scholarly journals Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+ T cell fate bifurcation

2016 ◽  
Author(s):  
Tapio Lönnberg ◽  
Valentine Svensson ◽  
Kylie R James ◽  
Daniel Fernandez-Ruiz ◽  
Ismail Sebina ◽  
...  

AbstractDifferentiation of naïve CD4+ T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to multiple levels of heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissection in vivo. By using single-cell RNA transcriptomics and computational modelling of temporal mixtures, we reconstructed the developmental trajectories of Th1 and Tfh cell populations during Plasmodium infection in mice at single-cell resolution. These cell fates emerged from a common, highly proliferative and metabolically active precursor. Moreover, by tracking clonality from T cell receptor sequences, we infer that ancestors derived from the same naïve CD4+ T cell can concurrently populate both Th1 and Tfh subsets. We further found that precursor T cells were coached towards a Th1 but not a Tfh fate by monocytes/macrophages. The integrated genomic and computational approach we describe is applicable for analysis of any cellular system characterized by differentiation towards multiple fates.One Sentence SummaryUsing single-cell RNA sequencing and a novel unsupervised computational approach, we resolve the developmental trajectories of two CD4+ T cell fates in vivo, and show that uncommitted T cells are externally influenced towards one fate by inflammatory monocytes.

Cytotherapy ◽  
2015 ◽  
Vol 17 (6) ◽  
pp. S9-S10
Author(s):  
Patrick Hanley ◽  
Joseph Melenhorst ◽  
Russell Cruz ◽  
Caridad Martinez ◽  
Helen Heslop ◽  
...  

2021 ◽  
Vol 11 ◽  
Author(s):  
Xi Yang ◽  
Quan Qi ◽  
Yuefen Pan ◽  
Qing Zhou ◽  
Yinhang Wu ◽  
...  

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.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2491-2491
Author(s):  
C.J.M. Halkes ◽  
I Jedema ◽  
H.M. van Egmond ◽  
L van der Fits ◽  
J.H.F. Falkenburg ◽  
...  

Abstract Abstract 2491 Alemtuzumab (ALT) is a monoclonal anti CD52 antibody used for the treatment of CD52 positive lymphoid malignancies and to deplete T cells in vivo and in vitro to prevent graft rejection or GVHD after allogeneic stem cell transplantation (alloSCT). Membrane CD52 expression depends on the presence of a glycosylphosphatidylinositol (GPI) anchor. GPI deficiency is frequently found in small populations of normal and malignant hematopoietic cells, including T and B cells (frequencies from <0.01 to 2%). These cells lack expression of GPI-linked proteins like CD52 as can be detected by absence of staining of FLAER, which is an aerolysin that specifically binds to mammalian GPI anchors. After alloSCT using ALT for T cell depletion, reconstitution of FLAER and CD52 double negative cells is seen, and outgrowth of CD52 negative malignant cell populations has been found after single agent treatment with ALT in malignant diseases. However, GPI deficient cells have been suggested to have a lower proliferative potential and a decreased survival due to their increased susceptibility to spontaneous complement mediated cell lysis, possibly explaining the infrequent dominant outgrowth of GPI deficient clones in healthy individuals. Sézary Syndrome (SS) is an aggressive cutaneous T cell lymphoma characterized by the presence of high numbers of neoplastic T cells expressing CD4 and CD52 in peripheral blood, lymph nodes and skin. Clinical responses in SS patients after single drug treatment with low dosed ALT have been described by several investigators. However, in 6 out of 6 patients analyzed, we found a small population of CD52 and FLAER negative Sézary cells, illustrating that a GPI negative subpopulation is frequently observed which may lead to outgrowth of CD52 negative Sézary cells. We treated 3 patients with successive courses of low dose ALT (10 mg subcutaneously once weekly until circulating malignant cells were < 1,000/mm3) and followed the kinetics of CD52- and CD52+ Sézary cells. Before ALT treatment, a CD4+CD52-FLAER- T cell population was found in all three patients (0.01–0.06% of all circulating CD4+ T cells). As expected, a rapid decrease in absolute numbers of CD4+CD52+FLAER+ cells was observed after ALT treatment (decrease 94 to 100%). Surprisingly, despite the absence of the CD52 target molecule, the absolute number of CD4+CD52-FLAER- T cells also decreased after the first and second treatment cycles in all three patients (decreases between 22 and 96%), indicating that the massive in vivo ALT mediated lysis of CD52+ Sézary cells coincided with collateral damage of CD52- Sézary cells. Between successive treatment courses in the absence of circulating ALT, the absolute numbers of CD4+CD52+FLAER+ T cells showed a more rapid increase compared to CD4+CD52-FLAER- T cells in all patients (median 193 fold increase (range 17–896) versus 9 fold increase (range 2–144) respectively), illustrating a decreased in vivo proliferative potential of these GPI negative cells. After repeated doses of ALT, one of the patients developed resistance to ALT treatment. Phenotype analysis revealed that 97% of the 23,000/mm3 circulating Sézary cells were CD4+CD52-FLAER-. Clonality analysis showed that CD4+CD52+FLAER+ and CD4+CD52-FLAER–Sézary cell populations expressed identical T cell receptor V-beta chains demonstrating that both cell populations are part of the same initial clone of Sézary cells. At present, one year after the start of ALT treatment, reponses are still observed in both other patients without overgrowth of a CD4+CD52-FLAER–Sézary cells. We conclude that despite presence of small populations of CD52 and GPI negative cells in patients with Sézary Syndrome, all patients respond to treatment with alemtuzumab. CD52 negative, GPI deficient Sézary cells showed high susceptibility to collateral damage during antibody treatment. During treatment intervals, CD52+ cells showed a faster recovery compared to CD52- cells, indicating a lower proliferative potential of the GPI deficient Sézary cells. Although, as shown in one patient, ultimate outgrowth of GPI deficient CD52- sezary cells can occur, the capacity to achieve long term control of both CD52+ and CD52- Sézary cells in several patients offers a rationale for treatment of SS with alemtuzumab, possibly in combination with a low dosed cytotoxic drug Disclosures: Off Label Use: Alemtuzumab for treatment of Sezary Syndrome.


