Single-cell RNA-seq profiling of individual Biomphalaria glabrata immune cells with a focus on immunologically relevant transcripts

2021 ◽  
Author(s):  
Hongyu Li ◽  
Abdullah A. Gharamah ◽  
Jacob R. Hambrook ◽  
Xinzhong Wu ◽  
Patrick C. Hanington
Keyword(s):  
Single Cell ◽  
Immune Cells ◽  
Biomphalaria Glabrata ◽  
Rna Seq

scholarly journals Different Glucose Metabolic Features According to Cancer and Immune Cells in the Tumor Microenvironment

2021 ◽  
Vol 11 ◽  
Author(s):  
Hongyoon Choi ◽  
Kwon Joong Na
Keyword(s):  
Tumor Microenvironment ◽  
Single Cell ◽  
Immune Cells ◽  
Human Cancer ◽  
Human Melanoma ◽  
The Cancer Genome Atlas ◽  
Enrichment Score ◽  
Metabolic Profiles ◽  
Rna Seq ◽  
Cancer Tissues

BackgroundA close metabolic interaction between cancer and immune cells in the tumor microenvironment (TME) plays a pivotal role in cancer immunity. Herein, we have comprehensively investigated the glucose metabolic features of the TME at the single-cell level to discover feasible metabolic targets for the tumor immune status.MethodsWe examined expression levels of glucose transporters (GLUTs) in various cancer types using The Cancer Genome Atlas (TCGA) data and single-cell RNA-seq (scRNA-seq) datasets of human cancer tissues including melanoma, head and neck, and breast cancer. In addition, scRNA-seq data of immune cells in the TME acquired from human melanoma after immune checkpoint inhibitors were analyzed to investigate the dynamics of glucose metabolic profiles of specific immune cells.ResultsPan-cancer bulk RNA-seq showed that the GLUT3-to-GLUT1 ratio was positively associated with immune cell enrichment score. The scRNA-seq datasets of various human cancer tissues showed that GLUT1 was highly expressed in cancer cells, while GLUT3 was highly expressed in immune cells in TME. The scRNA-seq data obtained from human melanoma tissues pre- and post-immunotherapy showed that glucose metabolism features of myeloid cells, particularly including GLUTs expression, markedly differed according to treatment response.ConclusionsDifferently expressed GLUTs in TME suggest that GLUT could be a good candidate a surrogate of tumor immune metabolic profiles and a target for adjunctive treatments for immunotherapy.

scholarly journals HGG-26. SINGLE-CELL RNA-SEQ OF PEDIATRIC HIGH-GRADE GLIOMAS IDENTIFIES COMMON ONCOGENIC PROCESSES AMONG DISTINCT TUMOR HISTOLOGIES

2021 ◽  
Vol 23 (Supplement_1) ◽  
pp. i22-i22
Author(s):  
John DeSisto ◽  
Andrew Donson ◽  
Rui Fu ◽  
Bridget Sanford ◽  
Kent Riemondy ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Single Cell ◽  
Immune Cells ◽  
Immune Cell ◽  
Treatment Modalities ◽  
Patient Specific ◽  
Cell Populations ◽  
High Grade ◽  
Methylation Data ◽  
Rna Seq

Abstract Background Pediatric high-grade glioma (PHGG) is a deadly childhood brain tumor that responds poorly to treatment. PHGG comprises two major subtypes: cortical tumors with wild-type H3K27 and diffuse midline gliomas (DMG) that occur in the midline and have characteristic H3K27M mutations. Cortical PHGG is heterogeneous with multiple molecular subtypes. In order to identify underlying commonalities in cortical PHGG that might lead to better treatment modalities, we performed molecular profiling, including single-cell RNA-Seq (scRNA-Seq), on PHGG samples from Children’s Hospital Colorado. Methods Nineteen cortical PHGG tumor samples, one DMG and one normal margin sample obtained at biopsy were disaggregated to isolate viable cells. Fifteen were glioblastomas (GBM), including five with epithelioid and/or giant cell features and five radiation-induced glioblastomas (RIG). There were also four non-GBM PHGG. We performed scRNA-Seq using 10X Genomics v.3 library preparation to enable capture of infiltrating immune cells. We also performed bulk RNA-Seq and DNA methylation profiling. Results After eliminating patient-specific and cell-cycle effects, RIG, epithelioid GBM, and other GBM each formed identifiable subgroups in bulk RNA-Seq and scRNA-Seq datasets. In the scRNA-Seq data, clusters with cells from multiple tumor samples included a PDGFRA-positive population expressing oligodendrocyte progenitor markers, astrocytic, mesenchymal and stemlike populations, macrophage/monocyte immune cells, and a smaller T-cell population. Analyses of DNA methylation data showed PDGFRA and CDK4 amplification and CDKN2A deletion are common alterations among PHGG. Inferred copy number variation analysis of the single-cell data confirmed that individual tumors include populations that both include and lack the molecular alterations identified in the methylation data. RNA velocity studies to define tumor cells of origin and further analyses of the immune cell populations are underway. Conclusions Single-cell analysis of PHGG confirms a large degree of tumor heterogeneity but also shows that PHGG have stemlike, mesenchymal and immune cell populations with common characteristics.

