059 Single-cell RNA sequencing reveals tissue compartment-specific plasticity of mycosis fungoides tumor cells

Mycosis fungoides (MF) is the most common primary cutaneous T-cell lymphoma. While initially restricted to the skin, malignant cells can appear in blood, bone marrow and secondary lymphoid organs in later disease stages. However, only little is known about phenotypic and functional properties of malignant T cells in relationship to tissue environments over the course of disease progression. We thus profiled the tumor micromilieu in skin, blood and lymph node in a patient with advanced MF using single-cell RNA sequencing combined with V-D-J T-cell receptor sequencing. In skin, we identified clonally expanded T-cells with characteristic features of tissue-resident memory T-cells (TRM, CD69+CD27-NR4A1+RGS1+AHR+). In blood and lymph node, the malignant clones displayed a transcriptional program reminiscent of a more central memory-like phenotype (KLF2+TCF7+S1PR1+SELL+CCR7+), while retaining tissue-homing receptors (CLA, CCR10). The skin tumor microenvironment contained potentially tumor-permissive myeloid cells producing regulatory (IDO1) and Th2-associated mediators (CCL13, CCL17, CCL22). Given their expression of PVR, TNFRSF14 and CD80/CD86, they might be under direct control by TIGIT+CTLA4+CSF2+TNFSF14+ tumor cells. In sum, this study highlights the adaptive phenotypic and functional plasticity of MF tumor cell clones. Thus, the TRM-like phenotype enables long-term skin residence of MF cells. Their switch to a TCM-like phenotype with persistent skin homing molecule expression in the circulation might explain the multi-focal nature of MF.

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IMMU-27. SINGLE CELL RNA-SEQUENCING IDENTIFIES NOVEL BONE MARROW DERIVED MYELOID CELLS IN GLIOBLASTOMA ASSOCIATED WITH TUMOR AGGRESSION

Neuro-Oncology ◽

10.1093/neuonc/noaa215.457 ◽

2020 ◽

Vol 22 (Supplement_2) ◽

pp. ii110-ii110

Author(s):

Christina Jackson ◽

Christopher Cherry ◽

Sadhana Bom ◽

Hao Zhang ◽

John Choi ◽

...

Keyword(s):

Bone Marrow ◽

Single Cell ◽

Tumor Cells ◽

Rna Sequencing ◽

Metabolic Pathways ◽

Myeloid Cells ◽

Tumor Grade ◽

Sequencing Data ◽

Single Cell Rna Sequencing ◽

Two Populations

Abstract BACKGROUND Glioma associated myeloid cells (GAMs) can be induced to adopt an immunosuppressive phenotype that can lead to inhibition of anti-tumor responses in glioblastoma (GBM). Understanding the composition and phenotypes of GAMs is essential to modulating the myeloid compartment as a therapeutic adjunct to improve anti-tumor immune response. METHODS We performed single-cell RNA-sequencing (sc-RNAseq) of 435,400 myeloid and tumor cells to identify transcriptomic and phenotypic differences in GAMs across glioma grades. We further correlated the heterogeneity of the GAM landscape with tumor cell transcriptomics to investigate interactions between GAMs and tumor cells. RESULTS sc-RNAseq revealed a diverse landscape of myeloid-lineage cells in gliomas with an increase in preponderance of bone marrow derived myeloid cells (BMDMs) with increasing tumor grade. We identified two populations of BMDMs unique to GBMs; Mac-1and Mac-2. Mac-1 demonstrates upregulation of immature myeloid gene signature and altered metabolic pathways. Mac-2 is characterized by expression of scavenger receptor MARCO. Pseudotime and RNA velocity analysis revealed the ability of Mac-1 to transition and differentiate to Mac-2 and other GAM subtypes. We further found that the presence of these two populations of BMDMs are associated with the presence of tumor cells with stem cell and mesenchymal features. Bulk RNA-sequencing data demonstrates that gene signatures of these populations are associated with worse survival in GBM. CONCLUSION We used sc-RNAseq to identify a novel population of immature BMDMs that is associated with higher glioma grades. This population exhibited altered metabolic pathways and stem-like potentials to differentiate into other GAM populations including GAMs with upregulation of immunosuppressive pathways. Our results elucidate unique interactions between BMDMs and GBM tumor cells that potentially drives GBM progression and the more aggressive mesenchymal subtype. Our discovery of these novel BMDMs have implications in new therapeutic targets in improving the efficacy of immune-based therapies in GBM.

