altered with aging. However, the quantity of RNA and protein recovery is affected by a 24-h delay in blood processing. This effect is more pronounced in the oldest, particularly for RNA, and may affect data interpretation of age-dependent gene expression studies.

Multiparametric Evaluation of Retinoic Acid-Induced Terminal Differentiation of Blastoid Cells from Acute Non-Lymphocytic Leukemia Patients in Vitro

Recent findings that retinoic acid (RA) induces terminal granulocytic differentiation of the human promyelocytic leukemia cell line HL-60 in vitro and blast cell maturation in patients suffering from acute non-lymphocytic leukemia (ANLL) prompted an investigation on the ability of this agent to induce terminal maturation in blast cells from ANLL patients in vitro. We tested the ability of RA at 3×10–6 M, 3×10–7 M and 3×108– M concentrations to induce differentiation in blastold cells from 16 patients with ANLL using cytochemical and cytologic parameters, in addition to cytofluorometric methods. Leukemic cells in primary culture from all the patients underwent cytochemical and biochemical changes after treatment with RA. However, the extent of differentiation-positive cell clones (D+ clones) varied from patient to patient. Morphologic maturation was observed in a significant number of bone marrow samples. Leukocyte alkaline phosphatase and NBT reduction ability of cells, which are biochemical markers of granulocytic differentiation, were also significantly increased with a simultaneous decrease in DNA and RNA synthesis (which was estimated using a Phywe ICP-11 impulse flow cytometer).

Surface immunoglobulin light chain expression in pre-B cell leukemias

Cytofluorographic analysis of surface immunoglobulin (sIg) light chain clonal excess (CE), defined as (%kappa+ - %lambda+)/(%kappa+ + %lambda+) cells per discrete level of fluorescence intensity, was carried out on mononuclear cells of 32 leukemic patients. Eight demonstrated sIg light chain CE, including four blastic chronic myeloid leukemias (BL-CML), three "null" acute lymphoblastic leukemias (ALL), and one leukemic lymphoblastic lymphoma. Six of the leukemias demonstrated a kappa CE and two had a lambda CE. Sorted kappa+ PB cells from a BL-CML patient were shown to have a diploid DNA stem line and to bear the "common" ALL antigen. To provide further support for our finding of the expression of sIg light chains in ALL, we studied the REH cell line, derived from a "common" ALL patient and found cytoplasmic mu heavy chain and surface Ig lambda CE. Nucleic acid blotting experiments on REH revealed that both kappa genes had been deleted and that lambda genes had been rearranged, as expected in B cells expressing lambda light chains. Moreover, REH cells contained mu and lambda RNA. When REH cells were treated with TPA the amount of mu chain RNA increased by approximately fivefold and the amount of lambda chain RNA increased by approximately twofold. The finding of sIg light chain in pre-B cell leukemias and in the REH cell line, suggests that these leukemic cells are further differentiated along the B-cell lineage than was previously believed.

Cell cycle analysis using flow cytometry

This manuscript reviews the utility of flow cytometry for the study of cell proliferation. The applications of univariate DNA distribution analysis to cytokinetic studies of asynchronous and perturbed cell populations are discussed briefly. The newly developed technique for simultaneous flow cytometric measurement of cellular DNA content and amount of incorporated bromodeoxyuridine is discussed in more detail. The cytochemistry required for this analysis is reviewed as are its applications to: determination of the fractions of cells in the G1-, S- and G2 + M-phases of the cell cycle; determination of the G1-, S- and G2 + M phase durations and dispersions and growth fraction for asynchronous cells; detection of ara-C resistant cells present at low frequency in an otherwise sensitive population; and analysis of the cytokinetic response of a solid murine tumour to treatment in vivo with a cell cycle specific agent.

Leprosy. XII. T-cell subsets in lepromatous leprosy

The authors quantitated T-rosette-forming cell (TRFC) and T-cell subsets (T mu, T gamma) in the peripheral blood of twenty patients with lepromatous leprosy. The results obtained in their studies are as follows: (1) They reconfirmed the low levels of TRFC in patients with lepromatous type of leprosy; (2) T-cell subsets, both T mu (helper) and T gamma (suppressor) cells, showed lower levels in all patients with lepromatous leprosy than mean values of normal healthy controls; (3) The degree of decreased levels of T mu cells (96%) was more severe than other parameters TRFC (70%) and T gamma cells (47%) in all patients with lepromatous leprosy; and (4) It may be concluded that the alteration of the T-cell subset, T mu-cells, reflects a more fundamental abnormality than TRFC aberration in demonstrating the impairment of cell-mediated immunity in patients with lepromatous leprosy.