scholarly journals Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Juber Herrera-Uribe ◽  
Jayne E. Wiarda ◽  
Sathesh K. Sivasankaran ◽  
Lance Daharsh ◽  
Haibo Liu ◽  
...  
Keyword(s):  
T Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Peripheral Blood ◽  
Cell Types ◽  
Cell Populations ◽  
Rna Seq ◽  
Cell Type ◽  
Transcriptomic Data ◽  
Single Cell Rna Sequencing

Pigs are a valuable human biomedical model and an important protein source supporting global food security. The transcriptomes of peripheral blood immune cells in pigs were defined at the bulk cell-type and single cell levels. First, eight cell types were isolated in bulk from peripheral blood mononuclear cells (PBMCs) by cell sorting, representing Myeloid, NK cells and specific populations of T and B-cells. Transcriptomes for each bulk population of cells were generated by RNA-seq with 10,974 expressed genes detected. Pairwise comparisons between cell types revealed specific expression, while enrichment analysis identified 1,885 to 3,591 significantly enriched genes across all 8 cell types. Gene Ontology analysis for the top 25% of significantly enriched genes (SEG) showed high enrichment of biological processes related to the nature of each cell type. Comparison of gene expression indicated highly significant correlations between pig cells and corresponding human PBMC bulk RNA-seq data available in Haemopedia. Second, higher resolution of distinct cell populations was obtained by single-cell RNA-sequencing (scRNA-seq) of PBMC. Seven PBMC samples were partitioned and sequenced that produced 28,810 single cell transcriptomes distributed across 36 clusters and classified into 13 general cell types including plasmacytoid dendritic cells (DC), conventional DCs, monocytes, B-cell, conventional CD4 and CD8 αβ T-cells, NK cells, and γδ T-cells. Signature gene sets from the human Haemopedia data were assessed for relative enrichment in genes expressed in pig cells and integration of pig scRNA-seq with a public human scRNA-seq dataset provided further validation for similarity between human and pig data. The sorted porcine bulk RNAseq dataset informed classification of scRNA-seq PBMC populations; specifically, an integration of the datasets showed that the pig bulk RNAseq data helped define the CD4CD8 double-positive T-cell populations in the scRNA-seq data. Overall, the data provides deep and well-validated transcriptomic data from sorted PBMC populations and the first single-cell transcriptomic data for porcine PBMCs. This resource will be invaluable for annotation of pig genes controlling immunogenetic traits as part of the porcine Functional Annotation of Animal Genomes (FAANG) project, as well as further study of, and development of new reagents for, porcine immunology.

scholarly journals LINE-1 Retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5’-single cell RNA-Seq

2021 ◽  
Author(s):  
Wilson McKerrow ◽  
Shane A. Evans ◽  
Azucena Rocha ◽  
John Sedivy ◽  
Nicola Neretti ◽  
...  
Keyword(s):  
Single Cell ◽  
Cancer Cells ◽  
Early Development ◽  
Immune Cells ◽  
Copy Number ◽  
Single Cells ◽  
Single Cell Level ◽  
Rna Seq ◽  
Cell Level ◽  
Mouse Hippocampus

