Single Cell Dynamics Causes Pareto-Like Effect in Stimulated T Cell Populations

ObjectiveThis study aimed to characterize the tumor-infiltrating T cells in moderately differentiated colorectal cancer.MethodsUsing single-cell RNA sequencing data of isolated 1632 T cells from tumor tissue and 1252 T cells from the peripheral blood of CRC patients, unsupervised clustering analysis was performed to identify functionally distinct T cell populations, followed by correlations and ligand-receptor interactions across cell types. Finally, differential analysis of the tumor-infiltrating T cells between colon cancer and rectal cancer were carried out.ResultsA total of eight distinct T cell populations were identified from tumor tissue. Tumor-Treg showed a strong correlation with Th17 cells. CD8+TRM was positively correlated with CD8+IEL. Seven distinct T cell populations were identified from peripheral blood. There was a strong correlation between CD4+TN and CD4+blood-TCM. Colon cancer and rectal cancer showed differences in the composition of tumor-infiltrating T cell populations. Tumor-infiltrating CD8+IEL cells were found in rectal cancer but not in colon cancer, while CD8+ TN cells were found in the peripheral blood of colon cancer but not in that of rectal cancer. A larger number of tumor-infiltrating CD8+ Tex (88.94%) cells were found in the colon cancer than in the rectal cancer (11.06%). The T cells of the colon and rectal cancers showed changes in gene expression pattern.ConclusionsWe characterized the T cell populations in the CRC tumor tissue and peripheral blood.

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158 Single cell analysis of emigrating cells from psoriasis lesion identifies distinct IL-17A and IL-17F producing T-cell populations and other novel disease-associated alterations

Journal of Investigative Dermatology ◽

10.1016/j.jid.2020.03.162 ◽

2020 ◽

Vol 140 (7) ◽

pp. S19

Author(s):

J. Kim ◽

J. Lee ◽

H. Kim ◽

N. Kameyama ◽

R. Nazarian ◽

...

Keyword(s):

T Cell ◽

Single Cell ◽

Single Cell Analysis ◽

Cell Populations ◽

Cell Analysis ◽

Psoriasis Lesion

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CAR T cell therapy drives endogenous locoregional T cell dynamics in a responding patient with glioblastoma

10.1101/2021.09.22.460392 ◽

2021 ◽

Author(s):

Vanessa D Jonsson ◽

Rachel Ng ◽

Natalie Dullerud ◽

Robyn A Wong ◽

Jonathan Hibbard ◽

...

Keyword(s):

T Cells ◽

Cerebrospinal Fluid ◽

T Cell ◽

Cell Therapy ◽

Single Cell ◽

Cell Dynamics ◽

T Cell Therapy ◽

Car T Cell ◽

Car T Cell Therapy ◽

Car T

CAR T cell therapy has transformed clinical care and management of patients with certain hematological cancers. However, it remains unclear whether the success of CAR T cell therapy relies solely on CAR T cell engagement with tumor antigen, or if it also requires the stimulation of an individual patient's endogenous T cell response. Here, we performed combined analysis of longitudinal, single cell RNA and T cell receptor sequencing on glioblastoma tumors, peripheral blood (PB), and cerebrospinal fluid (CSF) from a patient with recurrent multifocal glioblastoma that underwent a remarkable response followed by recurrence on IL13RA2-targeted CAR T cell therapy (Brown et al. 2016). Single cell analysis of a tumor resected prior to CAR T cell therapy revealed the existence of an inflamed tumor microenvironment including a CD8+ cytotoxic, clonally expanded and antigen specific T cell population that disappeared in the recurrent setting. Longitudinal tracking of T cell receptors uncovered distinct T cell dynamics classes in the CSF during CAR T cell therapy. These included T cell clones with transient dynamics, representing intraventricular CAR T cell delivery and endogenous T cell recruitment from the PB into the CSF; and a group of T cells in the cerebrospinal fluid, that tracked with clonally expanded tumor resident T cells and whose dynamics contracted concomitantly with tumor volume. Our results suggest the existence of an endogenous T cell population that was invigorated by intraventricular CAR T cell infusions, and combined with the therapy to produce a complete response.

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Investigating the tumor immune infiltrate for populations that predict immune-related adverse events (irAEs) in patients receiving PD-1 inhibitors.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.3116 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. 3116-3116

Author(s):

Steven Michael Blum ◽

Neal Smith ◽

Moshe Sade-Feldman ◽

Dennie T. Frederick ◽

Russell William Jenkins ◽

...

