scholarly journals Expression profiling of TCR-engineered T cells demonstrates overexpression of multiple inhibitory receptors in persisting lymphocytes

Blood ◽  
2013 ◽  
Vol 122 (8) ◽  
pp. 1399-1410 ◽  
Author(s):  
Daniel Abate-Daga ◽  
Ken-ichi Hanada ◽  
Jeremy L. Davis ◽  
James C. Yang ◽  
Steven A. Rosenberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Tumor Antigen ◽  
Expression Profiling ◽  
Inhibitory Receptors ◽  
Key Points ◽  
Engineered T Cells

Key Points Gene expression in TCR-engineered cells resembles that of virus-reactive cells more than native tumor antigen-reactive cells. Persisting TCR gene–engineered T cells are sensitive to PD-L1–PD-1 interaction but CD160-associated impairment is ligand-independent.

scholarly journals Gene expression profiling-based risk prediction and profiles of immune infiltration in diffuse large B-cell lymphoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Selin Merdan ◽  
Kritika Subramanian ◽  
Turgay Ayer ◽  
Johan Van Weyenbergh ◽  
Andres Chang ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
B Cell ◽  
Risk Prediction ◽  
Expression Profiling ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Gene Signatures ◽  
Large B Cell Lymphoma ◽  
Large B Cell

AbstractThe clinical risk stratification of diffuse large B-cell lymphoma (DLBCL) relies on the International Prognostic Index (IPI) for the identification of high-risk disease. Recent studies suggest that the immune microenvironment plays a role in treatment response prediction and survival in DLBCL. This study developed a risk prediction model and evaluated the model’s biological implications in association with the estimated profiles of immune infiltration. Gene-expression profiling of 718 patients with DLBCL was done, for which RNA sequencing data and clinical covariates were obtained from Reddy et al. (2017). Using unsupervised and supervised machine learning methods to identify survival-associated gene signatures, a multivariable model of survival was constructed. Tumor-infiltrating immune cell compositions were enumerated using CIBERSORT deconvolution analysis. A four gene-signature-based score was developed that separated patients into high- and low-risk groups. The combination of the gene-expression-based score with the IPI improved the discrimination on the validation and complete sets. The gene signatures were successfully validated with the deconvolution output. Correlating the deconvolution findings with the gene signatures and risk score, CD8+ T-cells and naïve CD4+ T-cells were associated with favorable prognosis. By analyzing the gene-expression data with a systematic approach, a risk prediction model that outperforms the existing risk assessment methods was developed and validated.

scholarly journals 88 Evidence of enhanced immune activation within the tumor microenvironment and the circulation of female patients with high-risk melanoma compared to males

2021 ◽  
Vol 9 (Suppl 3) ◽  
pp. A96-A96
Author(s):  
Mariam Saad ◽  
Aik Choon Tan ◽  
Issam El Naqa ◽  
Sandra Lee ◽  
F Stephen Hodi ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Expression Profiling ◽  
Female Gender ◽  
National Institutes Of Health ◽  
Female Patients ◽  
High Risk Melanoma ◽  
Risk Melanoma ◽  
Male Patients ◽  
Written Informed Consent

BackgroundSex differences in tumor immunity and response to immunotherapy were shown in murine models and descriptive analyses from recent clinical trials. We recently reported that female gender is a favorable prognostic marker for survival benefit following ipilimumab and high dose interferon-alfa (HDI) adjuvant therapy of high-risk melanoma in the ECOG-ACRIN E1609 trial (N=1670). Therefore, we investigated differences in candidate immune biomarkers in the circulation and tumor microenvironment (TME) of female and male patients.MethodsGene expression profiling (GEP) was performed on the tumor biopsies of 718 (454 male, 264 female) patients. The primary endpoint was mRNA expression profiling using U133A 2.0 Affymetrix gene chips. Raw microarray data sets were normalized by using the Robust Multi-array Average (RMA) method using Affymetrix Power Tools (APT) as previously published. Multiple probe sets representing the same genes were collapsed by using the probe with maximum gene expression. Gene set enrichment analysis (GSEA) was performed by comparing the female and male tumor samples, and gene sets with FDR q-value <0.1 were deemed as significant. Similarly, peripheral blood (serum and PBMC) samples were tested for soluble (Luminex) and cellular (multicolor flow cytometry) prognostic biomarkers in a subset of patients (N=321; 109 female and 212 male). All patients provided an IRB-approved written informed consent.ResultsAmong the subset of patients tested for circulating biomarkers, females were significantly younger than males (P=0.03). Testing PBMCs, the percentages of CD3+ T cells (P=0.04) and CD3+CD4+ helper T cells (P=0.0005) were significantly higher in female patients compared to males. Also, there were trends toward higher levels of proinflammatory cytokines IL1beta (P=0.07) and IL6 (P=0.06) in females. On the other hand, males had significantly higher percentages of monocytes (P=0.03). Further, there were trends toward higher percentages of CD3+/CD4+/CD25hi+/Foxp3+ (P=0.1) and CD3+/CD4+/CD25+/CD127low+ (P=0.1) T-reg in male patients compared to females. Among the cohort of patients (N=718) with tumor GEP data, females were significantly younger than males (P=0.0009). GEP identified pathways and genes related to immune cell infiltration and activation that were significantly enriched in the tumors of females compared to males (table 1).Abstract 88 Table 1Immune pathways significantly enriched in tumors of femalesConclusionsFemale gender was associated with adjuvant immunotherapeutic benefits and female patients were more likely to have evidence of immune activation within the TME and the circulation, supporting a potentially important role for female related factors in the immune response against melanoma, and these require further investigation.AcknowledgementsWe are grateful to the patients and family members who participated in the E1609 trial and the E1609 trial investigators. This study was conducted by the ECOG-ACRIN Cancer Research Group (Peter J. O’Dwyer, MD and Mitchell D. Schnall, MD, PhD, Group Co-Chairs) and supported by the National Cancer Institute of the National Institutes of Health under the following award numbers: U10CA180794, U10CA180820, U10CA180888, UG1CA233180, UG1CA233184. Biomarkers studies were supported under the following award number: P50CA12197310 (Tarhini and Kirkwood). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.Trial RegistrationNCT01274338Ethics ApprovalThe E1609 study protocol was approved by the institutional review board of each participating institution and conducted in accordance with Good Clinical Practice guidelines as defined by the International Conference on Harmonization. All patients provided an IRB-approved written informed consent.ConsentNot applicable.

