Abstract P5-04-03: Deconvoluting immune cell populations using ‘in silico flow cytometry’ with CIBERSORT: Association with neoadjuvant therapy response and genomic instability in TNBC

Author(s):  
Shaveta Vinayak ◽  
Aaron Newman ◽  
Sylvia Adams ◽  
Anosheh Afghahi ◽  
Kristin C Jensen ◽  
...  
2020 ◽  
pp. annrheumdis-2019-216786
Author(s):  
Margarita Ivanchenko ◽  
Gudny Ella Thorlacius ◽  
Malin Hedlund ◽  
Vijole Ottosson ◽  
Lauro Meneghel ◽  
...  

ObjectiveCongenital heart block (CHB) with immune cell infiltration develops in the fetus after exposure to maternal Ro/La autoantibodies. CHB-related serology has been extensively studied, but reports on immune-cell profiles of anti-Ro/La-exposed neonates are lacking. In the current study, we characterised circulating immune-cell populations in anti-Ro/La+mothers and newborns, and explored potential downstream effects of skewed neonatal cell populations.MethodsIn total, blood from mothers (n=43) and neonates (n=66) was sampled at birth from anti-Ro/La+ (n=36) and control (n=30) pregnancies with or without rheumatic disease and CHB. Flow cytometry, microarrays and ELISA were used for characterising cells and plasma.ResultsSimilar to non-pregnant systemic lupus erythematosus and Sjögren-patients, anti-Ro/La+mothers had altered B-cell subset frequencies, relative T-cell lymphopenia and lower natural killer (NK)-cell frequencies. Surprisingly, their anti-Ro/La exposed neonates presented higher frequencies of CD56dimCD16hi NK cells (p<0.01), but no other cell frequency differences compared with controls. Type I and II interferon (IFN) gene-signatures were revealed in neonates of anti-Ro/La+ pregnancy, and exposure of fetal cardiomyocytes to type I IFN induced upregulation of several NK-cell chemoattractants and activating ligands. Intracellular flow cytometry revealed IFNγ production by NK cells, CD8+ and CD4+ T cells in anti-Ro/La exposed neonates. IFNγ was also detectable in their plasma.ConclusionOur study demonstrates an increased frequency of NK cells in anti-Ro/La exposed neonates, footprints of type I and II IFN and an upregulation of ligands activating NK cells in fetal cardiac cells after type I IFN exposure. These novel observations demonstrate innate immune activation in neonates of anti-Ro/La+pregnancy, which could contribute to the risk of CHB.


2019 ◽  
Vol 6 (2) ◽  
pp. 51
Author(s):  
Jonathan E. Fogle ◽  
Jenna A. Scott ◽  
Glen W. Almond

Recent reports suggest that antibiotic therapy may either reduce or enhance the immune response to various porcine vaccines. Based upon these findings, we asked if antibiotic therapy alters immune cell populations, as measured by flow cytometry and/or vaccine-specific humoral immunity, as measured by sample to positive (S/P) antibody ratios. Here, we investigated the immuno-modulatory effects of enrofloxacin, ceftiofur, and tulathromycin on the immune response to a Mycoplasma hyopneumoniae (M. hyopneumoniae) and porcine circovirus type 2 (PCV-2) combination vaccine in weaned pigs. Maternal antibody likely interfered with the induction of immunity to M. hyopneumoniae. Antibiotic administration did not affect immune cell populations, as assessed by flow cytometry and did not affect the induction of humoral immunity to PCV-2.


2008 ◽  
Vol 29 (1) ◽  
pp. 137-143 ◽  
Author(s):  
Matthew C Loftspring ◽  
Jeremiah McDole ◽  
Aigang Lu ◽  
Joseph F Clark ◽  
Aaron J Johnson

Intracerebral hemorrhage (ICH) is a stroke subtype with high rates of mortality and morbidity. The immune system, particularly complement and cytokine signaling, has been implicated in brain injury after ICH. However, the cellular immunology associated with ICH has been understudied. In this report, we use flow cytometry to quantitatively profile immune cell populations that infiltrate the brain 1 and 4 days post-ICH. At 1 day CD45hi GR-1+ cells were increased 2.0-fold compared with saline controls ( P ≤ 0.05); however, we did not observe changes in any other cell populations analyzed. At 4 days ICH mice presented with a 2.4-fold increase in CD45hi cells, a 1.9-fold increase in CD45hi GR-1 cells, a 3.4-fold increase in CD45hi GR-1+ cells, and most notably, a 1.7-fold increase in CD4+ cells ( P ≤ 0.05 for all groups), compared with control mice. We did not observe changes in the numbers of CD8+ cells or CD45lo cells ( P = 0.43 and 0.49, respectively). Thus, we have shown the first use of flow cytometry to analyze leukocyte infiltration in response to ICH. Our finding of a CD4 T-cell infiltrate is novel and suggests a role for the adaptive immune system in the response to ICH.


