scholarly journals Papillary Thyroid Carcinoma Landscape and Its Immunological Link With Hashimoto Thyroiditis at Single-Cell Resolution

2021 ◽  
Vol 9 ◽  
Author(s):  
Jun Pan ◽  
Fang Ye ◽  
Chengxuan Yu ◽  
Qinsheng Zhu ◽  
Jiaqi Li ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Plasma Cells ◽  
Disease Free Survival ◽  
Hashimoto Thyroiditis ◽  
Carcinoma Cells ◽  
The Cancer Genome Atlas ◽  
Papillary Thyroid ◽  
Migration Potential

The tumor microenvironment heterogeneity of papillary thyroid cancer (PTC) is poorly characterized. The relationship between PTC and Hashimoto thyroiditis (HT) is also in doubt. Here, we used single-cell RNA sequencing to map the transcriptome landscape of PTC from eight PTC patients, of which three were concurrent with HT. Predicted copy number variation in epithelial cells and mesenchymal cells revealed the distinct molecular signatures of carcinoma cells. Carcinoma cells demonstrated intertumoral heterogeneity based on BRAF V600E mutation or lymph node metastasis, and some altered genes were identified to be correlated with disease-free survival in The Cancer Genome Atlas datasets. In addition, transcription factor regulons of follicular epithelial cells unveil the different transcription activation state in PTC patients with or without concurrent HT. The immune cells in tumors exhibited distinct transcriptional states, and the presence of tumor-infiltrating B lymphocytes was predominantly linked to concurrent HT origin. Trajectory analysis of B cells and plasma cells suggested their migration potential from HT adjacent tissues to tumor tissues. Furthermore, we revealed diverse ligand–receptor pairs between non-immune cells, infiltrating myeloid cells, and lymphocytes. Our results provided a single-cell landscape of human PTC. These data would deepen the understanding of PTC, as well as the immunological link between PTC and HT.

Preparation of Single Cell Suspension from Human Lung Tissue v1

2021 ◽  
Author(s):  
Steven B. Wells ◽  
Peter A. Szabo ◽  
Basak Ural ◽  
Maya M.L. Poon
Keyword(s):  
Epithelial Cells ◽  
Cell Suspension ◽  
Single Cell ◽  
Lung Tissue ◽  
Immune Cells ◽  
Human Lung ◽  
Dilution Factor ◽  
Single Cell Suspension ◽  
Human Lung Tissue ◽  
Defined Media

This protocol describes a method for the isolation of the immune cells, structural and epithelial cells, and progenitors from human lung sections of about two grams. By providing defined media formulations, volumes at each step, and a defined dilution factor for density centrifugation, it yields consistent single-cell suspensions across samples.

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 Single-cell transcriptomics reveal the heterogeneity and dynamic of cancer stem-like cells during breast tumor progression

2021 ◽  
Vol 12 (11) ◽  
Author(s):  
Guojuan Jiang ◽  
Juchuanli Tu ◽  
Lei Zhou ◽  
Mengxue Dong ◽  
Jue Fan ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Epithelial Cell ◽  
Epithelial Cells ◽  
Tumor Progression ◽  
Single Cell ◽  
Immune Cells ◽  
Breast Tumor ◽  
Immune Cell ◽  
Cell Lineage ◽  
Breast Tumor Progression

AbstractBreast cancer stem-like cells (BCSCs) play vital roles in tumorigenesis and progression. However, the origin and dynamic changes of BCSCs are still to be elucidated. Using the breast cancer mouse model MMTV-PyMT, we constructed a single-cell atlas of 31,778 cells from four distinct stages of tumor progression (hyperplasia, adenoma/MIN, early carcinoma and late carcinoma), during which malignant transition occurs. We identified that the precise cell type of ERlow epithelial cell lineage gave rise to the tumors, and the differentiation of ERhigh epithelial cell lineage was blocked. Furthermore, we discovered a specific signature with a continuum of gene expression profiles along the tumor progression and significantly correlated with clinical outcomes, and we also found a stem-like cell cluster existed among ERlow epithelial cells. Further clustering on this stem-like cluster showed several sub-clusters indicating heterogeneity of stem-like epithelial cells. Moreover, we distinguished normal and cancer stem-like cells in this stem-like epithelial cell cluster and profiled the molecular portraits from normal stem-like cell to cancer stem-like cells during the malignant transition. Finally, we found the diverse immune cell infiltration displayed immunosuppressive characteristics along tumor progression. We also found the specific expression pattern of cytokines and their corresponding cytokine receptors in BCSCs and immune cells, suggesting the possible cross-talk between BCSCs and the immune cells. These data provide a useful resource for illuminating BCSC heterogeneity and the immune cell remodeling during breast tumor progression, and shed new light on transcriptomic dynamics during the progression at the single-cell level.

