scholarly journals Single-cell transcriptional analysis of the immune tumour microenvironment during myeloma disease evolution

2021 ◽  
Author(s):  
Danielle C Croucher ◽  
Laura M Richards ◽  
Daniel Waller ◽  
Zhihua Li ◽  
Xian Fang Huang ◽  
...  
Keyword(s):  
Single Cell ◽  
Immune Cell ◽  
Killer Cell ◽  
Tumour Microenvironment ◽  
Transcriptional Analysis ◽  
Malignant Cells ◽  
Early Disease ◽  
Disease Evolution ◽  
Adaptive Immune ◽  
Overt Disease

Multiple myeloma is universally preceded by a premalignant disease state. However, efforts to develop preventative therapeutic strategies are hindered by an incomplete understanding of the immune mechanisms associated with progression. Using single-cell RNA-sequencing, we profiled 104,880 cells derived from the bone marrow of Vκ*MYC mice across the myeloma progression spectrum, of which 97,720 were identified as non-malignant cells of the tumour microenvironment. Analysis of the non-malignant cells comprising the immune microenvironment identified mechanisms associated with disease progression in innate and adaptive immune cell populations. This included activation of IL-17 signaling in myeloid cells from precursor mice, accompanied by upregulation of Il6 gene expression in basophils. In the T/Natural killer cell compartment, we identified Tox-expressing CD8+ T cells enriched in the tumour microenvironment of mice with overt disease, with co-expression of LAG3 and PD-1, as well as elevated T cell exhaustion signatures in mice with early disease. We subsequently showed that early intervention with combinatorial blockade of LAG3 and PD-1 using neutralizing monoclonal antibodies delayed tumor progression and improved survival of Vκ*MYC mice. Together, this work provides insight into the biology of myeloma evolution and nominates a treatment strategy for early disease.

scholarly journals Single cell transcriptional analysis reveals novel innate immune cell types

PeerJ ◽  
2014 ◽  
Vol 2 ◽  
pp. e452 ◽  
Author(s):  
Linda E. Kippner ◽  
Jinhee Kim ◽  
Greg Gibson ◽  
Melissa L. Kemp
Keyword(s):  
Single Cell ◽  
Immune Cell ◽  
Cell Types ◽  
Innate Immune ◽  
Innate Immune Cell ◽  
Transcriptional Analysis

scholarly journals Single-Cell RNA Sequencing of Peripheral Blood Reveals Immune Cell Signatures in Alzheimer’s Disease

2021 ◽  
Vol 12 ◽  
Author(s):  
Hui Xu ◽  
Jianping Jia
Keyword(s):  
Immune Response ◽  
T Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Peripheral Blood ◽  
Immune Cell ◽  
Adaptive Immune Response ◽  
Immune Repertoire ◽  
Adaptive Immune ◽  
Peripheral Immune Cells

The peripheral immune system is thought to affect the pathology of the central nervous system in Alzheimer’s disease (AD). However, current knowledge is inadequate for understanding the characteristics of peripheral immune cells in AD. This study aimed to explore the molecular basis of peripheral immune cells and the features of adaptive immune repertoire at a single cell level. We profiled 36,849 peripheral blood mononuclear cells from AD patients with amyloid-positive status and normal controls with amyloid-negative status by 5’ single-cell transcriptome and immune repertoire sequencing using the cell ranger standard analysis procedure. We revealed five immune cell subsets: CD4+ T cells, CD8+ T cells, B cells, natural killer cells, and monocytes–macrophages cells, and disentangled the characteristic alterations of cell subset proportion and gene expression patterns in AD. Thirty-one cell type-specific key genes, comprising abundant human leukocyte antigen genes, and multiple immune-related pathways were identified by protein–protein interaction network and pathway enrichment analysis. We also found high-frequency amplification clonotypes in T and B cells and decreased diversity in T cells in AD. As clone amplification suggested the activation of an adaptive immune response against specific antigens, we speculated that the peripheral adaptive immune response, especially mediated by T cells, may have a role in the pathogenesis of AD. This finding may also contribute to further research regarding disease mechanism and the development of immune-related biomarkers or therapy.

scholarly journals FB5P-seq: FACS-based 5-prime end single-cell RNAseq for integrative analysis of transcriptome and antigen receptor repertoire in B and T cells

2019 ◽  
Author(s):  
Noudjoud Attaf-Bouabdallah ◽  
Iñaki Cervera-Marzal ◽  
Chuang Dong ◽  
Laurine Gil ◽  
Amédée Renand ◽  
...  
Keyword(s):  
T Cells ◽  
Single Cell ◽  
Immune Cell ◽  
Antigen Receptor ◽  
Adaptive Immune System ◽  
Integrative Analysis ◽  
T Cell Subsets ◽  
Bioinformatics Pipeline ◽  
Human Tonsil ◽  
Adaptive Immune

