The tumour microenvironment shapes innate lymphoid cells in patients with hepatocellular carcinoma

Gut ◽  
2021 ◽  
pp. gutjnl-2021-325288
Author(s):  
Bernd Heinrich ◽  
E Michael Gertz ◽  
Alejandro A Schäffer ◽  
Amanda Craig ◽  
Benjamin Ruf ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Flow Cytometry ◽  
Single Cell ◽  
Rna Sequencing ◽  
Mononuclear Cells ◽  
Innate Lymphoid Cells ◽  
Lymphoid Cells ◽  
Cancer Tissue ◽  
Single Cell Rna Sequencing ◽  
Cytokine Milieu

ObjectiveHepatocellular carcinoma (HCC) represents a typical inflammation-associated cancer. Tissue resident innate lymphoid cells (ILCs) have been suggested to control tumour surveillance. Here, we studied how the local cytokine milieu controls ILCs in HCC.DesignWe performed bulk RNA sequencing of HCC tissue as well as flow cytometry and single-cell RNA sequencing of enriched ILCs from non-tumour liver, margin and tumour core derived from 48 patients with HCC. Simultaneous measurement of protein and RNA expression at the single-cell level (AbSeq) identified precise signatures of ILC subgroups. In vitro culturing of ILCs was used to validate findings from in silico analysis. Analysis of RNA-sequencing data from large HCC cohorts allowed stratification and survival analysis based on transcriptomic signatures.ResultsRNA sequencing of tumour, non-tumour and margin identified tumour-dependent gradients, which were associated with poor survival and control of ILC plasticity. Single-cell RNA sequencing and flow cytometry of ILCs from HCC livers identified natural killer (NK)-like cells in the non-tumour tissue, losing their cytotoxic profile as they transitioned into tumour ILC1 and NK-like-ILC3 cells. Tumour ILC composition was mediated by cytokine gradients that directed ILC plasticity towards activated tumour ILC2s. This was liver-specific and not seen in ILCs from peripheral blood mononuclear cells. Patients with high ILC2/ILC1 ratio expressed interleukin-33 in the tumour that promoted ILC2 generation, which was associated with better survival.ConclusionOur results suggest that the tumour cytokine milieu controls ILC composition and HCC outcome. Specific changes of cytokines modify ILC composition in the tumour by inducing plasticity and alter ILC function.

scholarly journals Single cell RNA sequencing reveals regional heterogeneity of hepatobiliary innate lymphoid cells in a tissue-enriched fashion

PLoS ONE ◽  
2019 ◽  
Vol 14 (4) ◽  
pp. e0215481 ◽  
Author(s):  
Anna L. Peters ◽  
Zhenhua Luo ◽  
Jun Li ◽  
Reena Mourya ◽  
Yunguan Wang ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Innate Lymphoid Cells ◽  
Lymphoid Cells ◽  
Regional Heterogeneity ◽  
Single Cell Rna Sequencing

The heterogeneity of human CD127+ innate lymphoid cells revealed by single-cell RNA sequencing

2016 ◽  
Vol 17 (4) ◽  
pp. 451-460 ◽  
Author(s):  
Åsa K Björklund ◽  
Marianne Forkel ◽  
Simone Picelli ◽  
Viktoria Konya ◽  
Jakob Theorell ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Innate Lymphoid Cells ◽  
Lymphoid Cells ◽  
Single Cell Rna Sequencing

scholarly journals SAT0302 INNATE LYMPHOID CELLS INDUCE A FIBROTIC PHENOTYPE OF FIBROBLASTS

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1096.2-1096
Author(s):  
S. Weber ◽  
C. G. Anchang ◽  
S. Rauber ◽  
M. Luber ◽  
M. G. Raimondo ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Tissue Remodeling ◽  
Innate Lymphoid Cells ◽  
Lymphoid Cells ◽  
Research Support ◽  
Fibroblast Activation ◽  
Fibrotic Tissue ◽  
Single Cell Rna Sequencing ◽  
Fibrotic Diseases