scholarly journals Systematic Profiling of Diagnostic and Prognostic Value of Autophagy-Related Genes for Sarcoma Patients

2020 ◽  
Author(s):  
Yuanhe Wang ◽  
Jianyi Li ◽  
Cheng Shao ◽  
Xiaojie Tang ◽  
Yukun Du ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Immune Cells ◽  
Disease Free Survival ◽  
Independent Set ◽  
Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Immune Checkpoints ◽  
Systematic Analysis

Abstract Background: Autophagy-related genes (ARGs) have been confirmed to have an important role in tumorigenesis and tumor microenvironment formation. Nevertheless, a systematic analysis of ARGs and their clinical significance in sarcoma patients is lacking.Methods: Gene expression files from The Cancer Genome Atlas (TCGA) database and Genotype-Tissue Expression (GTEx) were used to select differentially expressed genes (DEGs). Differentially expressed ARGs (DEARGs) were determined by matching the DEG and HADb gene sets, which were evaluated by functional enrichment analysis. Unsupervised clustering of the identified DEARGs was conducted, and associations with tumor microenvironment (TME), immune checkpoints, and immune cells were analyzed simultaneously. Two prognostic signatures, one for overall survival (OS) and one for disease-free survival (DFS), were established and validated in an independent set. Results: In total, 84 DEIRGs and two clusters were identified. TME scores, five immune checkpoints, and several types of immune cells were found to be significantly different between twp clusters. Two prognostic signatures incorporating DEARGs showed favorable discrimination and were successfully validated. Two nomograms combining signature and clinical variables were generated. The C-indexes were 0.818 and 0.636 for the OS and DFS nomograms, respectively.Conclusion: This comprehensive analyses of the ARG landscape in sarcoma showed novel ARGs related to carcinogenesis and the immune microenvironment. These findings have implications for prognosis and therapeutic responses, which reveal novel potential prognostic biomarkers, promote precision medicine, and provide potential novel targets for immunotherapy.

Preparation of a Single Cell Suspension from Bronchoalevolar Lavage v1

2021 ◽  
Author(s):  
Peter A. Szabo ◽  
Steven B. Wells ◽  
Basak Ural
Keyword(s):  
Epithelial Cells ◽  
Cell Suspension ◽  
Single Cell ◽  
Immune Cells ◽  
Human Lung ◽  
Lavage Fluid ◽  
Cell Suspensions ◽  
Dilution Factor ◽  
Single Cell Suspension ◽  
Defined Media

This protocol describes a method for the isolation of the immune cells, structural and epithelial cells, and progenitors from lavage fluid collected from human lung. By providing defined media formulations, volumes at each step, and a defined dilution factor for density centrifugation, it yields consistent single-cell suspensions across samples.

scholarly journals Co-evolution of tumor and immune cells during progression of multiple myeloma

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ruiyang Liu ◽  
Qingsong Gao ◽  
Steven M. Foltz ◽  
Jared S. Fowles ◽  
Lijun Yao ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Single Cell ◽  
Plasma Cell ◽  
Immune Cells ◽  
Plasma Cells ◽  
Genetic Alterations ◽  
Patient Specific ◽  
Integrated Analysis ◽  
Cell Subpopulations ◽  
Disease Stages

AbstractMultiple myeloma (MM) is characterized by the uncontrolled proliferation of plasma cells. Despite recent treatment advances, it is still incurable as disease progression is not fully understood. To investigate MM and its immune environment, we apply single cell RNA and linked-read whole genome sequencing to profile 29 longitudinal samples at different disease stages from 14 patients. Here, we collect 17,267 plasma cells and 57,719 immune cells, discovering patient-specific plasma cell profiles and immune cell expression changes. Patients with the same genetic alterations tend to have both plasma cells and immune cells clustered together. By integrating bulk genomics and single cell mapping, we track plasma cell subpopulations across disease stages and find three patterns: stability (from precancer to diagnosis), and gain or loss (from diagnosis to relapse). In multiple patients, we detect “B cell-featured” plasma cell subpopulations that cluster closely with B cells, implicating their cell of origin. We validate AP-1 complex differential expression (JUN and FOS) in plasma cell subpopulations using CyTOF-based protein assays, and integrated analysis of single-cell RNA and CyTOF data reveals AP-1 downstream targets (IL6 and IL1B) potentially leading to inflammation regulation. Our work represents a longitudinal investigation for tumor and microenvironment during MM progression and paves the way for expanding treatment options.