2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii105-ii106
Author(s):  
Michael Strong ◽  
Aqila Ahmed ◽  
Anda-Alexandra Calinescu ◽  
Xiaofeng Zhou ◽  
Tyler Robinson ◽  
...  

Abstract Roughly 400,000 people have bone metastases in the U.S. with the vast majority of these occurring in the spine. The etiology of bone metastasis still remains to be fully elucidated. This study explored the differences in immune landscape between long bone and spine that may contribute to higher rates of bone metastasis to the spine. Spines and femurs from male C57BL6/J mice (N=10) were processed for flow cytometry and immunophenotyping using Mass Cytometry by Time-Of-Flight (CyTOF). The cells were analyzed with CyTOF using a 33-surface protein marker mouse antibody panel. Spines (N=3) and femurs (N=2) from patients were analyzed with CyTOF using the Maxpar Complete Human T cell Immuno-Oncology Panel Set. There are global differences in the immune cell composition between the long bone and spine microenvironment. Flow cytometry revealed slight increases in the CD45+ and Cd11b+ cell populations in the bone marrow of murine spines compared to murine long bone, which are markers for myeloid-derived suppressor cells (MDSCs). Using CyTOF, significant differences in the immune cell landscape between long bone and spine were observed. In the murine long bone, an increase in monocytes/macrophages, myeloid progenitors, granulocytic MDSCs, granulocytes, and mast cells was observed compared to the spine. In the murine spine an elevation of CD8a+ DC cells, classical monocytes, MDSCs, pDCs, memory T helper cells, and NK T cells was seen. Evaluation of human long bone and spine revealed similar trends with a predominance of myeloid progenitor cells and monocytes in the human vertebra compared to the human long bone marrow. Significant differences in the immune microenvironment exist between the spine and long bone marrow in both murine and human samples. This is the first report of significant differences in immune cell populations between different skeletal locations. However, the functional significance of these differences has yet to be determined.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3933-3933
Author(s):  
Julie Wilkinson ◽  
Cecilia Smith ◽  
Sybil D’Costa ◽  
Enrique Rabellino

Abstract The utility of the ex-vivo evaluation of immune cell functionality in the context of a) Determining an efficacious vaccine strategy for infectious diseases/cancer, b) Determining a tolerance profile in autoimmunity and transplantation, and c) understanding the basic mechanisms of immune cell responses in disease pathogenesis is well recognized. However, the benefit of these assays as surrogate markers of immune cell activity in vivo has not been fully realized due to the variable nature of these in vitro assays which is particularly pronounced in T cell functional assays. This variability arises from a variety of factors ranging from choice of assay, source of the cells, the sample processing methodology (isolation, freezing, thawing, and culturing), sample staining protocol for the chosen assay and ultimately data analysis, and data reduction. With a view to reducing variability and standardizing targeted steps of T cell functional assays, an automated methodology for simultaneous staining and analysis of multiple intracellular cytokines and cytotoxicity markers via flow cytometry was developed and validated. A 5-color flow cytometry assay (2–3 surface markers; 2 intracellular markers) was developed to characterize the restricted polyclonal (SEB/CD28) and antigen specific (CEF peptide pool) cytokine and cytotoxic profile response in human PBMCs. A modification to available sample preparation instruments was performed that enabled the automated pipetting, incubation, and staining of intracellular and surface molecules of stimulated human peripheral blood mononuclear cell populations (PBMC) for flow cytometric analysis. Statistically significant reductions in both inter and intra assay variability was observed in the automated methodology as compared to the manual assay with improvements in CVs for positive cell numbers and mean fluorescence intensity. For example, the inter assay CVs for IFNg cytokine producing CD4+ T cell populations improved from approximately 15 to 5, while the mean fluorescence intensity improved nearly 5 fold with automation. Importantly, the automated methodology furnished comparable responses in percent positive cytokine/cytotoxicity profiles as compared to the manual method while reducing the “handson” sample preparation and analysis time from 2 hours to 20 minutes. With the standardization of functional assays, other sources of variability in assays result can now be addressed specifically e.g. specimen handling, freezing, thawing, culturing, or biological. Standardized multiparametric functional profiling of the cells thus reveals the complex nature of the immune response and lends credence to their use as surrogate markers of efficacy and functionality.