AbstractLINE-1 retrotransposons are known to be expressed in early development, in tumors and in the germline. Less is known about LINE-1 expression at the single cell level, especially outside the context of cancer. Because LINE-1 elements are present at a high copy number, many transcripts that are not driven by the LINE-1 promoter nevertheless terminate at the LINE-1 3’ UTR. Thus, 3’ targeted single cell RNA-seq datasets are not appropriate for studying LINE-1. However, 5’ targeted single cell datasets provide an opportunity to analyze LINE-1 expression at the single cell level. Most LINE-1 copies are 5’ truncated, and a transcript that contains the LINE-1 5’ UTR as its 5’ end is likely to have been transcribed from its promoter. We developed a method, L1-sc (LINE-1 expression for single cells), to quantify LINE-1 expression in 5’ targeted 10x genomics single cell RNA-seq datasets. Our method confirms that LINE-1 expression is high in cancer cells, but low or absent from immune cells. We also find that LINE-1 expression is elevated in epithelial compared to immune cells outside of the context of cancer and that it is also elevated in neurons compared to glia in the mouse hippocampus.

scholarly journals OP0013 SINGLE CELL PROFILE OF SKIN STROMAL AND IMMUNE CELLS AND PERIPHERAL BLOOD IMMUNE CELLS OF SCLERODERMA PATIENTS TOWARDS IDENTIFICATION OF DISEASE MECHANISM, PROGNOSTIC BIOMARKERS AND POTENTIAL THERAPEUTIC TARGETS

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 9.2-9
Author(s):  
C. Gur ◽  
A. Balbir-Gurman ◽  
H. Peleg ◽  
S. Aamar ◽  
F. Kharouf ◽  
...  
Keyword(s):  
Single Cell ◽  
Immune Cells ◽  
Stromal Cells ◽  
Stromal Cell ◽  
Immune Cell ◽  
Healthy Controls ◽  
Rna Seq ◽  
High Quality ◽  
Cell Compartment

Background:Despite many years of research, our understanding of Systemic Sclerosis (SSc) pathogenic processes, patient-to-patient variability, and diversity of stromal and immune cells within the involved tissues microenvironment, their interaction, as well as the genes and pathways leading to the pathogenesis remains largely unclear. Current technologies for characterizing SSc have limited depth and resolution, which needed for molecular define the small skin stromal and immune cells sub-populations supposed to drive SSc pathogenesis. Single-cell sequencing technologies hold a great potential in genomic medicine since they offer high resolution and sensitivity for unbiased profiling of disease versus normal niches.Objectives:Comprehensive characterization of stromal and immune cells in the skin and blood of SSc patients, and healthy controls, their specific intra-skin cell states, pathways, cell-cell interactions, and unbiased characterization of cell types profile, biomarkers, drivers, and regulatory pathways associated with specific SSc patient subgroups.Methods:We applied the massively parallel single cell RNA-seq (MARS-seq) developed in our laboratory to conduct a comprehensive single-cell genomics analysis of skin stromal and immune cells obtained through punch biopsy and blood immune cells from 73 SSc patients (39 DcSSc, 34 LcSSc) and 30 healthy controls. We used the MetaCell analytical method to identify homogeneous and robust groups of cells from single cell RNA-seq data. The perturbed signaling pathways, pathogenic stromal or immune cell subsets are characterized using CyTOF, immunohistochemistry,PhysicalInteractingCell sequencing (PIC-seq), andin vitrofunctional assays.Results:We collected data from a total of 46,742 high-quality skin stromal cells, and 57,475 high-quality blood and skin immune cells. Analysis of stromal cell compartment led to a detailed map of 261 meta cells organized into 16 broad lineages including: Fibroblasts, Pericytes, Vascular cells, and other cells. In the immune cell compartment, we found 361 meta cells organized into 14 broad lineages (e.g unique skin T, B, NK and dendritic cells). We observed a unique population of stromal and immune cells in the skin and blood of SSc patients as compared to controls. The major and dramatic changes were observed in the stromal cell compartment of the patient’s skin compared to controls. In the fibroblast lineage we found a small cluster of cells that were significantly diminished in the SSc patients compared with control, expressed genes associated with fibrosis and vascular remodeling. Significantly higher number of specific subsets of pericytes and vascular cells was found in SSc patients compared to controls. Analysis of the immune cell compartment revealed only minor changes in the immune cell composition in patients compared with controls. Finally, we found known and novel pathways (e.g Wnt/Notch signaling, IFN type I/II, AP-1 pathway, complement cascade activation) and cell-cell interactions that play crucial roles in SSc pathogenicity.Conclusion:Our study provides a detailed and unprecedented high-resolution atlas of the immune and stromal cells that make up the skin and peripheral blood in a large cohort of SSc patients with diverse disease duration and clinical settings. Our findings of candidate stromal and immune cell subpopulation, genes and pathways constitute the basis for understanding of SSc pathogenesis and heterogeneity and holds great potential to provide clinicians with new and powerful molecular tools for understanding of the immune-stromal cell crosstalk, for finding new biomarkers for SSc activity and complications and for tailoring and identification of new therapeutic targets.Disclosure of Interests:Chamutal Gur: None declared, Alexandra Balbir-Gurman Consultant of: Novartis, Hagit Peleg: None declared, Suhail Aamar: None declared, Fadi Kharouf: None declared, Yolanda Braun-Moscovici: None declared, Shuang-Yin Wang: None declared, Ido Amit: None declared

