scholarly journals A simple strategy for sample annotation error detection in cytometry datasets

2021 ◽  
Author(s):  
Megan Smithmyer ◽  
Alice E Wiedeman ◽  
David A.G. Skibinski ◽  
Adam K Savage ◽  
Carolina Acosta-Vega ◽  
...  
Keyword(s):  
Error Detection ◽  
Immune Cell ◽  
Hla Class I ◽  
Cell Types ◽  
Class I ◽  
Cross Sectional ◽  
Simple Strategy ◽  
Three Samples ◽  
Allele Expression

Mislabeling samples or data with the wrong participant information can impact study integrity and lead investigators to draw inaccurate conclusions. Quality control to prevent these types of errors is commonly embedded into the analysis of genomic datasets, but a similar identification strategy is not standard for cytometric data. Here, we present a method for detecting sample identification errors in cytometric data using expression of HLA class I alleles. We measured HLA-A*02 and HLA-B*07 expression in 3 longitudinal samples from 41 participants using a 33-marker CyTOF panel designed to identify major immune cell types. 3/123 samples (2.4%) showed HLA allele expression that did not match their longitudinal pairs. Furthermore, these same three samples cytometric signature did not match qPCR HLA class I allele data, suggesting that they were accurately identified as mismatches. We conclude that this technique is useful for detecting sample labeling errors in cytometric analyses of longitudinal data. This technique could also be used in conjunction with another method, like GWAS or PCR, to detect errors in cross-sectional data. We suggest widespread adoption of this or similar techniques will improve the quality of clinical studies that utilize cytometry.

scholarly journals P102 Host gene background and concentration influence the butyrate effect on modulating IECs proliferation

2020 ◽  
Vol 14 (Supplement_1) ◽  
pp. S186-S187
Author(s):  
H He ◽  
J Hu ◽  
W Wang ◽  
M Zhang ◽  
M Zheng ◽  
...  
Keyword(s):  
Immune Cell ◽  
Imaging System ◽  
Cell Types ◽  
Pathological Feature ◽  
Intestinal Epithelial ◽  
Barrier Dysfunction ◽  
Cross Sectional ◽  
Mucosal Regeneration ◽  
Intestinal Organoids ◽  
Stability And Accuracy

Abstract Background Intestinal epithelial barrier dysfunction is a major pathological feature of inflammatory bowel disease (IBD). Stability and accuracy of intestinal epithelial cells (IECs) self-renew are the fundament of intestinal mucosal regeneration and repair. Fermentable dietary fibre and short-chain fatty acid (SCFA) play a role in cell proliferation, histone acetylation and immune responses. However, the results about SCFA modulating IECs proliferation are not coincided. There are several reason that SCFA can have an impact on IECs through immune cell in animal experiment and that also include animal gene background, SCFA concentration, cell types used in cell experiment l. So we adopted intestinal organoids to investigate the effect of butyrate on IECs self-renew to avoid the immune cell influence and signal type cell experiments limitation. Methods Six to 8 weeks wide-type mice and IL10−/− mice were used. Mouse intestinal crypt isolation and organoid culture were according to previously published methods (H. Clevers et al., Gastroenterology 2011). Re-suspended isolated ISCs were seeded onto 10 ml MatrigelTM (Corning 356237) in CellCarrier-96 Ultra Microplates per well (Perkinelmer 6055302). Sodium butyrate (SB) was administered at a final concentration (from 0 to 0.2mM) at Day1. Organoids’ cross-sectional area was measured and calculated, as well as all images were captured using an Operetta High-Content Imaging System and Harmony software 4.8. Results SB promoted intestinal organoids proliferation in a narrow effective concentration from 0.02 to 0.09 mM (Figure 1). The effective SB concentration applied to WT mice-derived organoids other than IL10−/− mice-derived organoids. SB can effectively and rapidly promote organoid proliferation (Figures 2 and 4). SB can continuously promote the proliferation of organoids-derived organoids (Figures 3 and 4). Conclusion There is a narrow effective SB concentrationpromotes WT mice-derived organoids other than IL10−/− mice-derived organoids. This result may be used to illustrate the phenomenon that IBD-associated microbiota and metabolites, butyrate, has different effects on IBD patient and IBD model mice.

Metabolic profile and quality of life in class I sarcopenic overweight and obese postmenopausal women: a MONET study

2009 ◽  
Vol 34 (1) ◽  
pp. 18-24 ◽  
Author(s):  
Virginie Messier ◽  
Antony D. Karelis ◽  
Marie-Eve Lavoie ◽  
Martin Brochu ◽  
May Faraj ◽  
...  
Keyword(s):  
Quality Of Life ◽  
Postmenopausal Women ◽  
Lean Body Mass ◽  
Body Mass ◽  
Cross Sectional Study ◽  
Class I ◽  
Model Assessment ◽  
Cross Sectional ◽  
Metabolic Complications