Flow cytometry in the diagnosis and classification of malignant lymphoma and leukemia

DNA content and light scatter were measured by flow cytometry (FCM) in 103 patients including 43 patients with non-Hodgkin's lymphoma (NHL), eight patients with Hodgkin's disease (HD), 17 patients with acute lymphoblastic leukemia (ALL), ten patients with acute nonlymphocytic leukemia (ANLL), and 25 patients with chronic lymphoid leukemias. Controls consisted of 42 nonneoplastic specimens obtained from lymph nodes, spleen, bone marrow, and peripheral blood. Each specimen was analyzed after staining with a hypotonic solution of propidium iodide using nuclei isolated from chicken erythrocytes as an internal standard. The DNA content and light scatter of the human populations was expressed as a ratio between the DNA content (or light scatter) of the human G0--G1 cells and that of the chicken erythrocytes nuclei. The mean DNA ratio for the 42 nonneoplastic samples was 2.58 +/- 0.045 (SD). In these samples the DNA coefficient of variation of the human G0--G1 peak ranged from 1.48--3.28% (mean, 2.33 +/- 0.54%). The FCM data in the NHL was compared to morphologic diagnoses made according to the "working formulation of NHL for clinical usage" recently proposed by a panel of international experts. Eight of 17 (47%) low grade NHL, one of two (50%) mycosis fungoides, ten of 14 (71%) intermediate grade NHL, nine of ten (90%) high grade NHL, nine of 17 (53%) ALL, three of ten (30%) ANLL, and seven of 25 (28%) chronic lymphoid leukemias had abnormal DNA ratios indicative of aneuploidy. In addition, several cases had normal DNA ratios but G0--G1 coefficients of variation outside of the normal range. All cases of HD had normal DNA values except one case with a small percentage of near tetraploid cells. The mean percentage of cells with S-phase DNA content for the low grade NHL (2.2 +/- 0.8%) was significantly lower than that of the intermediate grade NHL (12.1 +/- 4.9%; P less than 0.0001). The mean S-phase value for the intermediate grade NHL was significantly lower than that of the high grade NHL (22.6 +/- 11.1%; P less than 0.001). The three prognostic categories of NHL designated by the new formulation were clearly distinguishable by the FCM data. Light scatter was not particularly useful for distinguishing nonneoplastic from neoplastic populations. The mean light scatter coefficient of variation of the ALL (15.2%) was significantly lower than that of ANLL (20.5%), however (P less than 0.04).

Abnormalities in the content of nucleic acids of peripheral blood mononuclear cells from patients with systemic lupus erythematosus

We have completed 59 cytofluorographic studies of DNA/RNA content in acridine orange-stained peripheral blood mononuclear cells from 44 patients with systemic lupus erythematosus, most of whom received no medications. Most such cells were in resting phases of the cell cycle, particularly those from patients with inactive disease. Nine patients with systemic lupus erythematosus had increased percentages of these cells in the synthesis and postsynthesis phases of the cell cycle; the B lymphocyte had a greatest proportions of activated cells. In 11 patients, we found that cells, particularly T lymphocytes, had increased RNA content without a proportional increase in DNA. This DNA block occurred primarily in patients with serum antibodies to DNA and it could be reproduced in normal mitogen-stimulated mononuclear cells incubated in heat-inactivated sera from patients with systemic lupus erythematosus whose own cells showed abnormalities of DNA/RNA content or in purified native DNA antibody. The DNA blocking potential of the DNA antibody was dependent on its Fc portion and on the presence of Fc receptors on T cells. Thus, saturation of Fc receptors by pretreatment with aggregated IgG or incubation with the whole antibody in the cold prevented the DNA block, indicating that it was an active process.

Human T-lymphocyte subset production of immune (gamma) interferon

Human T micron, T gamma, and T PHI lymphocyte subpopulations have the capacity to respond to phytohemagglutinin (PHA) in vitro with proliferation and the production of a pH 2 and heat-labile gamma interferon. This occurs both when the subsets are isolated by direct rosetting techniques or by negative selection. Macrophages enhance the production of the gamma interferon by each lymphocyte subset and do not themselves produce gamma interferon in response to products of PHA-activated lymphocyte subsets. Thus our studies indicate that subpopulations of T lymphocytes known to differ with regard to morphology, surface receptors, RNA content, response to corticosteroids and X-irradiation, and other functional capabilities do not differ with regard to their capacity to produce gamma interferon.