AbstractSingle-cell RNA sequencing (scRNA-seq) allows the identification, characterization, and quantification of cell types in a tissue. When focused on B and T cells of the adaptive immune system, scRNA-seq carries the potential to track the clonal lineage of each analyzed cell through the unique rearranged sequence of its antigen receptor (BCR or TCR, respectively), and link it to the functional state inferred from transcriptome analysis. Here we introduce FB5P-seq, a FACS-based 5’-end scRNA-seq method for cost-effective integrative analysis of transcriptome and paired BCR or TCR repertoire in phenotypically defined B and T cell subsets. We describe in details the experimental workflow and provide a robust bioinformatics pipeline for computing gene count matrices and reconstructing repertoire sequences from FB5P-seq data. We further present two applications of FB5P-seq for the analysis of human tonsil B cell subsets and peripheral blood antigen-specific CD4 T cells. We believe our novel integrative scRNA-seq method will be a valuable option to study rare adaptive immune cell subsets in immunology research.

scholarly journals P13: CHARACTERISATION OF THE TUMOUR MICROENVIRONMENT IN MESENCHYMAL GASTRIC TUMOURS USING SINGLE-CELL RNA SEQUENCING

2021 ◽  
Vol 108 (Supplement_1) ◽  
Author(s):  
J Harrington ◽  
M Lloyd ◽  
N Mabrouk ◽  
R Walker ◽  
B Grace ◽  
...  
Keyword(s):  
B Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cell ◽  
Therapeutic Targets ◽  
Tumour Microenvironment ◽  
Cell Populations ◽  
Limited Information ◽  
Single Cell Rna Sequencing ◽  
Mesenchymal Tumours

Abstract Introduction Gastric mesenchymal tumours are a rare group of neoplasms, which include gastrointestinal stromal tumours (GISTs) and leiomyomas. To date, there is limited information on the tumour microenvironment (TME) in these neoplasms, despite the TME widely known to influence the hallmarks of cancer. In this study we used single cell RNA sequencing (scRNAseq) to profile individual cells of the TME in GIST and leiomyoma. Method The two gastric mesenchymal tumours and two normal gastric samples were analysed using DropSeq, where single cell transcriptomes are captured onto barcoded beads using a microfluidic device before next generation sequencing. For comparison, we performed bulk RNA-sequencing and CIBERSORT to estimate the abundance of 22 immune cell populations. Furthermore, we used immunohistochemistry to elucidate the presence and location of several immune cells. Result Both neoplasms had diverse immune and stromal cell populations with a greater proportion of macrophages but less B cells than normal gastric tissue. ScRNAseq was able to identify subpopulations of B cells and T cells not detected with CIBERSORT. Interstitial cells of cajal, believed to be the pre-cursor to GISTs, were observed through scRNAseq and confirmed through immunohistochemistry. Conclusion To our knowledge, this is the first study to utilise scRNAseq on GISTs and leiomyomas, which enabled characterisation of the TME at a cellular level. Using this platform in future studies will enable better characterisation of the TME and may inform the discovery of therapeutic targets. Take-home message Single cell RNA sequencing enables the ability to explore the tumour microenvironment of mesenchymal tumours at an enhanced resolution, paving the way for potential future therapeutic targets.

scholarly journals Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma

Cell Research ◽  
2020 ◽  
Vol 30 (11) ◽  
pp. 1024-1042 ◽  
Author(s):  
Yu-Pei Chen ◽  
Jian-Hua Yin ◽  
Wen-Fei Li ◽  
Han-Jie Li ◽  
Dong-Ping Chen ◽  
...  
Keyword(s):  
Dendritic Cells ◽  
Nasopharyngeal Carcinoma ◽  
Single Cell ◽  
Plasma Cells ◽  
Immune Cell ◽  
Cellular Heterogeneity ◽  
Normal Sample ◽  
Malignant Cells ◽  
Promising Therapeutic Approach ◽  
Cell Diversity

