scholarly journals Developmental heterogeneity of microglia and brain myeloid cells revealed by deep single-cell RNA sequencing

2018 ◽  
Author(s):  
Qingyun Li ◽  
Zuolin Cheng ◽  
Lu Zhou ◽  
Spyros Darmanis ◽  
Norma Neff ◽  
...  
Keyword(s):  
White Matter ◽  
Single Cell ◽  
Rna Sequencing ◽  
Myeloid Cells ◽  
Brain Regions ◽  
Adult Brain ◽  
Specific Gene ◽  
List Type ◽  
Immune Functions ◽  
Single Cell Rna Sequencing

SummaryMicroglia are increasingly recognized for their major contributions during brain development and neurodegenerative disease. It is currently unknown if these functions are carried out by subsets of microglia during different stages of development and adulthood or within specific brain regions. Here, we performed deep single-cell RNA sequencing (scRNA-seq) of microglia and related myeloid cells sorted from various regions of embryonic, postnatal, and adult mouse brains. We found that the majority of adult microglia with homeostatic signatures are remarkably similar in transcriptomes, regardless of brain region. By contrast, postnatal microglia represent a more heterogeneous population. We discovered that postnatal white matter-associated microglia (WAM) are strikingly different from microglia in other regions and express genes enriched in degenerative disease-associated microglia. These postnatal WAM have distinct amoeboid morphology, are metabolically active, and phagocytose newly formed oligodendrocytes. This scRNA-seq atlas will be a valuable resource for dissecting innate immune functions in health and disease.HighlightsMyeloid scRNA-seq atlas across brain regions and developmental stagesLimited transcriptomic heterogeneity of homeostatic microglia in the adult brainPhase-specific gene sets of proliferating microglia along cell cycle pseudotimePhagocytic postnatal white matter-associated microglia sharing DAM gene signatures

scholarly journals Single-cell RNA sequencing reveals functional heterogeneity of glioma-associated brain macrophages

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Natalia Ochocka ◽  
Pawel Segit ◽  
Kacper Adam Walentynowicz ◽  
Kamil Wojnicki ◽  
Salwador Cyranowski ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Myeloid Cells ◽  
Specific Gene ◽  
Molecular Heterogeneity ◽  
Marker Proteins ◽  
Single Cell Rna Sequencing ◽  
Diffuse Gliomas ◽  
The Central Nervous System ◽  
Encoding Genes

AbstractMicroglia are resident myeloid cells in the central nervous system (CNS) that control homeostasis and protect CNS from damage and infections. Microglia and peripheral myeloid cells accumulate and adapt tumor supporting roles in human glioblastomas that show prevalence in men. Cell heterogeneity and functional phenotypes of myeloid subpopulations in gliomas remain elusive. Here we show single-cell RNA sequencing (scRNA-seq) of CD11b+ myeloid cells in naïve and GL261 glioma-bearing mice that reveal distinct profiles of microglia, infiltrating monocytes/macrophages and CNS border-associated macrophages. We demonstrate an unforeseen molecular heterogeneity among myeloid cells in naïve and glioma-bearing brains, validate selected marker proteins and show distinct spatial distribution of identified subsets in experimental gliomas. We find higher expression of MHCII encoding genes in glioma-activated male microglia, which was corroborated in bulk and scRNA-seq data from human diffuse gliomas. Our data suggest that sex-specific gene expression in glioma-activated microglia may be relevant to the incidence and outcomes of glioma patients.

scholarly journals Single-cell RNA sequencing reveals functional heterogeneity and sex differences of glioma-associated brain macrophages

2019 ◽  
Author(s):  
Natalia Ochocka ◽  
Pawel Segit ◽  
Kacper Adam Walentynowicz ◽  
Kamil Wojnicki ◽  
Salwador Cyranowski ◽  
...  
Keyword(s):  
Sex Differences ◽  
Single Cell ◽  
Rna Sequencing ◽  
Myeloid Cells ◽  
Specific Gene ◽  
Molecular Heterogeneity ◽  
Marker Proteins ◽  
Single Cell Rna Sequencing ◽  
Diffuse Gliomas ◽  
The Central Nervous System

AbstractMicroglia are resident myeloid cells in the central nervous system (CNS) that control homeostasis and protect CNS from damage and infections. Microglia and peripheral myeloid cells accumulate and adapt tumor supporting roles in human glioblastomas that show prevalence in men. Cell heterogeneity and functional phenotypes of myeloid subpopulations in gliomas remain elusive. Single-cell RNA sequencing (scRNA-seq) of CD11b+ myeloid cells in naïve and GL261 glioma-bearing mice revealed distinct profiles of microglia, infiltrating monocytes/macrophages and CNS border-associated macrophages. We demonstrated an unforeseen molecular heterogeneity among myeloid cells in naïve and glioma-bearing brains, validated selected marker proteins and showed distinct spatial distribution of identified subsets in experimental gliomas. We found higher expression of MHCII encoding genes in glioma-activated male microglia, which was corroborated in bulk and scRNA-seq data from human diffuse gliomas. Sex-specific gene expression in glioma-activated microglia may be relevant to sex differences in incidence and outcomes of glioma patients.