Background:Fibrotic diseases are characterized by excessive extracellular matrix production as a result of immune-mediated permanent fibroblast activation. Innate lymphoid cells type II (ILC2) are an only recently discovered cell type involved in barrier integrity and tissue homeostasis. There is upcoming evidence that ILC2s play a central role in mediating fibrotic diseases.Objectives:The aim of the study was to further elucidate the role of ILC2s in fibrotic tissue remodeling and fibroblast activation.Methods:Skin biopsies of patients with systemic sclerosis (SSc) or sclerodermatous chronic graft versus host disease (scGvHD) as well as lung biopsies of patients with idiopathic pulmonary fibrosis (IPF) were analyzed by immunofluorescence (IF) staining. Single cell RNA-sequencing (scRNA-seq) was performed on ILCs from fibrotic skin and lung of bleomycin-challenged mice. Further characterization of ILC2 phenotypes in fibrosis models was done by flow cytometry.In vitroculture of fibroblasts and ILC2s was used to study cellular interaction and fibrotic activation. Quantitative realtime-PCR, western blot, IF staining and ELISA were used as readouts.Results:Two different subtypes of ILC2s were found in skin of SSc and scGvHD patients as well as in lungs of IPF patients with one subpopulation being particularly increased in fibrotic tissue. Single cell RNA-sequencing confirmed the existence of two major populations of ILC2s in experimental fibrosis. One subtype showed features of immature ILC2 progenitors and was actively recruited from the bone marrow during fibrotic tissue remodeling. The other ILC2 subset was highly activated and expressed pro-fibrotic cytokines. These profibrotic ILC2s directly interacted with fibroblasts in a cell contact dependent manner. Semaphorin 4A (SEMA4A) expressed by ILC2s bound to Plexin D1 (PLXND1) on fibroblasts. This interaction resulted into fibrotic imprinting with high expression levels of the transcription factor PU.1 which was recently described as central regulator of the pro-fibrotic gene expression program (Wohlfahrt et al. 2019). Signaling through Jagged 1 (JAG1) and Notch receptor 2 (NOTCH2) was identified as a second mechanism of interaction between fibroblasts and ILC2s. JAG1 expressed by fibroblasts activated NOTCH2 signaling in ILC2s which emphazised the secretion of pro-fibrotic cytokines.Conclusion:We identified a bidirectional interaction between ILCs and fibroblasts incorporating a vicious circle of fibrotic tissue remodelling. As ILCs are still not accessible as therapeutic targets these results might contribute to the development of new strategies for anti-fibrotic therapies.References:[1]Wohlfahrt, Thomas, Simon Rauber, Steffen Uebe, Markus Luber, Alina Soare, Arif Ekici, Stefanie Weber, Alexandru-Emil Matei, Chih-Wei Chen, Christiane Maier, Emmanuel Karouzakis, Hans P. Kiener, Elena Pachera, Clara Dees, Christian Beyer, Christoph Daniel, Kolja Gelse, Andreas E. Kremer, Elisabeth Naschberger, Michael Stürzl, Falk Butter, Michael Sticherling, Susetta Finotto, Alexander Kreuter, Mark H. Kaplan, Astrid Jüngel, Steffen Gay, Stephen L. Nutt, David W. Boykin, Gregory M. K. Poon, Oliver Distler, Georg Schett, Jörg H. W. Distler, and Andreas Ramming. 2019. ‘PU.1 controls fibroblast polarization and tissue fibrosis’,Nature, 566: 344-49.Disclosure of Interests:Stefanie Weber: None declared, Charles Gwellem Anchang: None declared, Simon Rauber: None declared, Markus Luber: None declared, Maria Gabriella Raimondo Grant/research support from: Celgene, Partner Fellowship, Yuko Ariza Employee of: Ono Pharmaceutical Co., Ltd., Aleix Rius Rigau: None declared, Alexander Kreuter: None declared, Georg Schett Speakers bureau: AbbVie, BMS, Celgene, Janssen, Eli Lilly, Novartis, Roche and UCB, Jörg Distler Grant/research support from: Boehringer Ingelheim, Consultant of: Boehringer Ingelheim, Paid instructor for: Boehringer Ingelheim, Speakers bureau: Boehringer Ingelheim, Andreas Ramming Grant/research support from: Pfizer, Novartis, Consultant of: Boehringer Ingelheim, Novartis, Gilead, Pfizer, Speakers bureau: Boehringer Ingelheim, Roche, Janssen

scholarly journals Porcine intestinal innate lymphoid cells and lymphocyte spatial context revealed through single-cell RNA sequencing

