Single-cell TCR repertoire analysis of regulatory T cells suggests different immunological pathophysiology of preeclampsia and miscarriage, in humans

2018 ◽  
Vol 130 ◽  
pp. 38
Author(s):  
Sayaka Tsuda ◽  
Xiaoxin Zhang ◽  
Hiroshi Hamana ◽  
Tomoko Shima ◽  
Akemi Ushijima ◽  
...  
Keyword(s):  
T Cells ◽  
Regulatory T Cells ◽  
Single Cell ◽  
Repertoire Analysis ◽  
Tcr Repertoire

scholarly journals CTLA-4 controls the thymic development of both conventional and regulatory T cells through modulation of the TCR repertoire

2012 ◽  
Vol 110 (3) ◽  
pp. E221-E230 ◽  
Author(s):  
J. Verhagen ◽  
R. Genolet ◽  
G. J. Britton ◽  
B. J. Stevenson ◽  
C. A. Sabatos-Peyton ◽  
...  
Keyword(s):  
T Cells ◽  
Regulatory T Cells ◽  
Thymic Development ◽  
Tcr Repertoire

Activated and Expanded T Cells for Potential Therapy of Patients with Autoimmune Diseases.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3854-3854
Author(s):  
Alice Long ◽  
Mark Bonyhadi ◽  
Christophe Ferrand ◽  
Mark Frohlich ◽  
Ronald J. Berenson
Keyword(s):  
T Cells ◽  
Immune System ◽  
T Cell ◽  
Side Effects ◽  
Autoimmune Diseases ◽  
Current Therapy ◽  
High Dose ◽  
Autoreactive T Cells ◽  
Repertoire Analysis ◽  
Tcr Repertoire

Abstract Autoreactive T cells have been implicated as central players in many autoimmune diseases. Current therapy for autoimmune diseases involves chronic immunosuppression, which increases the risk of infection and cancer, and is associated with other side effects. Recently, high-dose chemotherapy combined with stem cell transplantation has been used, but is often associated with severe toxicities. To avoid the side effects associated with these therapies, we are developing an alternative therapeutic approach in which patients are treated with relatively non-toxic therapy to reduce T cell numbers, and then administered healthy T cells to restore the immune system. Most autoimmune patients have oligoclonal populations of T cells as measured by T cell receptor (TCR) repertoire analysis. These may represent autoreactive T cells which contribute to TCR repertoire skewing. Clinical studies have shown a positive correlation between post-therapy TCR repertoire normalization and remission of autoimmune diseases. We have developed the Xcellerate™ Technology for the ex vivo activation and expansion of T cells. To expand T cells, peripheral blood mononuclear cells (PBMCs) are cultured with microscopic paramagnetic beads conjugated with anti-CD3 and anti-CD28 mAbs (Xcyte™Dynabeads®). T cells manufactured using this or a similar technology have been administered to patients with cancer and HIV in several clinical trials. In these studies, we and others have shown that the Xcellerate Technology can normalize skewed TCR repertoires in these patient populations. In the present study, we evaluated the use of the Xcellerate Technology to grow T cells from patients with autoimmune diseases such as rheumatoid arthritis, scleroderma, Crohn’s disease and systemic lupus erythematosus. We collected data on cytokine secretion, activation marker expression, cell expansion and TCR repertoire. T cells expanded an average of 1,325 fold (±1,592; range=16–6,532; n=35 patients), with nearly all cultures displaying marked CD25 and CD154 upregulation, and secretion of high levels of IFNγ and GM-CSF. Similar to results observed in cancer patients, TCR repertoire analysis showed that the Xcellerate Technology can normalize the skewed repertoires observed in autoimmune patients. Out of 12 PBMCs examined by spectratype analysis, one showed no TCR Vβ skewing prior to expansion, whereas the remaining 11 tissues displayed varying degrees of skewedness. After expansion, repertoire skewedness was decreased for all 11 samples. Repertoire normalization was dependent upon high-levels of TCR/CD28 engagement, which was achieved by initiating cultures using high bead to T cell ratios (Figure 1). Neither type of autoimmune disease, disease severity nor patient treatment (including: steroids, melphalan, infliximab, rapamycin, etc.) at the time of blood collection had an adverse effect on the ability to expand the patients’ T cells. Based on these results, the Xcellerate Technology may prove useful for generating healthy T cells from patients with autoimmune diseases which could then be used to restore the immune system following lymphoablative therapy. Studies are underway to further evaluate this approach. Figure Figure