2004 ◽  
Vol 284 (1-2) ◽  
pp. 7-14 ◽  
Author(s):  
Simonetta Di Fabio ◽  
Franco Corrias ◽  
Francesca Monardo ◽  
Fausto Titti

2021 ◽  
Vol 9 (Suppl 3) ◽  
pp. A350-A350
Author(s):  
Michelle Winkler ◽  
Michael Curran

BackgroundAnti-checkpoint antibodies blocking T cell co-inhibitory molecules (e.g. αPD-1, αCTLA-4) allow immune effector cells to persist, expand, and maintain cytotoxic function in the tumor microenvironment (TME). Despite being effective in immune ”hot” tumors that are infiltrated by effector anti-tumor cells, immune ”cold” tumors fail to respond to checkpoint blockade. ”Cold” tumors are populated with immune suppressive cells including regulatory T cells, M2 macrophages, and myeloid derived suppressor cells, which inhibit immune effector infiltration and function. These suppressive populations, along with tumor cells, express co-inhibitory checkpoints already targeted with current immunotherapeutics, but also some checkpoints in need of further investigation. We hypothesized that by targeting these checkpoints with cytoreductive antibodies which selectively deplete suppressive populations and tumor cells via ADCC/ADCP, we will compromise ”cold” immune privilege and restore an efficient anti-tumor immune response.MethodsTo identify novel targets to produce checkpoint cytoreductive antibodies we conducted in silico analysis that prioritized immune-inhibitory targets with tumor-specific or tumor-selective expression on cell surface. We cross-referenced a previously published list of transmembrane proteins against publicly sourced datasets including TCGA, HPA, GTEx, BioGPS, and SAGE.1 We then characterized the expression profile of each selected target on tumor cells in vitro and on cell populations in the TME ex vivo via multiparameter flow cytometry. Finally, we assessed the impact of existing checkpoint-targeting cytoreductive antibodies on survival and tumor growth in murine ”hot” and ”cold” tumors.ResultsVISTA and DLL3 were identified via in silico analysis as co-inhibitory surface proteins specifically and selectively in the TME and not in healthy tissues. DLL3 is mainly expressed on tumor cells while VISTA was described mostly on immunosuppressive myeloid cells. An anti-DLL3 antibody was produced by a previous laboratory as an IgG1 antibody, and we engineered a version in the depletive (IgG2a) isotype, which will enable us to target this checkpoint with either a blocking or a depleting antibody. Flow cytometry analysis identified VISTA on multiple myeloid cell populations in ”cold” 4T1 murine mammary tumors while its expression was low in spleen. To start assessing the efficiency of depleting versus non-depleting antibodies, ”hot” CT26 murine tumors and 4T1 tumors were treated with an αCTLA-4-IgG2a or αCTLA-4-IgG1. Groups treated with depleting antibodies showed increased survival compared to groups treated with non-depleting antibodies.ConclusionsNovel immune-inhibitory checkpoints can be identified and targeting them with cytoreductive antibodies leads to a higher anti-tumor immune response. This investigation opens the door to more efficient combination therapies.AcknowledgementsSupported by a training fellowship from The University of Texas Health Science Center at Houston Center for Clinical and Translational Sciences TL1 Program (Grant No. TL1 TR003169).ReferencesWang J, et al. Siglec-15 as an immune suppressor and potential target for normalization cancer immunotherapy. Nat Med 25,(2019).


2021 ◽  
Author(s):  
Arrianna Zirbes ◽  
Jesuchristopher Joseph ◽  
Jennifer C Lopez ◽  
Rosalyn W Sayaman ◽  
Mudaser Basam ◽  
...  

Abstract Background : A majority of breast cancers (BC) are age-related and we seek to determine what cellular and molecular changes occur in breast tissue with age that make women more susceptible to cancer initiation. Immune-epithelial cell interactions are important during mammary gland development and the immune system plays an important role in BC progression. The composition of human immune cell populations is known to change in peripheral blood with age and in breast tissue during BC progression. Less is known about changes in immune populations in normal breast tissue and how their interactions with mammary epithelia change with age. Methods : We quantified densities of T cells, B cells, and macrophage subsets in pathologically normal breast tissue from 122 different women who ranged in age from 24 to 74 years old. Donor-matched peripheral blood from a subset of 20 donors was analyzed by flow cytometry. Tissue immune cell densities and localizations relative to the epithelium were quantified in situ with machine learning-based analyses of multiplex immunohistochemistry-stained tissue sections. In situ results were corroborated with flow cytometry analyses of peri-epithelial immune cells from primary organoid preparations and transcriptome analyses of public data from bulk tissue reduction mammoplasties. Results : Proportions of immune cell subsets in breast tissue and donor-matched peripheral blood were not correlated. Density (cells/mm 2 ) of T and B lymphocytes in situ decreased with age. T cells and macrophages preferentially localized near or within epithelial bilayers, rather than the intralobular stroma. M2:M1 macrophage ratio increased with age and was accompanied by an increased density of M2 in the intralobular stroma. Transcriptional signature analyses suggested age-dependent decline in adaptive immune cell populations and functions and increased innate immune cell activity. Conclusions : T cells and macrophages are so intimately associated with the epithelia that they are embedded within the bilayer, suggesting an important role for immune-epithelial cell interactions. Age-associated decreased T cell density in peri-epithelial regions, and increased M2 macrophage density in intralobular stroma suggests the emergence of a tissue microenvironment that is simultaneously immune-senescent and immunosuppressive with age .