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

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.

scholarly journals SCALE: modeling allele-specific gene expression by single-cell RNA sequencing

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Yuchao Jiang ◽  
Nancy R. Zhang ◽  
Mingyao Li
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Scale Modeling ◽  
Single Cell Rna Sequencing ◽  
Allele Specific

scholarly journals Massively parallel, time-resolved single-cell RNA sequencing with scNT-Seq

2019 ◽  
Author(s):  
Qi Qiu ◽  
Peng Hu ◽  
Kiya W. Govek ◽  
Pablo G. Camara ◽  
Hao Wu
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Temporal Dynamics ◽  
Embryonic Stem ◽  
Droplet Microfluidics ◽  
Massively Parallel ◽  
Specific Gene ◽  
Time Resolved ◽  
Single Cell Rna Sequencing ◽  
Rna Biogenesis

ABSTRACTSingle-cell RNA sequencing offers snapshots of whole transcriptomes but obscures the temporal dynamics of RNA biogenesis and decay. Here we present single-cell new transcript tagging sequencing (scNT-Seq), a method for massively parallel analysis of newly-transcribed and pre-existing RNAs from the same cell. This droplet microfluidics-based method enables high-throughput chemical conversion on barcoded beads, efficiently marking metabolically labeled newly-transcribed RNAs with T-to-C substitutions. By simultaneously measuring new and old transcriptomes, scNT-Seq reveals neuronal subtype-specific gene regulatory networks and time-resolved RNA trajectories in response to brief (minutes) versus sustained (hours) neuronal activation. Integrating scNT-Seq with genetic perturbation reveals that DNA methylcytosine dioxygenases may inhibit stepwise transition from pluripotent embryonic stem cell state to intermediate and totipotent two-cell-embryo-like (2C-like) states by promoting global RNA biogenesis. Furthermore, pulse-chase scNT-Seq enables transcriptome-wide measurements of RNA stability in rare 2C-like cells. Time-resolved single-cell transcriptomic analysis thus opens new lines of inquiry regarding cell-type-specific RNA regulatory mechanisms.

scholarly journals Single-Cell RNA-Sequencing Identifies Infrapatellar Fat Pad Macrophage Polarization in Acute Synovitis/Fat Pad Fibrosis and Cell Therapy

2021 ◽  
Vol 8 (11) ◽  
pp. 166
Author(s):  
Dimitrios Kouroupis ◽  
Thomas M. Best ◽  
Lee D. Kaplan ◽  
Diego Correa ◽  
Anthony J. Griswold
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Transcriptional Profiling ◽  
Macrophage Polarization ◽  
Myeloid Cells ◽  
Cellular Heterogeneity ◽  
Joint Disease ◽  
Infrapatellar Fat Pad ◽  
Fat Pad ◽  
Single Cell Rna Sequencing

The pathogenesis and progression of knee inflammatory pathologies is modulated partly by residing macrophages in the infrapatellar fat pad (IFP), thus, macrophage polarization towards pro-inflammatory (M1) or anti-inflammatory (M2) phenotypes is important in joint disease pathologies. Alteration of M1/M2 balance contributes to the initiation and progression of joint inflammation and can be potentially altered with mesenchymal stem cell (MSC) therapy. In an acute synovial/IFP inflammation rat model a single intra-articular injection of IFP-MSC was performed, having as controls (1) diseased rats not receiving IFP-MSC and (2) non-diseased rats. After 4 days, cell specific transcriptional profiling via single-cell RNA-sequencing was performed on isolated IFP tissue from each group. Eight transcriptomically distinct cell populations were identified within the IFP across all three treatment groups with a noted difference in the proportion of myeloid cells across the groups. Largely myeloid cells consisted of macrophages (>90%); one M1 sub-cluster highly expressing pro-inflammatory markers and two M2 sub-clusters with one of them expressing higher levels of canonical M2 markers. Notably, the diseased samples (11.9%) had the lowest proportion of cells expressing M2 markers relative to healthy (14.8%) and MSC treated (19.4%) samples. These results suggest a phenotypic polarization of IFP macrophages towards the pro-inflammatory M1 phenotype in an acute model of inflammation, which are alleviated by IFP-MSC therapy inducing a switch towards an alternate M2 status. Understanding the IFP cellular heterogeneity and associated transcriptional programs may offer insights into novel therapeutic strategies for disabling joint disease pathologies.

scholarly journals Single-Cell RNA Sequencing in Human Retinal Degeneration Reveals Distinct Glial Cell Populations

Cells ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 438 ◽  
Author(s):  
Andrew P. Voigt ◽  
Elaine Binkley ◽  
Miles J. Flamme-Wiese ◽  
Shemin Zeng ◽  
Adam P. DeLuca ◽  
...  
Keyword(s):  
Single Cell ◽  
Retinal Degeneration ◽  
Rna Sequencing ◽  
Glial Cell ◽  
Glial Cells ◽  
Peripheral Retina ◽  
Cell Populations ◽  
Specific Gene ◽  
Autoimmune Retinopathy ◽  
Single Cell Rna Sequencing