Keyword(s):

T Cell ◽

Adverse Events ◽

Single Cell ◽

Immune Cells ◽

Checkpoint Inhibitors ◽

Advanced Melanoma ◽

Cell Populations ◽

Data Set ◽

Systemic Immunosuppression ◽

Definition Of

3116 Background: The mechanistic relationship between clinical benefit and immune-related adverse events (irAEs) in response to immune checkpoint inhibitors (ICIs) remains unclear, with several clinical studies reporting that irAEs are biomarkers of responses. Single-cell RNA sequencing (scRNAseq) analysis of tumors from patients with advanced melanoma before and after treatment with ICIs have identified immune cells that correlate with response to ICIs. We sought to evaluate if these populations were also associated with irAEs. Methods: A published scRNAseq data set generated with the Smart-Seq2 protocol (Sade-Feldman M, et al. Cell 2018.) was re-analyzed, stratified by two definitions of irAEs: (1) toxicity requiring systemic immunosuppression (prednisone > 10mg/day) or (2) systemic immunosuppression and/or endocrinopathy. Unbiased single-cell analysis was performed, followed by sub-clustering of T cell populations. The percentage of cells in each cluster was determined on a per sample basis. Results: 13,184 immune cells from 39 samples collected from 25 patients were re-analyzed. 27 samples were from patients who did not respond to ICIs, while 12 samples came from responding patients. 21 samples came from patients who required immunosuppression, 5 samples from patients with isolated thyroiditis, and 13 samples from patients who met neither irAE criteria. Unsupervised scRNAseq analyses focused on ICI efficacy re-capitulated published associations between response and populations that included B-cells (p < 0.01) and TCF7 expressing T-cells (p < 0.01). While these cell populations were not associated with either definition of toxicity, we observed a non-Treg CD4 expressing T cell population (0.8-10.5% cells/sample) that positively correlated with either definition of toxicity (p < 0.05) but not efficacy. Conclusions: In a patient cohort with advanced melanoma, tumor-infiltrating immune cell populations associated with response to ICI therapy were not associated with irAEs. This suggests that biomarkers of ICI response may not function as biomarkers of irAEs, and ongoing analysis will seek to validate this result. Understanding the differences between ICI response and irAEs may identify new therapeutic targets for maximizing efficacy while mitigating toxicity.

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Single-cell lineage trajectories and chromatin regulators that initialize antiviral CD8 T cell ontogeny

10.1101/2021.08.11.456014 ◽

2021 ◽

Author(s):

Huitian Diao ◽

Runqiang Chen ◽

Shanel M Tsuda ◽

Dapeng Wang ◽

Megan A Frederick ◽

...

Keyword(s):

T Cell ◽

Single Cell ◽

Interleukin 2 ◽

Cell Lineage ◽

Cd8 T Cell ◽

Effector Memory ◽

Cell Populations ◽

Chronic Infections ◽

Chromatin Regulators

Individual naive CD8 T cells activated in lymphoid organs differentiate into functionally diverse and anatomically distributed T cell phylogenies in response to intracellular microbes. During infections that resolve rapidily, including live viral vaccines, distinct effector (TEFF) and memory (TMEM) cell populations develop that ensure long term immunity. During chronic infections, responding cells progressively become dysfunctional and exhaust. A diverse taxonomy of TEFF, TMEM and exhausted (TEX) CD8 T cell populations is known, but the initial developmental basis of this phenotypic variation remains unclear. Here, we defined single-cell trajectories and identified chromatin regulators that establish antiviral CD8 T cell heterogeneity using unsupervised analyses of single-cell RNA dynamics and an in vivo RNAi screen. Activated naive cells differentiate linearly into uncommitted effector-memory progenitor (EMP) cells, which initially branch into an analogous manifold during either acute or chronic infection. Disparate RNA velocities in single EMP cells initiate divergence into stem, circulating, and tissue-resident memory lineages that generate diverse TMEM and TEX precursor states in specific developmental orders. Interleukin-2 receptor (IL-2R) signals are essential for formation and transcriptional heterogeneity of EMP cells, and promote trajectories toward TEFF rather than TEX states. Nucleosome remodelers Smarca4 and Chd7 differentially promote transcription that delineates divergent TMEM lineages before cooperatively driving terminal TEFF cell differentiation. Thus, the lineage architecture is established by specific chromatin regulators that stabilize diverging transcription in uncommitted progenitors.

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Integrative bulk and single-cell profiling of pre-manufacture T-cell populations reveals factors mediating long-term persistence of CAR T-cell therapy

Cancer Discovery ◽

10.1158/2159-8290.cd-20-1677 ◽

2021 ◽

pp. candisc.1677.2020

Author(s):

Gregory M Chen ◽

Changya Chen ◽

Rajat K Das ◽

Peng Gao ◽

Chia-Hui Chen ◽

...