Double Negative T Cells Influence TCR VB Variablity to Induce Allotolerance.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 759-759
Author(s):  
Zachariah A. McIver ◽  
Marcin Wlodarski ◽  
Jennifer Powers ◽  
Christine O’Keefe ◽  
Tao Jin ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
T Cells ◽  
T Cell ◽  
Regulatory T Cells ◽  
Peripheral Tolerance ◽  
Double Negative ◽  
Clonal Deletion ◽  
Tcr Repertoire ◽  
Double Negative T Cells

Abstract Immune alloresponsiveness following allogeneic HSCT is influenced by the dynamics of immune reconstitution and development of allotolerance. In general, tolerance is induced by thymic clonal deletion (central) and apoptosis or suppression of alloresponsive lymphocytes by regulatory T cells in the periphery. We have recently demonstrated that the size of the TCR repertoire within the CD4 and CD8 compartments can be assessed using VB spectrum by flow cytometry, and expansions/losses of individual TCR VB families can be used as a surrogate marker of TCR variability. (Exp. Hem.32: 1010–1022; Br. J. Haematol.129:411–419). Additionally, regulatory T cells can also impact the clonal contractions and expansions within the TCR VB repertoire. Various types of regulatory T cells have been described including CD4+CD25+, CD8+, NK T−cells, and CD3+CD4/CD8− double negative T cells (DN Tregs). In our current study we investigated the role of DN Tregs on the restoration of immune repertoire diversity. We hypothesized that alloresponsiveness clinically detected as a manifestation of GvHD may be associated with oligoclonal T−cell expansions, and in this context decreased numbers of regulatory T cells suggest deficient tolerizing function by regulatory T cells including DN Tregs. Here we studied a cohort of 60 HSCT recipients (AML, CML, CLL, NHL, AA, and PV), of which 25 patients received matched unrelated donor grafts and 35 received matched sibling donor grafts. Blood was sampled between 2003–2006 at monthly intervals after HSCT, and flow cytometry for TCR repertoire in CD4 and CD8 cells as well as the numbers of DN cells were recorded. Additionally, separate samples were collected for measurement of chimerism and were included in analysis when donor lymphoid chimerism was > 60%. A subset analysis was performed based on the presence/absence of GvHD. For the 27/60 (45%) patients with episodes of GvHD, results were obtained at the time of diagnosis of GvHD (grade > 2), while for patients in whom notable GvHD was not captured, the steady−state values at corresponding times were used for analysis. For all patients serial evaluations were available. For the purpose of this study, significant VB expansions/contractions were defined as +/− 2 standard deviation over the average VB family size. Using Cox proportional hazards analysis to identify univariate risk factors for GVHD, CD8 VB TCR contractions > 14 VB families (58.3% contraction of entire CD4 VB repertoire) constituted a strong indicator for increased risk (HR=7.61, p=0.011). This observation is consistent with the fact that oligoclonality of alloreactive T cell clones is frequently accompanied by a significant contraction/loss of remaining VB families and may herald heightened alloresponsiveness as a manifestation of GvHD. Estimation for correlation by Pearson’s correlation coefficient also demonstrated that percentage of DN cells strongly correlated with a normalization of CD4 VB TCR repertoire (lower number of expansions; N=57, R= −0.51, p=0.027), supporting our hypothesis that DN cells participate in peripheral tolerance and suppress proliferative, alloresponsive CD4 clones. In summary, our results further characterize TCR variability post HSCT and define the role of DN cells in the induction of allotolerance.

scholarly journals Targeted reconstruction of T cell receptor sequence from single cell RNA-sequencing links CDR3 length to T cell differentiation state

2016 ◽  
Author(s):  
Shaked Afik ◽  
Kathleen B. Yates ◽  
Kevin Bi ◽  
Samuel Darko ◽  
Jernej Godec ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cell Response ◽  
T Cell Response ◽  
Effector Memory ◽  
Cell State ◽  
Tcr Repertoire ◽  
Single Cell Rna Sequencing