2020 ◽  
Author(s):  
Jessica A. Engel ◽  
Hyun Jae Lee ◽  
Cameron G. Williams ◽  
Rachel Kuns ◽  
Stuart Olver ◽  
...  

AbstractAcute gastrointestinal Graft-versus-Host-Disease (GVHD) is a primary determinant of mortality after allogeneic hematopoietic stem-cell transplantation (alloSCT). It is mediated by alloreactive donor CD4+ T cells that differentiate into pathogenic subsets expressing IFNγ, IL-17A or GM-CSF, and is regulated by subsets expressing IL-10 and/or Foxp3. Developmental relationships between T-helper states during priming in mesenteric lymph nodes (mLN) and effector function in the GI tract remain undefined at genome-scale. We used scRNA-seq and computational modelling to create an atlas of putative differentiation pathways during GVHD. Computational trajectory inference suggested emergence of pathogenic and regulatory states along a single developmental trajectory in mLN. Importantly, we identified an unexpected second trajectory, categorised by little proliferation or cytokine expression, reduced glycolysis, and high TCF1 expression. TCF1hi cells upregulated α4β7 prior to gut migration and failed to express cytokines therein. Nevertheless, they demonstrated recall potential and plasticity following secondary transplantation, including cytokine or Foxp3 expression, but reduced TCF1. Thus, scRNA-seq revealed divergence of allo-reactive CD4+ T cells into quiescent and effector states during gut GVHD, reflecting putative heterogenous priming in vivo. These findings, the first at a single-cell level during GVHD over time, can now be used to interrogate T cell differentiation in patients undergoing alloSCT.


2021 ◽  
Author(s):  
Jack A. Collora ◽  
Delia Pinto-Santini ◽  
Siavash Pasalar ◽  
Neal Ravindra ◽  
Carmela Ganoza ◽  
...  