2022 ◽  
Author(s):  
Jayne E Wiarda ◽  
Julian M Trachsel ◽  
Sathesh K Sivasankaran ◽  
Christopher K Tuggle ◽  
Crystal L Loving
Keyword(s):  
T Cells ◽  
B Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Innate Lymphoid Cells ◽  
Lymphoid Cells ◽  
Spatial Context ◽  
Intestinal Lymphocytes ◽  
Single Cell Rna Sequencing ◽  
Group 1

Intestinal lymphocytes are crucial members of the mucosal immune system with impact over outcomes of intestinal health versus dysbiosis. Resolving intestinal lymphocyte complexity and function is a challenge, as the intestine provides cellular snapshots of a diverse spectrum of immune states. In pigs, intestinal lymphocytes are poorly described relative to humans or traditional model species. Enhanced understanding of porcine intestinal lymphocytes will promote food security and improve utility of pigs as a biomedical model for intestinal research. Single-cell RNA sequencing (scRNA-seq) was performed to provide transcriptomic profiles of lymphocytes in the porcine ileum, with 31,983 cells annotated into 26 cell types. Deeper interrogation revealed previously undescribed cells in porcine ileum, including SELLhi γδ T cells, group 1 and group 3 innate lymphoid cells (ILCs), and four subsets of B cells. Single-cell transcriptomes in ileum were compared to those in porcine blood, and subsets of activated lymphocytes were detected in ileum but not periphery. Comparison to scRNA-seq human and murine ileum data revealed a general consensus of ileal lymphocytes across species. Lymphocyte spatial context in porcine ileum was conferred through differential tissue dissection prior to scRNA-seq. Antibody-secreting cells, B cells, follicular αβ T cells, and cycling T/ILCs were enriched in ileum with Peyer's patches, while non-cycling γδ T, CD8 αβ T, and group 1 ILCs were enriched in ileum without Peyer's patches. scRNA-seq findings were leverages to develop advanced toolsets for further identification of ILCs in porcine ileum via flow cytometry and in situ staining. Porcine ileal ILCs identified via scRNA-seq did not transcriptionally mirror peripheral ILCs (corresponding to natural killer cells) but instead had gene signatures indicative of tissue- and activation-specific functions, indicating potentially similar roles to intestinal ILCs identified in humans. Overall, the data serve as a highly-resolved transcriptomic atlas of the porcine intestinal immune landscape and will be useful in further understanding intestinal immune cell function.

scholarly journals Predicting anti-PD-1 responders in malignant melanoma from the frequency of S100A9+ monocytes in the blood

2021 ◽  
Vol 9 (5) ◽  
pp. e002171
Author(s):  
Soudabeh Rad Pour ◽  
Yago Pico de Coaña ◽  
Xavier Martinez Demorentin ◽  
Jeroen Melief ◽  
Manjula Thimma ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Overall Survival ◽  
Single Cell ◽  
Rna Sequencing ◽  
Mononuclear Cells ◽  
Predictive Biomarkers ◽  
University Hospital ◽  
Detailed Knowledge ◽  
Monocytic Cell ◽  
Single Cell Rna Sequencing

BackgroundWhile programmed cell death receptor 1 (PD-1) blockade treatment has revolutionized treatment of patients with melanoma, clinical outcomes are highly variable, and only a fraction of patients show durable responses. Therefore, there is a clear need for predictive biomarkers to select patients who will benefit from the treatment.MethodTo identify potential predictive markers for response to PD-1 checkpoint blockade immunotherapy, we conducted single-cell RNA sequencing analyses of peripheral blood mononuclear cells (PBMC) (n=8), as well as an in-depth immune monitoring study (n=20) by flow cytometry in patients with advanced melanoma undergoing treatment with nivolumab at Karolinska University Hospital. Blood samples were collected before the start of treatment and at the time of the second dose.ResultsUnbiased single-cell RNA sequencing of PBMC in patients with melanoma uncovered that a higher frequency of monocytes and a lower ratio of CD4+ T cells to monocyte were inversely associated with overall survival. Similarly, S100A9 expression in the monocytic subset was correlated inversely with overall survival. These results were confirmed by a flow cytometry-based analysis in an independent patient cohort.ConclusionOur results suggest that monocytic cell populations can critically determine the outcome of PD-1 blockade, particularly the subset expressing S100A9, which should be further explored as a possible predictive biomarker. Detailed knowledge of the biological role of S100A9+ monocytes is of high translational relevance.