Keyword(s):

T Cell ◽

Cell Therapy ◽

Single Cell ◽

Cell Populations ◽

T Cell Therapy ◽

Car T Cell ◽

Car T Cell Therapy ◽

Car T ◽

Single Cell Profiling

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Single cell immune profiling reveals a developmentally distinct CD4+ GM-CSF+ T cell lineage that induces GI tract GVHD

Blood Advances ◽

10.1182/bloodadvances.2021006084 ◽

2022 ◽

Author(s):

Clint Piper ◽

Emma Hainstock ◽

Cheng Yin-Yuan ◽

Yao Chen ◽

Achia Khatun ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Single Cell ◽

Cell Population ◽

Cell Populations ◽

Sequencing Analysis ◽

Gi Tract ◽

Gm Csf ◽

Mediators Of Inflammation ◽

Ifn Γ

Gastrointestinal (GI) tract involvement is a major determinant for subsequent morbidity and mortality arising during graft versus host disease (GVHD). CD4+ T cells that produce GM-CSF have emerged as central mediators of inflammation in this tissue site as GM-CSF serves as a critical cytokine link between the adaptive and innate arms of the immune system. However, cellular heterogeneity within the CD4+ GM-CSF+ T cell population due to the concurrent production of other inflammatory cytokines has raised questions as to whether these cells have a common ontology or if there exists a unique CD4+ GM-CSF+ subset that differs from other defined T helper (TH) subtypes. Using single cell RNA sequencing analysis, we identified two CD4+ GM-CSF+ T cell populations that arose during GVHD and were distinguishable by the presence or absence of IFN-γ co-expression. CD4+ GM-CSF+ IFN-γ- T cells which emerged preferentially in the colon had a distinct transcriptional profile, employed unique gene regulatory networks, and possessed a non-overlapping TCR repertoire when compared to CD4+ GM-CSF+ IFN-γ+ T cells as well as all other transcriptionally defined CD4+ T cell populations in the colon. Functionally, this CD4+ GM-CSF+ T cell population contributed to pathological damage in the GI tract which was critically dependent upon signaling through the IL-7 receptor but was independent of type 1 interferon signaling. Thus, these studies help to unravel heterogeneity within CD4+ GM-CSF+ T cells that arise during GVHD and define a developmentally distinct colitogenic TH GM-CSF+ subset that mediates immunopathology.

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Chicken peripheral blood lymphocyte response to ALV-J infection assessed by single-cell RNA sequencing

10.1101/2021.01.12.426350 ◽

2021 ◽

Author(s):

Manman Dai ◽

Min Feng ◽

Ziwei Li ◽

Weisan Chen ◽

Ming Liao

Keyword(s):

T Cells ◽

T Cell ◽

Viral Infection ◽

Single Cell ◽

Rna Sequencing ◽

Peripheral Blood ◽

Cell Populations ◽

Control Group ◽

Marker Genes ◽

Single Cell Rna Sequencing

ABSTRACTChicken peripheral blood lymphocytes (PBLs) exhibit wide-ranging cell types, but current understanding of their subclasses, immune cell classification, and function is limited and incomplete. Previously, we found that viremia caused by avian leukosis virus subgroup J (ALV‐J) was eliminated by 21 days post infection (DPI), accompanied by increased CD8+ T cell ratio in PBLs and low antibody levels. Here we performed single-cell RNA sequencing (scRNA-seq) of PBLs in ALV-J infected and control chickens at 21 DPI to determine chicken PBL subsets and their specific molecular and cellular characteristics, before and after viral infection. Eight cell clusters and their potential marker genes were identified in chicken PBLs. T cell populations (clusters 6 and 7) had the strongest response to ALV-J infection at 21 DPI, based on detection of the largest number of differentially expressed genes (DEGs). T cell populations of clusters 6 and 7 could be further divided into four subsets: activated CD4+ T cells (cluster A0), Th1-like cells (cluster A2), Th2-like cells (cluster A1), and cytotoxic CD8+ T cells. Hallmark genes for each T cell subset response to viral infection were initially identified. Furthermore, pseudotime analysis results suggested that chicken CD4+ T cells could potentially differentiate into Th1-like and Th2-like cells. Moreover, ALV-J infection probably induced CD4+ T cell differentiation into Th1-like cells in which the most immune related DEGs were detected. With respect to the control group, ALV-J infection also had an obvious impact on PBL cell composition. B cells showed inconspicuous response and their numbers decreased in PBLs of the ALV-J infected chickens at 21 DPI. Percentages of cytotoxic Th1-like cells and CD8+ T cells were increased in the T cell population of PBLs from ALV-J infected chicken, which were potentially key mitigating factors against ALV-J infection. More importantly, our results provided a rich resource of gene expression profiles of chicken PBL subsets for a systems-level understanding of their function in homeostatic condition as well as in response to viral infection.

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