AbstractDespite antiretroviral therapy (ART), HIV-1 persists in proliferating T cell clones that increase over time. To understand whether early ART affects HIV-1 persistence in vivo, we performed single-cell ECCITE-seq and profiled 89,279 CD4+ T cells in paired samples during viremia and after immediate versus delayed ART in six people in the randomized interventional Sabes study. We found that immediate ART partially reverted TNF responses while delayed ART did not. Antigen and TNF responses persisted despite immediate ART and shaped the transcriptional landscape of CD4+ T cells, HIV-1 RNA+ cells, and T cell clones harboring them (cloneHIV-1). Some HIV-1 RNA+ cells reside in the most clonally expanded cytotoxic T cell populations (GZMB and GZMK Th1 cells). CloneHIV-1+ were larger in clone size, persisted despite ART, and exhibited transcriptional signatures of antigen, cytotoxic effector, and cytokine responses. Using machine-learning algorithms, we identified markers for HIV-1 RNA+ cells and cloneHIV-1+ as potential therapeutic targets. Overall, by combining single-cell immune profiling and T cell expansion dynamics tracking, we identified drivers of HIV-1 persistence in vivo.


2021 ◽  
Author(s):  
Aparna Nathan ◽  
Samira Asgari ◽  
Kazuyoshi Ishigaki ◽  
Tiffany Amariuta ◽  
Yang Luo ◽  
...  

Many non-coding genetic variants cause disease by modulating gene expression. However, identifying these expression quantitative trait loci (eQTLs) is complicated by gene-regulation differences between cell states. T cells, for example, have fluid, multifaceted functional states in vivo that cannot be modeled in eQTL studies that aggregate cells. Here, we modeled T cell states and eQTLs at single-cell resolution. Using >500,000 resting memory T cells from 259 Peruvians, we found over one-third of the 6,511 cis-eQTLs had state-dependent effects. By integrating single-cell RNA and surface protein measurements, we defined continuous cell states that explained more eQTL variation than discrete states like CD4+ or CD8+ T cells and could have opposing effects on independent eQTL variants in a locus. Autoimmune variants were enriched in cell-state-dependent eQTLs, such as a rheumatoid-arthritis variant near ORMDL3 strongest in cytotoxic CD8+ T cells. These results argue that fine-grained cell state context is crucial to understanding disease-associated eQTLs.


2020 ◽  
Vol 8 (Suppl 2) ◽  
pp. A48.1-A48
Author(s):  
D Liu ◽  
P Paczkowski ◽  
S MacKay ◽  
J Zhou

Chimeric antigen receptor (CAR) T cell therapy has already paved the way for successful immunotherapies to fight against liquid tumors and is quickly expanding to solid tumors. Nevertheless, the biggest challenges are how to evaluate the quality of CAR-T cells and how to predict their in vivo behaviors once reinfused into a patient. In this report, we review single-cell polyfunctional profiling results obtained from several different sets of pre-infusion CAR-T samples, including CD19 CAR-T products from Novartis and Kite Pharma (Gilead), GoCAR-T cell products targeting Prostate Stem Cell Antigen from Bellicum, bispecific CD19/22 CAR-T cells from the NIH, trimeric APRIL-based CAR-T cells targeting both BCMA and TACI from MGH and CAR-T cells targeting glypican 3 in hepatocellular carcinoma from NIH. In each case, CD4+ and CD8+ CAR-T cells were stimulated and subsequently analyzed at a single-cell level using IsoPlexis’ IsoCode proteomic chips. Our single-cell data revealed highly polyfunctional and heterogeneous responses across each cohorts. The polyfunctional strength index (PSI) of the pre-infused CAR-T products is significantly associated with the clinical outcome of the patients after receiving the treatment, as well as post-infusion grade 3+ CRS. The CAR-T cells secreted a wide range of cytokines/chemokines in response to antigen specific stimulation and a significant portion of the CAR-T cells were polyfunctional (2+cytokines/cell). These results highlight the potential benefits of single-cell proteomics to comprehensively understand how CAR-T products behave in response to antigen-specific stimulation. Analyzing the single-cell polyfunctionality of CAR-T profiles also provides a valuable quality check for optimizing the manufacturing process and a powerful tool for next generation biomarker developments.Disclosure InformationD. Liu: None. P. Paczkowski: None. S. MacKay: None. J. Zhou: None.