Sarcopenia is believed to be associated with disability and metabolic complications. The objective of this study was to examine the metabolic and quality-of-life profile of sarcopenic overweight and obese postmenopausal women. In this cross-sectional study of 136 healthy overweight and obese postmenopausal women, 9 class I sarcopenic women were identified. Class I sarcopenia was defined as an appendicular lean body mass index (ALBMI) ≤ 6.44 kg·m–2 (appendicular lean body mass/height). Outcome measures were body composition (dual energy X-ray absorptiometry and computed tomography), blood lipids, inflammation markers, blood pressure, insulin sensitivity (homeostasis model assessment and hyperinsulinemic-euglycemic clamp), cardiorespiratory fitness, and quality of life (Medical Outcomes Study General Health Survey questionnaire). By design, class I sarcopenic women (n = 9) had a significantly lower ALBMI and appendicular lean body mass than nonsarcopenic women (n = 127). In addition, class I sarcopenic women tended to have lower levels of insulin resistance (p = 0.070) and fasting glucose (p = 0.054). However, no difference between the groups was observed for quality of life. This study showed that, in our sample of class I sarcopenic overweight and obese postmenopausal women, subjects did not present an unfavourable metabolic or quality-of-life profile, compared with nonsarcopenic overweight and obese postmenopausal women.

scholarly journals Changes in impact of HLA class I allele expression on HIV-1 plasma virus loads at a population level over time

2010 ◽  
Vol 54 (4) ◽  
pp. 196-205 ◽  
Author(s):  
Michiko Koga ◽  
Ai Kawana-Tachikawa ◽  
David Heckerman ◽  
Takashi Odawara ◽  
Hitomi Nakamura ◽  
...  
Keyword(s):  
Population Level ◽  
Hla Class I ◽  
Class I ◽  
Plasma Virus ◽  
Allele Expression ◽  
Hiv 1 ◽  
Over Time

scholarly journals Human leucocyte antigen class I in hormone receptor-positive, HER2-negative breast cancer: association with response and survival after neoadjuvant chemotherapy

2019 ◽  
Vol 21 (1) ◽  
Author(s):  
Bruno Valentin Sinn ◽  
Karsten E. Weber ◽  
Wolfgang Daniel Schmitt ◽  
Peter A. Fasching ◽  
William Fraser Symmans ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Hormone Receptor ◽  
Triple Negative ◽  
Immune Cell ◽  
Hla Class I ◽  
Class I ◽  
Endocrine Treatment ◽  
Hormone Receptor Positive ◽  
Tumor Immunogenicity

Abstract Background Clinical application of cancer immunotherapy requires a better understanding of tumor immunogenicity and the tumor microenvironment. HLA class I molecules present antigens to CD8+ cytotoxic cells. Their loss or downregulation is frequently found in tumors resulting in reduced T cell responses and worse prognosis. Methods We evaluated HLA class I heavy chain expression by immunohistochemistry in 863 biopsies (GeparTrio trial). Patients received neoadjuvant chemotherapy and adjuvant endocrine treatment if tumors were hormone receptor-positive (HR+). In parallel, the expression of HLA-A was analyzed using a microarray cohort of 320 breast cancer patients from the MD Anderson Cancer Center. We evaluated its association with clinical outcome, tumor-infiltrating lymphocytes (TILs), and immune cell metagenes. Results In HR+/HER2− breast cancer, HLA class I heavy chain expression was associated with increased TILs and better response to chemotherapy (7% vs. 14% pCR rate, P = 0.029), but worse disease-free survival (hazard ratio (HR) 1.6 (1.1–2.4); P = 0.024). The effect was significant in a multivariate model adjusted for clinical and pathological variables (HR 1.7 (1.1–2.6); P = 0.016) and was confirmed by analysis of HLA-A in a microarray cohort. HLA-A was correlated to most immune cell metagenes. There was no association with response or survival in triple-negative or HER2+ disease. Conclusions The study confirms the negative prognostic role of lymphocytes in HR+ breast cancer and points at a complex interaction between chemotherapy, endocrine treatment, and tumor immunogenicity. The results point at a subtype-specific and potentially treatment-specific role of tumor-immunological processes in breast cancer with different implications in triple-negative and hormone receptor-positive disease.

scholarly journals P14.47 Tissue immune markers for central nervous system germinoma

2019 ◽  
Vol 21 (Supplement_3) ◽  
pp. iii77-iii78 ◽  
Author(s):  
A K CHAN ◽  
Z F Shi ◽  
K W Lo ◽  
H K Ng ◽  
C C Lau
Keyword(s):  
T Cells ◽  
T Cell ◽  
Immune Cells ◽  
Immune Cell ◽  
Hla Class I ◽  
Class I ◽  
Cytotoxic T Cell ◽  
T Helper ◽  
The Mean ◽  
Immune Cell Infiltrates