scholarly journals Erratum: Corrigendum: The heterogeneity of human CD127+ innate lymphoid cells revealed by single-cell RNA sequencing

2016 ◽  
Vol 17 (6) ◽  
pp. 740-740 ◽  
Author(s):  
Åsa K Björklund ◽  
Marianne Forkel ◽  
Simone Picelli ◽  
Viktoria Konya ◽  
Jakob Theorell ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Innate Lymphoid Cells ◽  
Lymphoid Cells ◽  
Single Cell Rna Sequencing

scholarly journals Single-Cell RNA Sequencing Analysis of the Immunometabolic Rewiring and Immunopathogenesis of Coronavirus Disease 2019

2021 ◽  
Vol 12 ◽  
Author(s):  
Furong Qi ◽  
Wenbo Zhang ◽  
Jialu Huang ◽  
Lili Fu ◽  
Jinfang Zhao
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Mononuclear Cells ◽  
Plasma Cells ◽  
Severe Disease ◽  
Sequencing Analysis ◽  
Sequencing Data ◽  
Metabolic Remodeling ◽  
Single Cell Rna Sequencing ◽  
Antibody Secretion

Although immune dysfunction is a key feature of coronavirus disease 2019 (COVID-19), the metabolism-related mechanisms remain elusive. Here, by reanalyzing single-cell RNA sequencing data, we delineated metabolic remodeling in peripheral blood mononuclear cells (PBMCs) to elucidate the metabolic mechanisms that may lead to the progression of severe COVID-19. After scoring the metabolism-related biological processes and signaling pathways, we found that mono-CD14+ cells expressed higher levels of glycolysis-related genes (PKM, LDHA and PKM) and PPP-related genes (PGD and TKT) in severe patients than in mild patients. These genes may contribute to the hyperinflammation in mono-CD14+ cells of patients with severe COVID-19. The mono-CD16+ cell population in COVID-19 patients showed reduced transcription levels of genes related to lysine degradation (NSD1, KMT2E, and SETD2) and elevated transcription levels of genes involved in OXPHOS (ATP6V1B2, ATP5A1, ATP5E, and ATP5B), which may inhibit M2-like polarization. Plasma cells also expressed higher levels of the OXPHOS gene ATP13A3 in COVID-19 patients, which was positively associated with antibody secretion and survival of PCs. Moreover, enhanced glycolysis or OXPHOS was positively associated with the differentiation of memory B cells into plasmablasts or plasma cells. This study comprehensively investigated the metabolic features of peripheral immune cells and revealed that metabolic changes exacerbated inflammation in monocytes and promoted antibody secretion and cell survival in PCs in COVID-19 patients, especially those with severe disease.

scholarly journals Single-Cell RNA Sequencing Reveals the Expansion of Cytotoxic CD4+ T Lymphocytes and a Landscape of Immune Cells in Primary Sjögren’s Syndrome

2021 ◽  
Vol 11 ◽  
Author(s):  
Xiaoping Hong ◽  
Shuhui Meng ◽  
Donge Tang ◽  
Tingting Wang ◽  
Liping Ding ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
T Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cell ◽  
Susceptibility Genes ◽  
Primary Sjögren’S Syndrome ◽  
Healthy Controls ◽  
Immune Cell Subsets ◽  
Single Cell Rna Sequencing