ABSTRACTThe T cell compartment must contain diversity in both TCR repertoire and cell state to provide effective immunity against pathogens1,2. However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell state at the single cell level because most analysis of the TCR repertoire has, to date, aggregated information from populations of cells. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current protocols to directly sequence the TCR require the use of long sequencing reads, increasing the cost and decreasing the number of cells that can be feasibly analyzed. Here we present a tool that can efficiently extract TCR sequence information from standard, short-read scRNA-seq libraries of T cells: TCR Reconstruction Algorithm for Paired-End Single cell (TRAPeS). We apply it to investigate heterogeneity in the CD8+T cell response in humans and mice, and show that it is accurate and more sensitive than previous approaches3,4. We applied TRAPeS to single cell RNA-seq of CD8+T cells specific for a single epitope from Yellow Fever Virus5. We show that the recently-described "naive-like" memory population of YFV-specific CD8+T cells have significantly longer CDR3 regions and greater divergence from germline sequence than do effector-memory phenotype CD8+T cells specific for YFV. This suggests that TCR usage contributes to heterogeneity in the differentiation state of the CD8+T cell response to YFV. TRAPeS is publicly available, and can be readily used to investigate the relationship between the TCR repertoire and cellular phenotype.

scholarly journals Selective Cell State in the Clonally Expanded T-Cell Compartment of Vκ*MYC Mice Responding to Treatment with Checkpoint Inhibitors

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1581-1581
Author(s):  
Danielle C Croucher ◽  
Laura M Richards ◽  
Zhihua Li ◽  
Ellen nong Wei ◽  
Xian Fang Huang ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
T Cell ◽  
Mouse Model ◽  
Single Cell ◽  
Research Funding ◽  
Genetically Engineered ◽  
Cell State ◽  
Genetically Engineered Mouse Model ◽  
Tcr Repertoire

Abstract Introduction: Immune checkpoint receptor (ICR) blockade has emerged as an effective anti-tumour modality, but only in a subset of cancer patients. Moreover, in Multiple myeloma (MM), single-agent activity has not been observed, highlighting the need to better understand the mechanism of action of this class of drugs. We recently showed that combinatorial ICR blockade using αLAG3 and αPD-1 delays disease progression and improves survival in the transplantable Vκ*MYC model of MM (Croucher et al. ASH 2018). However, despite this being a controlled study with genetically-homogeneous tumours, anti-tumour immune responses were heterogeneous, with only a subset of mice demonstrating a delay in tumour progression (17/29 mice, response rate = 58.6%). Thus, using this model, we set out to define mechanisms underlying variability in response to ICR blockade. Methods: We established a cohort of mice by engrafting 5-week-old C57BL/6 mice with Vκ12598 cells via tail vein injection. Treatment with αLAG3/αPD-1 or Ig-control was initiated 1-week post-engraftment and bone marrow (BM) samples were collected 3 weeks after the start of treatment. Following FACS-enrichment of T cells and plasma cells (PCs), single cell suspensions were subjected to matched single-cell gene expression (5' scRNA-seq) and T cell receptor (TCR)/B cell receptor (BCR) profiling (10x Genomics). Results: Samples were selected for profiling based on response to treatment, with responders (n=4) defined by significantly lower disease burden compared to non-responders (n=3) and control-treated mice (n=5), as measured by serum M-protein and %PCs in BM/spleen at sacrifice. Unsupervised clustering of scRNA-seq data from PCs (n=3,318 cells) identified no gene expression or BCR repertoire differences between control and treated, or between responder and non-responder samples, supporting that variability in response was not related to malignant Vκ12598 cells themselves. Across all samples, a statistically significant difference was not detected between the total number of unique TCR sequences (clonotypes) comparing control-treated (351-2369), non-responders (1185-2327) and responders (1378-1698), with no overlapping TCR sequences between top clonotypes. Evaluation of TCR repertoire diversity revealed that αLAG3/αPD-1 treatment induces clonal T cell expansion in control versus treated mice, but this was not significantly different between responders and non-responders. Analysis of paired scRNA-seq data (n=21,520 cells) revealed that expanded T cells from αLAG3/αPD-1-treated mice occupy a different cell state in responder vs. non-responder mice. We speculate that underlying differences in the TCR repertoire may dictate the downstream phenotype of expanded, anti-tumour T cells in mice treated with combinatorial αLAG3/αPD-1. Tumour control following treatment was associated with clonal expansion of T cells expressing genes related to cytoxicity and activation (Ccl5, Ifng, Fasl, Gzmb), whereas tumour progression was associated with clonal expansion of proliferative T cells (Cdkn3, Birc5, Ccna2, Aurka, Mki67). Although T cell proliferation is typically a phenotype ascribed to effector T cells, recent studies have similarly observed this proliferative cell state in dysfunctional T cells within melanoma tumours. Moreover, emerging evidence supports suppression of T cell proliferation by CDK4/6 inhibitors as a means to augment anti-tumour activity of ICR-based therapy. Thus, studies exploring whether reversal of the observed proliferative T cell state can restore response to αLAG3/αPD-1 treatment in non-responding Vκ12598 mice are ongoing and will be reported. Conclusions: ICR inhibitors demonstrate significant activity in some cancers, however many patients fail to respond and a similarly promising level of efficacy has not been achieved in MM. Studies aimed at unraveling the mechanisms of response and resistance to ICR inhibitors are therefore needed to improve the utility of this class of drugs for all patients. Our approach of using paired single-cell gene expression and TCR repertoire profiling has enabled identification of molecular cell states specifically in expanded T cells of responder vs. non-responder mice. In turn, our work nominates novel mechanisms that may be used as potential biomarkers for anti-tumour immune responses as well as potential targets to augment responses to ICR blockade therapy. Disclosures Chesi: Abcuro: Patents & Royalties: Genetically engineered mouse model of myeloma; Novartis: Consultancy, Patents & Royalties: human CRBN transgenic mouse; Pfizer: Consultancy; Pi Therapeutics: Patents & Royalties: Genetically engineered mouse model of myeloma; Palleon Pharmaceuticals: Patents & Royalties: Genetically engineered mouse model of myeloma. Bergsagel: GSK: Consultancy, Honoraria; Genetech: Consultancy, Honoraria; Janssen: Consultancy, Honoraria; Oncopeptides: Consultancy, Honoraria; Novartis: Consultancy, Honoraria, Patents & Royalties: human CRBN mouse; Pfizer: Consultancy, Honoraria; Celgene: Consultancy, Honoraria. Sebag: Janssen: Research Funding; Bristol Myers-Squibb: Consultancy, Honoraria; Takeda: Consultancy, Honoraria; Novartis: Consultancy, Honoraria; Amgen: Consultancy, Honoraria; Sanofi: Consultancy, Honoraria; Karyopharm Therapeutics: Consultancy, Honoraria. Trudel: BMS/Celgene: Consultancy, Honoraria, Research Funding; Amgen: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; GlaxoSmithKline: Consultancy, Honoraria, Research Funding; Roche: Consultancy; Sanofi: Honoraria; Pfizer: Honoraria, Research Funding; Genentech: Research Funding.