scholarly journals High-dimensional single cell mass cytometry analysis of the murine hematopoietic system reveals signatures induced by ageing and physiological pathogen challenges

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Christos Nikolaou ◽  
Kerstin Muehle ◽  
Stephan Schlickeiser ◽  
Alberto Sada Japp ◽  
Nadine Matzmohr ◽  
...  
Keyword(s):  
T Cells ◽  
Nk Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Plasma Cells ◽  
Cell Mass ◽  
Mass Cytometry ◽  
Preclinical Research ◽  
Hematopoietic System ◽  
Adaptive Immune Cells

Abstract Background Immune ageing is a result of repetitive microbial challenges along with cell intrinsic or systemic changes occurring during ageing. Mice under ‘specific-pathogen-free’ (SPF) conditions are frequently used to assess immune ageing in long-term experiments. However, physiological pathogenic challenges are reduced in SPF mice. The question arises to what extent murine experiments performed under SPF conditions are suited to analyze immune ageing in mice and serve as models for human immune ageing. Our previous comparisons of same aged mice with different microbial exposures, unambiguously identified distinct clusters of immune cells characteristic for numerous previous pathogen encounters in particular in pet shop mice. Results We here performed single cell mass cytometry assessing splenic as secondary and bone marrow as primary lymphoid organ-derived leukocytes isolated from young versus aged SPF mice in order to delineate alterations of the murine hematopoietic system induced during ageing. We then compared immune clusters from young and aged SPF mice to pet shop mice in order to delineate alterations of the murine hematopoietic system induced by physiological pathogenic challenges and those caused by cell intrinsic or systemic changes during ageing. Notably, distinct immune signatures were similarly altered in both pet shop and aged SPF mice in comparison to young SPF mice, including increased frequencies of memory T lymphocytes, effector-cytokine producing T cells, plasma cells and mature NK cells. However, elevated frequencies of CD4+ T cells, total NK cells, granulocytes, pDCs, cDCs and decreased frequencies of naïve B cells were specifically identified only in pet shop mice. In aged SPF mice specifically the frequencies of splenic IgM+ plasma cells, CD8+ T cells and CD4+ CD25+ Treg were increased as compared to pet shop mice and young mice. Conclusions Our study dissects firstly how ageing impacts both innate and adaptive immune cells in primary and secondary lymphoid organs. Secondly, it partly distinguishes murine intrinsic immune ageing alterations from those induced by physiological pathogen challenges highlighting the importance of designing mouse models for their use in preclinical research including vaccines and immunotherapies.

scholarly journals Systematic profiling of diagnostic and prognostic value of autophagy-related genes for sarcoma patients

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yuanhe Wang ◽  
Jianyi Li ◽  
Cheng Shao ◽  
Xiaojie Tang ◽  
Yukun Du ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Immune Cells ◽  
Disease Free Survival ◽  
Independent Set ◽  
Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Immune Checkpoints ◽  
Systematic Analysis

Abstract Background Autophagy-related genes (ARGs) have been confirmed to have an important role in tumorigenesis and tumor microenvironment formation. Nevertheless, a systematic analysis of ARGs and their clinical significance in sarcoma patients is lacking. Methods Gene expression files from The Cancer Genome Atlas (TCGA) database and Genotype-Tissue Expression (GTEx) were used to select differentially expressed genes (DEGs). Differentially expressed ARGs (DEARGs) were determined by matching the DEG and HADb gene sets, which were evaluated by functional enrichment analysis. Unsupervised clustering of the identified DEARGs was conducted, and associations with tumor microenvironment (TME), immune checkpoints, and immune cells were analyzed simultaneously. Two prognostic signatures, one for overall survival (OS) and one for disease-free survival (DFS), were established and validated in an independent set. Results In total, 84 DEARGs and two clusters were identified. TME scores, five immune checkpoints, and several types of immune cells were found to be significantly different between two clusters. Two prognostic signatures incorporating DEARGs showed favorable discrimination and were successfully validated. Two nomograms combining signature and clinical variables were generated. The C-indexes were 0.818 and 0.747 for the OS and DFS nomograms, respectively. Conclusion This comprehensive analyses of the ARG landscape in sarcoma showed novel ARGs related to carcinogenesis and the immune microenvironment. These findings have implications for prognosis and therapeutic responses, which reveal novel potential prognostic biomarkers, promote precision medicine, and provide potential novel targets for immunotherapy.