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Faculty Opinions recommendation of Hydro-Seq enables contamination-free high-throughput single-cell RNA-sequencing for circulating tumor cells.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.735763461.793573386 ◽

2020 ◽

Author(s):

Vijay Tiwari ◽

Mohammed Inayatullah

Keyword(s):

Single Cell ◽

Tumor Cells ◽

Rna Sequencing ◽

Circulating Tumor Cells ◽

High Throughput ◽

Single Cell Rna Sequencing

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Single-Cell RNA Sequencing Identifies Extracellular Matrix Gene Expression by Pancreatic Circulating Tumor Cells

Cell Reports ◽

10.1016/j.celrep.2014.08.029 ◽

2014 ◽

Vol 8 (6) ◽

pp. 1905-1918 ◽

Cited By ~ 253

Author(s):

David T. Ting ◽

Ben S. Wittner ◽

Matteo Ligorio ◽

Nicole Vincent Jordan ◽

Ajay M. Shah ◽

...

Keyword(s):

Gene Expression ◽

Extracellular Matrix ◽

Single Cell ◽

Tumor Cells ◽

Rna Sequencing ◽

Circulating Tumor Cells ◽

Matrix Gene ◽

Single Cell Rna Sequencing

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Single-cell RNA sequencing reveals heterogeneous tumor and immune cell populations in early-stage lung adenocarcinomas harboring EGFR mutations

Oncogene ◽

10.1038/s41388-020-01528-0 ◽

2020 ◽

Cited By ~ 1

Author(s):

Di He ◽

Di Wang ◽

Ping Lu ◽

Nan Yang ◽

Zhigang Xue ◽

...

Keyword(s):

Gene Expression ◽

T Cells ◽

Single Cell ◽

Tumor Cells ◽

Rna Sequencing ◽

Early Stage ◽

Cell Types ◽

Egfr Mutations ◽

Advanced Tumor ◽

Single Cell Rna Sequencing

Abstract Lung adenocarcinoma (LUAD) harboring EGFR mutations prevails in Asian population. However, the inter-patient and intra-tumor heterogeneity has not been addressed at single-cell resolution. Here we performed single-cell RNA sequencing (scRNA-seq) of total 125,674 cells from seven stage-I/II LUAD samples harboring EGFR mutations and five tumor-adjacent lung tissues. We identified diverse cell types within the tumor microenvironment (TME) in which myeloid cells and T cells were the most abundant stromal cell types in tumors and adjacent lung tissues. Within tumors, accompanied by an increase in CD1C+ dendritic cells, the tumor-associated macrophages (TAMs) showed pro-tumoral functions without signature gene expression of defined M1 or M2 polarization. Tumor-infiltrating T cells mainly displayed exhausted and regulatory T-cell features. The adenocarcinoma cells can be categorized into different subtypes based on their gene expression signatures in distinct pathways such as hypoxia, glycolysis, cell metabolism, translation initiation, cell cycle, and antigen presentation. By performing pseudotime trajectory, we found that ELF3 was among the most upregulated genes in more advanced tumor cells. In response to secretion of inflammatory cytokines (e.g., IL1B) from immune infiltrates, ELF3 in tumor cells was upregulated to trigger the activation of PI3K/Akt/NF-κB pathway and elevated expression of proliferation and anti-apoptosis genes such as BCL2L1 and CCND1. Taken together, our study revealed substantial heterogeneity within early-stage LUAD harboring EGFR mutations, implicating complex interactions among tumor cells, stromal cells and immune infiltrates in the TME.

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Abstract NG04: Diversity of circulating tumor cells in a mouse pancreatic cancer model identified by single cell RNA sequencing

10.1158/1538-7445.am2014-ng04 ◽

2014 ◽

Cited By ~ 2

Author(s):

David T. Ting ◽

Ben S. Wittner ◽

Ajay M. Shah ◽

David T. Miyamoto ◽

Brian W. Brannigan ◽

...

Keyword(s):

Pancreatic Cancer ◽

Single Cell ◽

Tumor Cells ◽

Rna Sequencing ◽

Circulating Tumor Cells ◽

Cancer Model ◽

Single Cell Rna Sequencing

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Abstract IA09: Single cell RNA-sequencing of circulating tumor cells

10.1158/1557-3265.pmsclingen15-ia09 ◽

2016 ◽

Author(s):

David T. Miyamoto ◽

Yu Zheng ◽

Ben S. Wittner ◽

Richard J. Lee ◽

Huili Zhu ◽

...