2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e15021-e15021
Author(s):  
Zishan Zhou ◽  
Yue Pu ◽  
Shanshan Xiao ◽  
Ping Wang ◽  
Yang Yu ◽  
...  

e15021 Background: T-cell receptor (TCR)-engineered T cells are a novel option for adoptive cell therapy used for the treatment of several advanced forms of cancers. Unlike many shared tumor-specific antigens, such as melanoma-associated antigen (MAGE)-A3, MAGE-A4, and New York esophageal squamous cell carcinoma (NY-ESO)-1, neoantigen has garnered much attention as a potential precision immunotherapy. Personalized neoantigen selection serves a broader and more precision future for cancer patients. Methods: Dendritic cells (DCs) derived from adherent monocytes were pulsed with mixed peptides during the maturation phase. CD8+ cells positively selected from PBMCs were incubated with washed DCs. After 21day culture in X-VIVO medium with IL-7 and IL-15, cells were harvested and stimulated with peptides for 6 h. CD137+ cells were sorted by flow cytometric and immediately processed using the 10x Genomic Chromium Single Cell 5' Library & Gel Bead Kit and Chromium Single Cell V(D)J Enrichment Kit. The T-cell TCR libraries were constructed and sequenced on the Illumina HiSeq X Ten platform. The sequencing reads were aligned to the hg38 human reference genome and analyzed using the 10x Genomics Cell Ranger pipeline. The paired TCR α and β chain sequence of each cell was demonstrated with V(D)J analysis. TCR-T cells were constructed using the information of neoantigen specific TCR, and infused to patients. Results: Two patients were treated with the personalized TCR-T treatment. At the first stage, specialized immune cells were harvested and proceeded to single-cell TCR profiling. Then, the single cell sequencing of the first patient's sample revealed the top five neoantigen specific TCR CDR3 clonotypes with the proportion of 25%, 7.67%, 4.81%, 2.79%, and 2.54%, respectively. Similarly, the other patient had the top five TCR CDR3 sequenced with the proportion of 13.38%, 7.04%, 4.21%, 2.83%, and 1.94%, respectively. The results demonstrated that both patients had one or two dominant CDR3 clonotypes, which might reflect the strength of neoantigen in vivo. At the third stage, TCR-T cells were constructed, and infused to the patients. The clinical outcome will be evaluated in the near future. Conclusions: We have generated a pipeline for a highly personalized cancer therapy using TCR-engineered T cells. Although some questions remain to be answered, this novel approach may result in better clinical responses in future treatment.


Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 38-38
Author(s):  
Jun Shen ◽  
Yingxi Xu ◽  
Shuo Zhang ◽  
Shuzhen Lyu ◽  
Zack Wang ◽  
...  

Human pluripotent stem cells (hPSCs) provide a powerful platform for generating functional hematopoietic cells for blood disease modeling and therapeutic testing. However, the quantity and quality of hPSC-derived blood cells remain to be improved. Here, by performing extensive single-cell transcriptomic analyses to map fate choices and gene expression programs during hematopoietic differentiation of hPSCs, we construct the first hematopoietic landscape of hPSCs at the single-cell level and identify strategies to promote hematopoietic progenitor (HP) generation from hPSCs with functional T cell potential. By focusing specifically on cell populations and molecular events involved in endothelial-to-hematopoietic transition (EHT), we compared the difference of early hematopoiesis between hPSCs and human embryos (Yang Zeng et al. Cell Research. 2019) and found aerobic metabolism was dysregulated during in-vitro-directed differentiation. The decreased oxygen metabolism program was further deciphered as a key molecular event occurred during the EHT. Providing hypoxia at the stage of EHT enhanced hematopoietic differentiation of hPSCs via specifying arterial programs, including arterial hemogenic endothelium (AHE) and arterial endothelium cells (AE). To further determine the effect of AE on hematopoietic development, we isolated AE, venous endothelium and mesenchymal cells identified in our single-cell transcriptomic analyses and cocultured them with AHE respectively for HP generation. AE were finally validated as a critical regulator of definitive HP specification with more T cell potential. T cells generated from AE-primed HPs (AE-T) were highly functional and exhibited polyfunctional production of interferon (IFN)-γ, tumor necrosis factor alpha (TNF-α), and IL-2 in response to phorbol 12-myristate 13-acetate (PMA) and ionomycin. To further evaluate the function of AE-T, we engineered T cells with CD19-CAR. The in vitro cytotoxicity of CAR-engineered AE-T was performed both in CD19+ cell lines (Nalm-6 and Raji) and human primary B-ALL samples. The efficacy of CAR-engineered AE-T in vivo was evaluated in a mouse xenograft model inoculated intravenously with luciferase-expressing Nalm-6 cells. Similar to CD19 CAR-transduced peripheral blood T cells, the AE-T potently inhibited tumor growth both in vitro and in vivo. Collectively, our study provides benchmark datasets to understand the origins of human hematopoiesis and presents an advance for guiding the generation of functional T cells in vitro for clinical applications. Disclosures No relevant conflicts of interest to declare.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 3172-3172
Author(s):  
Melinda Roskos ◽  
Robert B. Levy