Abstract BACKGROUND Germinoma is the commonest CNS germ cell tumor. An important histological feature is prominent immune cell infiltrates. The composition of such immune cell infiltrates remains under-investigated in the literature. MATERIAL AND METHODS We collected a cohort of 40 cases of intra-cranial germinomas and examined the clinical and histopathological features. The tumor infiltrating immune cells were characterized by immunohistochemistry and image analysis. RESULTS Across the cohort, the mean positivity ± SE of CD3-positive T cell and CD20-positive B cells was 31.2% ± 3.1% and 15.2% ± 2.2%, respectively (p<0.001). The mean positivity of CD4-positive T helper cell and CD8-positive cytotoxic T cell was 19% ± 2.3% and 14.3% ± 1.7%, respectively (p<0.001). PD-L1 expression was detected in 50% of the cases and was observed exclusively in immune cells but not in neoplastic cells. Germinomas with positive PD-L1 expression had significantly more abundant CD3-positive T cells (p=0.001), CD4-positive T helper cells (p<0.001) and CD8-positive cytotoxic T cells (p=0.004) as compared with those lacking PD-L1 expression. Immunostain for HLA-A and HLA-B revealed loss of HLA class I expression occurring in 92.5% of the germinomas. Loss of HLA class I expression was associated with less abundant CD3-positive T cells (p=0.04). CONCLUSION Taken together, the predominant T cells infiltrate and PD-L1 expression suggest anti-PD-L1 therapeutic agents as potential novel treatment option for germinoma patients. The loss of HLA class I may represent one of the mechanisms for tumor immune escape in germinoma.

scholarly journals 4473 Immune control of plasma cell disorders – in-depth analysis of Sox2 immunity in MGUS

2020 ◽  
Vol 4 (s1) ◽  
pp. 136-136
Author(s):  
Sandra Patricia Susanibar Adaniya ◽  
Casey L. Cummins ◽  
Miren L. Baroja ◽  
Beatriz Carreno ◽  
Gerald P. Linette ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Cd8 T Cells ◽  
Hla Class I ◽  
Cross Sectional Study ◽  
Class I ◽  
Cell Reactivity ◽  
Cross Sectional ◽  
Depth Analysis

OBJECTIVES/GOALS: We aim to identify and characterize anti-Sox2-specific CD8+ T cell responses in stable MUGS patients expressing HLA class I alleles-A*02:01 and /or -B*07:02. METHODS/STUDY POPULATION: Cross sectional study of patients with stable MGUS defined as stable serum paraprotein for ≥ 12 months from the MM Research Clinic at the Abramson Cancer Institute. Sox2 T cell reactivity will be assessed by IFN-γ ELISPOT assays. Rested PBMC will be pulsed with candidate Sox2-derived peptides predicted to display high affinity to HLA class I alleles and known to be processed and presented as determined by “targeted MS/MS” (mass spectrometry). The presence of anti-Sox2-specific CD8+ T cells will be confirmed in peptide/HLA multimer assays using flow cytometry. Anti-Sox2-specific CD8+ T cells will be characterized for HLA restriction and TCR αβ composition. RESULTS/ANTICIPATED RESULTS: Our work is still in progress. From Aug to Dec 2019, 22 MGUS subjects have been analyzed, 11 of which were found to have the HLA of interest. Positive Sox-2 reactivity by ELISpot was found in 3 subjects. DISCUSSION/SIGNIFICANCE OF IMPACT: Anti-Sox2 immune responses may maintain MGUS in a clinical indolent state by eliminating Sox2-expressing clonogenic MM cells. A detailed characterization of anti-Sox2 T cells followed by in-vivo assessment of their anti-myeloma activity could provide the foundation for a Sox2 based immunotherapy approach in MM.

scholarly journals Making Insulin and Staying Out of Autoimmune Trouble: The Beta-Cell Conundrum

2021 ◽  
Vol 12 ◽  
Author(s):  
Alexia Carré ◽  
Roberto Mallone
Keyword(s):  
Beta Cell ◽  
Beta Cells ◽  
Mhc Class I ◽  
Antigen Processing ◽  
Cell Function ◽  
Immune Cell ◽  
Current Knowledge ◽  
Cell Types ◽  
Class I ◽  
Cellular Models

Autoimmune type 1 diabetes (T1D) results from the intricate crosstalk of various immune cell types. CD8+ T cells dominate the pro-inflammatory milieu of islet infiltration (insulitis), and are considered as key effectors of beta-cell destruction, through the recognition of MHC Class I-peptide complexes. The pathways generating MHC Class I-restricted antigens in beta cells are poorly documented. Given their specialized insulin secretory function, the associated granule processing and degradation pathways, basal endoplasmic reticulum stress and susceptibility to additional stressors, alternative antigen processing and presentation (APP) pathways are likely to play a significant role in the generation of the beta-cell immunopeptidome. As direct evidence is missing, we here intersect the specificities of beta-cell function and the literature about APP in other cellular models to generate some hypotheses on APPs relevant to beta cells. We further elaborate on the potential role of these pathways in T1D pathogenesis, based on the current knowledge of antigens presented by beta cells. A better understanding of these pathways may pinpoint novel mechanisms amenable to therapeutic targeting to modulate the immunogenicity of beta cells.

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