scholarly journals Prostate Epithelial Genes Define Docetaxel-Sensitive Prostate Cancer Molecular Subtype

2020 ◽  
Author(s):  
Hyunho Han ◽  
Kwibok Choi ◽  
Young Jun Moon ◽  
Ji Eun Heo ◽  
Won Sik Ham ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Epithelial Cells ◽  
Single Cell ◽  
Molecular Subtype ◽  
Prostate Gland ◽  
Specific Antigen ◽  
Prostate Adenocarcinoma ◽  
The Cancer Genome Atlas ◽  
Subtype B ◽  
Prostate Epithelial Cells

ABSTRACTBACKGROUND & OBJECTIVESAnalysis of the transcriptomic landscape of prostate adenocarcinoma shows multidimensional gene expression variability. Understanding cancer transcriptome complexity can provide biological insight and therapeutic guidance. To avoid potential confounding factors, such as stromal contamination and stress-related material degradation, we utilized a set of genes expressed by prostate epithelial cells from single-cell transcriptome data of the human prostate gland.MATERIALS & METHODSAnalyzing publicly available bulk and single-cell RNA sequencing data, we defined 1,629 genes expressed by prostate epithelial cells. Consensus clustering and CIBERSORT deconvolution were used for class discovery and proportion estimate analysis. The Cancer Genome Atlas Prostate Adenocarcinoma (TCGA-PRAD) dataset served as a training set. The resulting clusters were analyzed in association with clinical, pathologic, and genomic characteristics and impact on survival.RESULTSTCGA-PRAD tumors were separated into four subtypes: A (30.0%), B (26.0%), C (14.7%), D (4.2%), and mixed (25.0%). Subtype A was characterized by low frequency of ETS-family fusions and high expression of KLK3, which encodes prostate-specific antigen (PSA). Subtype B showed the highest expression of ACP3, encoding PAP (prostatic acid phosphatase). Subtypes C and D were commonly associated with advanced T/N stages, high Gleason grades, and p53 or PIK3CA mutations. In silico drug-sensitivity screening suggested that subtype B is likely sensitive to docetaxel and paclitaxel. Serum PSA/PAP ratio was predictive of a radiographic response to docetaxel in metastatic castration-resistant prostate cancer patients.CONCLUSIONWe propose four prostate adenocarcinoma subtypes with distinct transcriptomic, genomic, and pathologic characteristics. PSA/PAP ratio in advanced cancer may aid in determining which patients would benefit from maximized androgen receptor inhibition or early use of antimicrotubule agents. Molecular subtypes and biomarkers must be validated in a prospective cohort study.

scholarly journals Identification of a Signature Comprising 5 Soluble Carrier Family Genes to Predict the Recurrence of Papillary Thyroid Carcinoma

2021 ◽  
Vol 20 ◽  
pp. 153303382110363
Author(s):  
Rui Han ◽  
Wei Sun ◽  
Hao Zhang
Keyword(s):  
Gene Expression ◽  
High Risk ◽  
Cox Regression ◽  
Disease Free Survival ◽  
Risk Groups ◽  
The Cancer Genome Atlas ◽  
Papillary Thyroid ◽  
Cox Regression Analysis ◽  
Expression Levels ◽  
Clinicopathological Variables

RNA-sequencing data and relevant clinical data in The Cancer Genome Atlas for 502 samples of papillary thyroid cancer (PTC) were analyzed to determine the prognostic value of soluble carrier family genes in PTC. We analyzed soluble carrier family gene expression and function in the samples. Clustering identified 2 clusters in the data. Risk characteristics were identified using LASSO and Univariate Cox regression analysis, which divided the patients into low and high-risk groups. The expression levels of 88 soluble carrier genes were significantly different between tumors and normal tissue. The 2 PTC clusters had different clinical outcomes and distributions of gene expression. The expression levels of SFXN1, SLC12A4, SLC35A1, SLC35E1, and SLCO1C1 were markedly different between the 2 groups. The high risk and low risk groups had significant different prognoses ( P < 0.05). Significant differences were identified for disease free survival (DFS), sex and T stage between the 2 subgroups. The risk score was identified as an independent prognostic variable ( P < 0.05) and as a predictor of clinicopathological variables. In patients with PTC, solute carrier gene expression showed differential associations with clinicopathological variables. The 5 genes could be used as prognostic factors for PTC, particularly to predict PTC recurrence.

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