Abstract There is currently significant interest in the transplant field to develop adoptive-transfer strategies utilizing T cell populations to provide immediate immune function as well as long-term immune reconstitution following hematopoietic cell transplantation (HCT). Presumably, these pre-selected T cell populations could then be further expanded in the transplant recipient as a consequence of lymphopenia-induced proliferation. However, clinical application of adoptive transfer strategies has been limited by practical (time, expense) and technical (isolation and expansion of antigen-specific T cell populations) difficulties, hence more efficient approaches need to be identified. Recent reports have demonstrated the feasibility for the rapid ex vivo generation of transgenic memory CD8 populations. We investigated the potential of applying this ex vivo approach to generate and expand an immunodominant antigen-specific memory population from primary CD8 T cells. CD8 cells recognizing the mouse H60 epitope were selected as the antigen-specific CD8 population. The H60 glycoprotein is the ligand for NKG2D and the LTFNYRNL peptide is an immunodominant minor transplantation antigen. H60 is expressed by BALB.B (H2b) hematopoietic cells and recognized by C57BL/6 (B6) CD8 cells within the context of the H2Kb molecule. CD8 T cells from normal B6 spleens were positively selected using Miltenyi beads. The purified CD8 cells (97%) were then cultured with bone marrow-derived B6 DC, rmIL-2, and H60 peptide (1μM) for 3 days. Cells were harvested and re-cultured with rmIL-15 for 2–4 days. The resultant CD8 population was enriched 10 fold for tetramer-stained H60+ CD8 T cells (average: 3.0% of CD8 T cells). The H60+ CD8 cells displayed a memory phenotype as characterized by CD44+, Ly6C+, CD62Lintermed, and CD25lo expression. We hypothesized these H60+ CD8 T cells could be further expanded in transplant recipients by lymphopenia-induced proliferation. To determine the expansion and persistence of H60+ TM post-HCT, H60+-enriched CD8 cells were co-transplanted with T cell-depleted B6 bone marrow into 9.0Gy-conditioned syngeneic recipients. The phenotype and number of H60+ cells in recipient spleens and bone marrow were assessed beginning 3 days post-HCT. Notably, the H60+ CD8 cells maintained their memory phenotype and persisted at least 2 months post-transplant. The ex vivo-generated H60+ TM underwent a relative expansion of 1.5–2 fold as assessed in recipient spleens, similar to the post-transplant expansion of H60+ CD8 TM derived in vivo from B6 mice primed to BALB.B cells. Moreover, this post-HCT expansion was also similar to that by an ex vivo-generated, transgenic CD8 TM population. Both (ex vivo and in vivo generated) H60+ TM populations also exhibited expansion (1.5–2 fold) in the bone marrow. In total, an immunodominant antigen-specific CD8 TM population was selectively generated and enriched ex vivo and found to undergo expansion following transplant into ablatively conditioned HCT recipients. The similarities in expansion and persistence between ex vivo generated H60 and in vivo primed H60 populations suggest this approach may have useful applications towards the development of successful adoptive transfer strategies.


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