2021 ◽  
Vol 156 (Supplement_1) ◽  
pp. S3-S4
Author(s):  
Nicholas Borcherding ◽  
John Moley ◽  
Rachael Field ◽  
Jonathan R Brestoff

Abstract Obesity is a metabolic disease that promotes the development of a number of other pathologies. Despite its high disease burden, the underlying pathophysiology of obesity is poorly understood. Emerging research has indicated that adipocytes transfer their mitochondria to macrophages in white adipose tissue as a mechanism of cell-to-cell communication and that this process is impaired in obesity. However, the diversity of intercellular mitochondria transfer axes that occurs in adipose and its regulation in obesity are not known. Here, we utilized 31-color spectral flow cytometry of adipocyte-specific mitochondria reporter (MitoFat) mice to comprehensively analyze intercellular mitochondria transfer from adipocytes to other cell types in white, beige, and brown adipose tissues. Employing manifold machine learning, we generated reference clusters of cells in 5-month (young) and 20-month-old (aged) MitoFat mice fed a normal chow diet (low fat diet). Using the reference clusters and manifold, we then mapped differences in immune cell populations using nearest neighbor search approximations in MitoFat mice fed normal chow, high-fat diet (HFD), high-fat diet with low palmitate (LP-HFD). The degree of mitochondria transfer from adipocytes to each of the various cell clusters was determined for each tissue and for each condition. We observed that adipocytes transfer their mitochondria to a wide range of immune cell populations, most notably macrophages. Although aged mice develop obesity, surprisingly they do not exhibit decreased mitochondria transfer from adipocytes to macrophages in vivo in white, beige, or brown adipose tissue. In contrast, young mice fed a HFD highly enriched in palmitate exhibit obesity and markedly reduced mitochondria transfer from adipocytes to macrophages. The decrease in mitochondria transfer was largely ameliorated by the replacement of palmitate with medium chain fatty acids, suggesting a potential direct dietary mechanism in the alteration of mitochondria transfer. Overall, the 31-color quantification increased granularity, allowing us to quantify differences in immune populations and mitochondria transfer by tissue, age, and diet. Similar machine-learning approaches could be used to investigate both basic biological and clinical questions by effectively reducing dimensions, mitigating batch effect, and enabling comparisons across different tissues, timepoints, or conditions.


2016 ◽  
Author(s):  
Patrick Danaher ◽  
Sarah Warren ◽  
Lucas Dennis ◽  
Leonard D’Amico ◽  
Andrew White ◽  
...  

AbstractBackgroundAssays of the abundance of immune cell populations in the tumor microenvironment promise to inform immune oncology research and the choice of immunotherapy for individual patients. We propose to measure the intratumoral abundance of various immune cells populations with gene expression. In contrast to IHC and flow cytometry, gene expression assays yield high information content from a clinically practical workflow. Previous studies of gene expression in purified immune cells have reported hundreds of genes showing enrichment in a single cell type, but the utility of these genes in tumor samples is unknown. We describe a novel statistical method for using co-expression patterns in large tumor gene expression datasets to validate previously reported candidate cell type marker genes, and we use this method to winnow previously published gene lists down to a subset of high confidence marker genes.MethodsWe use co-expression patterns in 9986 samples from The Cancer Genome Atlas (TCGA) to validate previously reported cell type marker genes. We compare immune cell scores derived from these genes to measurements from flow cytometry and immunohistochemistry. We characterize the reproducibility of our cell scores in replicate runs of RNA extracted from FFPE tumor tissue.ResultsWe identify a list of 60 marker genes whose expression levels quantify 14 immune cell populations. Cell type scores calculated from these genes are concordant with flow cytometry and IHC readings, show high reproducibility in replicate RNA samples from FFPE tissue, and reveal an intricate picture of the immune infiltrate in TCGA. Most genes previously reported to be enriched in a single cell type have co-expression patterns inconsistent with cell type specificity.ConclusionsDue to their concise gene set, computational simplicity and utility in tumor samples, these cell type gene signatures may be useful in future discovery research and clinical trials to understand how tumors and therapeutic intervention shape the immune response.


Sign in / Sign up

Export Citation Format

Share Document