Immunological markers and DNA content in a case of giant lymph node hyperplasia (Castleman's disease)

Little is known about the immunologic characteristics of the cells in giant lymph node hyperplasia (GLNH). For this reason, cell surface markers and intracytoplasmic immunoglobulins were determined on a case of GLNH. In addition, cellular DNA content was determined by flow analysis. A 59-year-old male underwent thoracotomy for a posterior madiastinal mass, which was entirely excised. Histologically, the mass was diagnosed as GLNH with features of both the hyaline-vascular and plasma-cell types. Preoperatively, the patient had a broad-based hypergammaglobulinemia with an increase in serum IgG. Two months postoperatively, the serum protein electrophoresis had returned to normal. Surface immunoglobulins (SIg) were determined on fresh cells in suspension using a polyvalent antiserum and monospecific antisera against heavy and light chains. Ten percent of the cells had SIg. The distribution of SIg-bearing cells was polyclonal. Intracytoplasmic immunoglobulin (CIg), as determined by immunofluorescence on ethanol-fixed smears from the cell suspensions, showed 6% positive cells. The distribution of cytoplasmic immunoglobulin was similarly polyclonal. Ethanol-fixed frozen sections also showed a polyclonal pattern when stained for CIg. Fifty-two percent of fresh cells in suspension formed Erosettes. These immunologic characteristics do not differ from those observed in non-neoplastic lymphoid tissues. A DNA content histogram was obtained by flow microfluorometry using ethanol-fixed cells stained with propidium iodide following RNase treatment. The DNA content distribution was within the normal limits established by the study of non-neoplastic lymphoid tissues.

Subpopulations of human peripheral blood cells: analysis of granulocytic progenitor cells by flow cytometry and immunologic surface markers

Normal human peripheral blood cells were separated into different populations based upon isopycnic sedimentation, E rosetting, and EAC rosetting. Each population was characterized according to morphology, surface markers, granulocytic colony formation in semi-solid media, and stainable RNA content by acridine orange (AO) flow cytometry. These techniques enrich for a population of cells that is characterized by a lymphoid morphology, a high granulocytic-macrophage progenitor cell cloning efficiency, a lack of surface markers, and a high stainable RNA content not found in the other two populations of peripheral blood lymphocytes (T cells and B cells). The stainable RNA content serves as a new metabolic marker for the population of cells in which the preponderance of granulocytic progenitor cells reside.

Separation of human T lymphocyte subpopulations (Tmu, Tgamma) by density gradient electrophoresis

Purified human peripheral blood T lymphocytes were fractionated by density gradient electrophoresis on the basis of their surface charge. The high mobility cell fractions were found to be enriched in T cells having receptors for IgM (Tmu cells) with only minor proportions of T cells having receptors for IgG (Tgamma cells). In contrast, the low mobility cell fractions were enriched in Tgamma cells with very low numbers of contaminating Tmu cells. Both populations were of higher mobility than human peripheral blood B lymphocytes. High-affinity sheep erythrocyte resette-forming cells (E-RFC) were relatively enriched in the high and intermediate mobility fractions and appear to include the Tmu cells and the T cells without receptors for IgG or IgM (Tvarphi). The low affinity E-RFC were found only in the lower mobility fractions that included the Tgamma cell population. A direct correlation was observed between the number of Tgamma lymphocytes and the low affinity E-RFC in all the fractions. The separated cell fractions were treated in vitro with different concentrations of concanavalin A (Con A) and examined for the numbers of Tmu and Tgamma cells. Low concentrations of Con A (2.5 mug/ml) significantly increased the number of Tmu cells, whereas high concentrations of Con A (20 mug/ml and 40 mug/ml) markedly reduced the number of Tmu cells and increased the number of Tgamma cells. Furthermore, all fractions (both Tmu and Tgamma cell enriched) responded by proliferation to Con A, whereas only the high and intermediate mobility fractions (enriched in Tmu cells) responded to phytohemagglutinin. Fractions enriched in Tgamma cells responded very poorly to phytohemagglutinin. This method provides another technique for separating human Tmu- and Tgamma-enriched lymphocyte subpopulations and does not modulate the Fc receptors of the cells, in contrast to the rosetting techniques currently in use for the separation of these lymphocytes.

Relationship between RNA content and progression of lymphocytes through S phase of cell cycle

A flow cytometric technique for simultaneous measurements of RNA and DNA in individual cells has been applied to correlate the content of cellular RNA with the rate of progression of cells through the S phase. Human peripheral lymphocytes stimulated with phytohemagglutinin were blocked at the G1/S phase boundary by hydroxyurea or 5-fluorodeoxy-uridine treatment. Cells in the G1 phase as well as cells blocked at the G1/S phase boundary showed high heterogeneity with respect to stainable RNA content. After release from the block, the cells traversed the S phase at rates proportional to the quantity of stainable RNA per cell. Cells with the highest RNA content completed DNA replication 5 hr after release from the block; the cells with minimal RNA traversed the S phase at one-fifth of this rate. The large intercellular variation in stainable RNA and length of the S phase may be due to functional heterogeneity in the lymphocyte population. Our results suggest a correlation between the number of ribosomes and the rate of DNA replication in lymphocytes.