scholarly journals Single-cell RNA-seq reveals endoimmune cells in zebrafish

2020 ◽  
Author(s):  
Yunwei Shi ◽  
Peipei Qian ◽  
Jiajing Sheng ◽  
Xu Zhang ◽  
Xiaoning Wang ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Innate Immune ◽  
Marker Genes ◽  
Innate Immune Cells ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
And Function ◽  
Normal Physiological Function

AbstractEndothelial cells (ECs) constitute a monolayer that covers the interior surface of blood vessels and participates in various processes. Although vascular ECs share certain common properties, they differ in both structure and function. So far, the transcriptome profile and heterogeneity of the full repertoire of ECs in vertebrates remain poorly understood. The relatively small size of zebrafish embryos and larvae allows a feasible analysis of the broad spectrum of ECs within every tissue and organ of a whole organism. ECs have been suggested to be conditional innate immune cells. Whether ECs possess the comparable capacity of involvement in immune response is so far undetermined. Currently, through single-cell RNA sequencing analysis of total ECs of zebrafish we identified a fraction of endothelial cells expressing the marker genes of innate immune cells, named “endoimmune cells”. We found the percentage of these cells gradually increased along with the embryonic development. Then, we observed the patrolling mCherry+ cells displayed the morphology alike to the macrophages and neutrophils. Furthermore, we revealed that some of the kdrl:ras-mCherry ECs were labelled with coro1a:EGFP as well. In addition, we demonstrated that the mCherry+ EC from intersegmental vessel could gradually present the expression of GFP in Tg(kdrl:ras-mCherry∷coro1a:GFP) line, suggesting the endoimmune cells are derived from ECs. Importantly, we showed the endoimmune cells are responsive to the inflammation in zebrafish. Taken together, these data suggested the existence of endoimmune cells, a novel type of subpopulations of ECs. It will provide novel insights for understanding endothelial roles in both normal physiological function and human diseases and enable endoimmune cells-based target therapies.

scholarly journals The ratio of exhausted to resident infiltrating lymphocytes is prognostic for colorectal cancer patient outcome

2020 ◽  
Author(s):  
Momeneh Foroutan ◽  
Ramyar Molania ◽  
Aline Pfefferle ◽  
Corina Behrenbruch ◽  
Axel Kallies ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
T Cells ◽  
Nk Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Immune Cell ◽  
Colorectal Cancer Patient ◽  
Colon Adenocarcinoma ◽  
Rna Seq ◽  
Infiltrating Lymphocytes

AbstractImmunotherapy success in colorectal cancer (CRC) is mainly limited to patients whose tumours exhibit high microsatellite instability (MSI). However, there is variability in treatment outcomes within this group, which is in part driven by the frequency and characteristics of tumour infiltrating immune cells. Indeed, the presence of specific infiltrating immune cell subsets has been shown to correlate with immunotherapy responses and is in many cases prognostic of treatment outcome. Tumour-infiltrating lymphocytes (TILs) can undergo distinct differentiation programs such as acquire features of tissue-residency or exhaustion, a process during which T cells upregulate inhibitory receptors such as PD-1 and loose functionality. While residency and exhaustion programs of CD8 T cells are relatively well-studied, these programs have only recently been appreciated in CD4 T cells and remain largely unknown in tumour-infiltrating natural killer (NK) cells. In this study, we use single cell RNA-seq data to identify signatures of residency and exhaustion in CRC infiltrating lymphocytes, including CD8, CD4 and NK cells. We then test these signatures in independent single cell data from tumour and normal tissue infiltrating immune cells. Further, we use versions of these signatures adapted for bulk RNA-seq data to identify a list of tumour intrinsic mutations associated with residency and exhaustion from TCGA data. Finally, using two independent transcriptomic data sets from patients with colon adenocarcinoma, we show that combinations of these signatures, in particular NK signatures, as well as tumour-associated signatures, such as TGF-β signalling, are associated with distinct survival outcomes in colorectal cancer patients.

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