ObjectivePrimary Sjögren’s syndrome (pSS) is a systemic autoimmune disease, and its pathogenetic mechanism is far from being understood. In this study, we aimed to explore the cellular and molecular mechanisms that lead to pathogenesis of this disease.MethodsWe applied single-cell RNA sequencing (scRNA-seq) to 57,288 peripheral blood mononuclear cells (PBMCs) from five patients with pSS and five healthy controls. The immune cell subsets and susceptibility genes involved in the pathogenesis of pSS were analyzed. Flow cytometry was preformed to verify the result of scRNA-seq.ResultsWe identified two subpopulations significantly expand in pSS patients. The one highly expressing cytotoxicity genes is named as CD4+ CTLs cytotoxic T lymphocyte, and another highly expressing T cell receptor (TCR) variable gene is named as CD4+ TRAV13-2+ T cell. Flow cytometry results showed the percentages of CD4+ CTLs, which were profiled with CD4+ and GZMB+ staining; the total T cells of 10 patients with pSS were significantly higher than those of 10 healthy controls (P= 0.008). The expression level of IL-1β in macrophages, TCL1A in B cells, as well as interferon (IFN) response genes in most cell subsets was upregulated in the patients with pSS. Susceptibility genes including HLA-DRB5, CTLA4, and AQP3 were highly expressed in patients with pSS.ConclusionsOur data revealed disease-specific immune cell subsets and provided some potential new targets of pSS. Specific expansion of CD4+ CTLs may be involved in the pathogenesis of pSS, which might give valuable insights for therapeutic interventions of pSS.

scholarly journals Multiplexing droplet-based single cell RNA-sequencing using natural genetic barcodes

2017 ◽  
Author(s):  
Hyun Min Kang ◽  
Meena Subramaniam ◽  
Sasha Targ ◽  
Michelle Nguyen ◽  
Lenka Maliskova ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Mononuclear Cells ◽  
Specific Gene ◽  
Cell Capture ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Peripheral Blood Mononuclear ◽  
Single Cell Rna Sequencing ◽  
Sample Identity

Droplet-based single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes from tens of thousands of cells. Multiplexing samples for single cell capture and library preparation in dscRNA-seq would enable cost-effective designs of differential expression and genetic studies while avoiding technical batch effects, but its implementation remains challenging. Here, we introduce an in-silico algorithm demuxlet that harnesses natural genetic variation to discover the sample identity of each cell and identify droplets containing two cells. These capabilities enable multiplexed dscRNA-seq experiments where cells from unrelated individuals are pooled and captured at higher throughput than standard workflows. To demonstrate the performance of demuxlet, we sequenced 3 pools of peripheral blood mononuclear cells (PBMCs) from 8 lupus patients. Given genotyping data for each individual, demuxlet correctly recovered the sample identity of > 99% of singlets, and identified doublets at rates consistent with previous estimates. In PBMCs, we demonstrate the utility of multiplexed dscRNA-seq in two applications: characterizing cell type specificity and inter-individual variability of cytokine response from 8 lupus patients and mapping genetic variants associated with cell type specific gene expression from 23 donors. Demuxlet is fast, accurate, scalable and could be extended to other single cell datasets that incorporate natural or synthetic DNA barcodes.

scholarly journals Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design

GigaScience ◽  
2021 ◽  
Vol 10 (9) ◽  
Author(s):  
Lukas M Weber ◽  
Ariel A Hippen ◽  
Peter F Hickey ◽  
Kristofer C Berrett ◽  
Jason Gertz ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Experimental Design ◽  
Single Cell ◽  
Rna Sequencing ◽  
In Silico ◽  
Cost Savings ◽  
Cancer Tissue ◽  
Library Preparation ◽  
Natural Genetic Variation ◽  
Single Cell Rna Sequencing

Abstract Background Pooling cells from multiple biological samples prior to library preparation within the same single-cell RNA sequencing experiment provides several advantages, including lower library preparation costs and reduced unwanted technological variation, such as batch effects. Computational demultiplexing tools based on natural genetic variation between individuals provide a simple approach to demultiplex samples, which does not require complex additional experimental procedures. However, to our knowledge these tools have not been evaluated in cancer, where somatic variants, which could differ between cells from the same sample, may obscure the signal in natural genetic variation. Results Here, we performed in silico benchmark evaluations by combining raw sequencing reads from multiple single-cell samples in high-grade serous ovarian cancer, which has a high copy number burden, and lung adenocarcinoma, which has a high tumor mutational burden. Our results confirm that genetic demultiplexing tools can be effectively deployed on cancer tissue using a pooled experimental design, although high proportions of ambient RNA from cell debris reduce performance. Conclusions This strategy provides significant cost savings through pooled library preparation. To facilitate similar analyses at the experimental design phase, we provide freely accessible code and a reproducible Snakemake workflow built around the best-performing tools found in our in silico benchmark evaluations, available at https://github.com/lmweber/snp-dmx-cancer.

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