scholarly journals A peripheral CD4+ T cell precursor for naive, memory, and regulatory T cells

2010 ◽  
Vol 207 (13) ◽  
pp. 2883-2894 ◽  
Author(s):  
Chunfang Zhao ◽  
Joanna D. Davies
Keyword(s):  
T Cells ◽  
T Cell ◽  
Regulatory T Cells ◽  
Cell Receptor ◽  
Cd4 T Cell ◽  
Interleukin 7 ◽  
Cell Pool ◽  
Tcr Repertoire ◽  
B Cell Leukemia ◽  
Cd4 Cell

Mechanisms that control the size of the T cell pool, the ratio between naive cells and memory cells, the number and frequency of regulatory T cells, and T cell receptor (TCR) diversity are necessary to maintain immune integrity and avoid disease. We have previously shown that a subset of naive CD4+ T cells, defined by the expression on their surface of a very low density of CD44 (CD44v.low cells), can inhibit wasting and wasting-associated lymphopenia in mice with cancer. In this study, we further investigate the properties of CD44v.low cells and show that they are significantly more efficient than the remaining naive (CD44low or CD44int) and memory CD4+ cell subsets in reconstituting the overall size of the CD4+ T cell pool, creating a T cell pool with a diverse TCR repertoire, generating regulatory T cells that express forkhead box P3 (FoxP3), and promoting homeostatic equilibrium between naive, memory, and Foxp3+ regulatory T cell numbers. T cell population reconstitution by CD44v.low cells is thymus independent. Compared with CD44int cells, a higher percentage of CD44v.low cells express B cell leukemia/lymphoma 2, interleukin-7 receptor, and CD5. The data support a key role for CD4+ CD44v.low cells as peripheral precursors that maintain the integrity of the CD4+ T cell pool.

Sign in / Sign up

Export Citation Format

Share Document