Abstract Nasopharyngeal carcinoma (NPC) is an aggressive malignancy with extremely skewed ethnic and geographic distributions. Increasing evidence indicates that targeting the tumor microenvironment (TME) represents a promising therapeutic approach in NPC, highlighting an urgent need to deepen the understanding of the complex NPC TME. Here, we generated single-cell transcriptome profiles for 7581 malignant cells and 40,285 immune cells from fifteen primary NPC tumors and one normal sample. We revealed malignant signatures capturing intratumoral transcriptional heterogeneity and predicting aggressiveness of malignant cells. Diverse immune cell subtypes were identified, including novel subtypes such as CLEC9A+ dendritic cells (DCs). We further revealed transcriptional regulators underlying immune cell diversity, and cell–cell interaction analyses highlighted promising immunotherapeutic targets in NPC. Moreover, we established the immune subtype-specific signatures, and demonstrated that the signatures of macrophages, plasmacytoid dendritic cells (pDCs), CLEC9A+ DCs, natural killer (NK) cells, and plasma cells were significantly associated with improved survival outcomes in NPC. Taken together, our findings represent a unique resource providing in-depth insights into the cellular heterogeneity of NPC TME and highlight potential biomarkers for anticancer treatment and risk stratification, laying a new foundation for precision therapies in NPC.

Using single cell genomics to change the treatment of lung cancer.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e20563-e20563
Author(s):  
Venessa T. Chin ◽  
Ghamdan Al Eryani ◽  
Rachael McCloy ◽  
Emily Stone ◽  
Adrian Havryk ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Single Cell ◽  
Immune Activation ◽  
Immune Cell ◽  
Locally Advanced ◽  
Innate Immune ◽  
Endobronchial Ultrasound ◽  
Single Cell Genomics ◽  
Adaptive Immune ◽  
Adaptive Immune Cell

e20563 Background: Lung cancer (LC) is common with a dismal prognosis. Although treatment with immunotherapy (IO) has improved survival outcomes, these therapies remain expensive. Even using biomarker selection, response rates still fall short of 50%. The majority of immune cell profiling done previously uses samples taken from early stage patients focusing on a single immune cell subtype. Here we use single cell RNA sequencing (scRNA-seq) and Cellular Indexing of Transcriptome and Epitopes by sequencing (CITE-seq) to characterise the innate and adaptive immune cell activation state and assess the response to exposure to IO in vitro from patients with advanced LC. Methods: Patients with locally advanced or metastatic LC having an Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) have biopsies collected for analysis. Cells are grown in culture +/- nivolumab for 48 hours. scRNA-seq and CITE-seq is conducted using established protocols. Transcriptomic and proteomic data on the innate and adaptive immune cell subsets assess markers of immune activation and/or suppression and the changes after nivolumab are quantified. Results are correlated with clinical outcomes. Results: In a locally advanced/metastatic population, EBUS-TBNA biopsies yield highly cellular samples with a heterogeneous population of immune cells able to be cultured +/- IO using novel, inclusive techniques. Transcriptomic clustering reveals distinct sub-populations within the T-cell, B-cell and innate immune cell compartments. Within these clusters, CITE-seq shows protein expression on individual cells can determine states of exhaustion, cytolytic ability, migratory potential and innate immune activation. Conclusions: Single cell genomics is feasible and informative in patients with advanced LC. This work will form the basis of a functional, real-time assay to assess individualised responses to IO therapy that has the potential to predict IO response.

scholarly journals Tumour heterogeneity and intercellular networks of nasopharyngeal carcinoma at single cell resolution

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yang Liu ◽  
Shuai He ◽  
Xi-Liang Wang ◽  
Wan Peng ◽  
Qiu-Yan Chen ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Single Cell ◽  
Cell Receptor ◽  
Tumour Microenvironment ◽  
Treg Cells ◽  
Epstein Barr Virus Infection ◽  
Malignant Cells ◽  
Barr Virus ◽  
Epstein Barr ◽  
Barr Virus Infection

AbstractThe heterogeneous nature of tumour microenvironment (TME) underlying diverse treatment responses remains unclear in nasopharyngeal carcinoma (NPC). Here, we profile 176,447 cells from 10 NPC tumour-blood pairs, using single-cell transcriptome coupled with T cell receptor sequencing. Our analyses reveal 53 cell subtypes, including tumour-infiltrating CD8+ T, regulatory T (Treg), and dendritic cells (DCs), as well as malignant cells with different Epstein-Barr virus infection status. Trajectory analyses reveal exhausted CD8+ T and immune-suppressive TNFRSF4+ Treg cells in tumours might derive from peripheral CX3CR1+CD8+ T and naïve Treg cells, respectively. Moreover, we identify immune-regulatory and tolerogenic LAMP3+ DCs. Noteworthily, we observe intensive inter-cell interactions among LAMP3+ DCs, Treg, exhausted CD8+ T, and malignant cells, suggesting potential cross-talks to foster an immune-suppressive niche for the TME. Collectively, our study uncovers the heterogeneity and interacting molecules of the TME in NPC at single-cell resolution, which provide insights into the mechanisms underlying NPC progression and the development of precise therapies for NPC.

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