Degenerative diseases affecting retinal photoreceptor cells have numerous etiologies and clinical presentations. We clinically and molecularly studied the retina of a 70-year-old patient with retinal degeneration attributed to autoimmune retinopathy. The patient was followed for 19 years for progressive peripheral visual field loss and pigmentary changes. Single-cell RNA sequencing was performed on foveal and peripheral retina from this patient and four control patients, and cell-specific gene expression differences were identified between healthy and degenerating retina. Distinct populations of glial cells, including astrocytes and Müller cells, were identified in the tissue from the retinal degeneration patient. The glial cell populations demonstrated an expression profile consistent with reactive gliosis. This report provides evidence that glial cells have a distinct transcriptome in the setting of human retinal degeneration and represents a complementary clinical and molecular investigation of a case of progressive retinal disease.

scholarly journals Pancreatic cancer is marked by complement-high blood monocytes and tumor-associated macrophages

2021 ◽  
Vol 4 (6) ◽  
pp. e202000935
Author(s):  
Samantha B Kemp ◽  
Nina G Steele ◽  
Eileen S Carpenter ◽  
Katelyn L Donahue ◽  
Grace G Bushnell ◽  
...  
Keyword(s):  
Single Cell ◽  
Pancreatic Ductal Adenocarcinoma ◽  
Rna Sequencing ◽  
Gene Expression Signature ◽  
Ductal Adenocarcinoma ◽  
Specific Gene ◽  
Sequencing Analysis ◽  
Tumor Associated Macrophages ◽  
Primary Tumors ◽  
Single Cell Rna Sequencing

Pancreatic ductal adenocarcinoma (PDA) is accompanied by reprogramming of the local microenvironment, but changes at distal sites are poorly understood. We implanted biomaterial scaffolds, which act as an artificial premetastatic niche, into immunocompetent tumor-bearing and control mice, and identified a unique tumor-specific gene expression signature that includes high expression of C1qa, C1qb, Trem2, and Chil3. Single-cell RNA sequencing mapped these genes to two distinct macrophage populations in the scaffolds, one marked by elevated C1qa, C1qb, and Trem2, the other with high Chil3, Ly6c2 and Plac8. In mice, expression of these genes in the corresponding populations was elevated in tumor-associated macrophages compared with macrophages in the normal pancreas. We then analyzed single-cell RNA sequencing from patient samples, and determined expression of C1QA, C1QB, and TREM2 is elevated in human macrophages in primary tumors and liver metastases. Single-cell sequencing analysis of patient blood revealed a substantial enrichment of the same gene signature in monocytes. Taken together, our study identifies two distinct tumor-associated macrophage and monocyte populations that reflects systemic immune changes in pancreatic ductal adenocarcinoma patients.

scholarly journals Single-cell transcriptomics predicts relapse in MLL-rearranged acute lymphoblastic leukemia in infants

2020 ◽  
Author(s):  
Tito Candelli ◽  
Pauline Schneider ◽  
Patricia Garrido Castro ◽  
Luke A. Jones ◽  
Rob Pieters ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Lymphoblastic Leukemia ◽  
Risk Stratification ◽  
Single Cell ◽  
Rna Sequencing ◽  
Lymphoblastic Leukemia ◽  
Leukemic Cells ◽  
List Type ◽  
Relapse Risk ◽  
Single Cell Rna Sequencing

AbstractInfants with MLL-rearranged acute lymphoblastic leukemia (ALL) undergo intense therapy to counter a highly aggressive leukemia with survival rates of only 30-40%. The majority of patients initially show therapy response, but in two-thirds of cases the leukemia returns, typically during treatment. Accurate relapse prediction would enable treatment strategies that take relapse risk into account, with potential benefits for all patients. Through analysis of diagnostic bone marrow biopsies, we show that single-cell RNA sequencing can predict future relapse occurrence. By analysing gene modules derived from an independent study of the gene expression response to the key drug prednisone, individual leukemic cells are predicted to be either resistant or sensitive to treatment. Quantification of the proportion of cells classified by single-cell transcriptomics as resistant or sensitive, accurately predicts the occurrence of future relapse in individual patients. Strikingly, the single-cell based classification is even consistent with the order of relapse timing. These results lay the foundation for risk-based treatment of MLL-rearranged infant ALL, through single-cell classification. This work also sheds light on the subpopulation of cells from which leukemic relapse arises. Leukemic cells associated with high relapse risk are characterized by a smaller size and a quiescent gene expression program. These cells have significantly fewer transcripts, thereby also demonstrating why single-cell analyses may outperform bulk mRNA studies for risk stratification. This study indicates that single-cell RNA sequencing will be a valuable tool for risk stratification of MLL-rearranged infant ALL, and shows how clinically relevant information can be derived from single-cell genomics.Key PointsSingle-cell RNA sequencing accurately predicts relapse in MLL-rearranged infant ALLIdentification of cells from which MLL-rearranged infant ALL relapses occur

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