Keyword(s):

Single Cell ◽

Tumor Cells ◽

Rna Sequencing ◽

Circulating Tumor Cells ◽

Single Cell Rna Sequencing

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Single-cell RNA sequencing shows the immunosuppressive landscape and tumor heterogeneity of HBV-associated hepatocellular carcinoma

Nature Communications ◽

10.1038/s41467-021-24010-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Daniel Wai-Hung Ho ◽

Yu-Man Tsui ◽

Lo-Kong Chan ◽

Karen Man-Fong Sze ◽

Xin Zhang ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Single Cell ◽

Tumor Cells ◽

Rna Sequencing ◽

Immune Cells ◽

Tumor Heterogeneity ◽

Sequencing Analysis ◽

T Cell Infiltration ◽

Single Cell Rna Sequencing ◽

Immune Oncology

AbstractInteraction between tumor cells and immune cells in the tumor microenvironment is important in cancer development. Immune cells interact with the tumor cells to shape this process. Here, we use single-cell RNA sequencing analysis to delineate the immune landscape and tumor heterogeneity in a cohort of patients with HBV-associated human hepatocellular carcinoma (HCC). We found that tumor-associated macrophages suppress tumor T cell infiltration and TIGIT-NECTIN2 interaction regulates the immunosuppressive environment. The cell state transition of immune cells towards a more immunosuppressive and exhaustive status exemplifies the overall cancer-promoting immunocellular landscape. Furthermore, the heterogeneity of global molecular profiles reveals co-existence of intra-tumoral and inter-tumoral heterogeneity, but is more apparent in the latter. This analysis of the immunosuppressive landscape and intercellular interactions provides mechanistic information for the design of efficacious immune-oncology treatments in hepatocellular carcinoma.

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STEM-27. A PERIVASCULAR STEM CELL UNDERLIES VERTEBRATE MENINGEAL TUMORIGENESIS

Neuro-Oncology ◽

10.1093/neuonc/noab196.101 ◽

2021 ◽

Vol 23 (Supplement_6) ◽

pp. vi26-vi27

Author(s):

Abrar Choudhury ◽

Martha Cady ◽

Calixto Lucas ◽

Brisa Palikuqi ◽

Ophir Klein ◽

...

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Single Cell ◽

Tumor Cells ◽

Rna Sequencing ◽

Single Cells ◽

Cell Types ◽

Human Meningioma ◽

Single Cell Rna Sequencing ◽

Human Meningiomas

Abstract BACKGROUND Meningiomas are the most common primary intracranial tumors in humans and dogs, but biologic drivers and cell types underlying meningeal tumorigenesis are incompletely understood. Here we integrate meningioma single-cell RNA sequencing with stem cell approaches to define a perivascular stem cell underlying vertebrate meningeal tumorigenesis. METHODS Single-cell RNA sequencing was performed on 57,114 cells from 8 human meningiomas, 54,607 cells from 3 dog meningiomas, and human meningioma xenografts in mice. Results were validated using immunofluorescence (IF), immunohistochemistry (IHC), and deconvolution of bulk RNA sequencing of 200 human meningiomas. Mechanistic and functional studies were performed using clonogenic and limiting dilution assays, xenografts, and genetically engineered mouse models. RESULTS Copy number variant identification from human meningioma single cells distinguished tumor cells with loss of chr22q from non-tumor cells with intact chr22q. A single cluster distinguished by expression of Notch3 and other cancer stem cell genes had an intermediate level of loss of chr22q, suggesting this cluster may represent meningioma stem cells. In support of this hypothesis, pseudotime trajectory analysis demonstrated transcriptomic progression starting from Notch3+ cells and encompassing all other meningioma cell types. Notch3+ meningioma cells had transcriptomic concordance to mural pericytes, and IF/IHC of prenatal and adult human meninges, as well as lineage tracing using a Notch3-CreERT2 allele in mice, confirmed Notch3+ cells were restricted to the perivascular stem cell niche in mammalian meningeal development and homeostasis. Integrating human and dog meningioma single cells revealed Notch3+ cells in tumor and non-tumor clusters in dog meningiomas. Notch3 IF/IHC and cell-type deconvolution of bulk RNA sequencing showed Notch3+ cells were enriched in high-grade human meningiomas. Notch3 overexpression in human meningioma cells increased clonogenic growth in vitro, and increased tumorigenesis and tumor growth in vivo, decreasing overall survival. CONCLUSIONS Notch3+ stem cells in the perivascular niche underlie vertebrate meningeal tumorigenesis.

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