scholarly journals Preclinical targeting of human acute myeloid leukemia and myeloablation using chimeric antigen receptor–modified T cells

Blood ◽  
2014 ◽  
Vol 123 (15) ◽  
pp. 2343-2354 ◽  
Author(s):  
Saar Gill ◽  
Sarah K. Tasian ◽  
Marco Ruella ◽  
Olga Shestova ◽  
Yong Li ◽  
...  
Keyword(s):  
T Cells ◽  
Acute Myeloid Leukemia ◽  
Mouse Models ◽  
Chimeric Antigen Receptor ◽  
Myeloid Leukemia ◽  
Antigen Receptor ◽  
Key Points ◽  
Human Acute Myeloid Leukemia ◽  
Engineered T Cells ◽  
Acute Myeloid

Key Points Targeting of CD123 via CAR-engineered T cells results in rejection of human AML and myeloablation in mouse models.

scholarly journals Targetable subsets of non-Hodgkin lymphoma in Malawi define therapeutic opportunities

2016 ◽  
Vol 1 (1) ◽  
pp. 84-92 ◽  
Author(s):  
Elizabeth A. Morgan ◽  
M. Patrick Sweeney ◽  
Tamiwe Tomoka ◽  
Nadja Kopp ◽  
Daniel Gusenleitner ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Hodgkin Lymphoma ◽  
Expression Profiling ◽  
Resource Constraints ◽  
Objective Assessment ◽  
Non Hodgkin Lymphoma ◽  
Key Points ◽  
Targeted Gene Expression

Key Points NHL subclassification is lacking in Malawi due to resource constraints yet is critical for directing therapy. Targeted gene expression profiling facilitates objective assessment and segregation of biologically defined subsets of NHL from Malawi.

scholarly journals Cardiovascular toxicity and titin cross-reactivity of affinity-enhanced T cells in myeloma and melanoma

Blood ◽  
2013 ◽  
Vol 122 (6) ◽  
pp. 863-871 ◽  
Author(s):  
Gerald P. Linette ◽  
Edward A. Stadtmauer ◽  
Marcela V. Maus ◽  
Aaron P. Rapoport ◽  
Bruce L. Levine ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell Receptors ◽  
Cardiac Toxicity ◽  
Cross Reactivity ◽  
Cardiovascular Toxicity ◽  
Protein Motifs ◽  
Alternative Protein ◽  
Key Points ◽  
Engineered T Cells ◽  
Target Effects

Key Points Engineered T-cell receptors can have redundant recognition of alternative protein motifs, resulting in severe cardiac toxicity. The use of induced pleuripotent stem cells (iPSCs) is a promising approach to identify potential off-target effects of engineered T cells.

Nonsense-Mediated mRNA Decay Is Essential for the Hematopietic Compartement.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 506-506
Author(s):  
Joachim Weischenfeldt ◽  
Inge Damgaard ◽  
David Bryder ◽  
Claus Nerlov ◽  
Bo Porse
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
T Cells ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Mrna Decay ◽  
Double Positive ◽  
Mrna Pool ◽  
Nonsense Mediated Mrna Decay

Abstract Nonsense-mediated mRNA decay (NMD) is a conserved cellular surveillance system that degrades mRNAs with premature termination codons (PTCs). PTC-containing transcripts can arise from faulty events such as erroneous mRNA processing events as well as mutations, and their translation may lead to the synthesis of deleterious proteins. In addition to serving as a genomic protection system, experiments in tissue culture cells have demonstrated that NMD regulates 5% of the normal mRNA pool suggesting that the NMD pathway may have a broader role in gene regulation. Finally, NMD has also been proposed to be important during lymphocyte development as a tool of riding the cells of transcripts resulting from unproductive re-arrangements events of T cell receptor and immunoglobulin genes. Although NMD has been studied extensively at the biochemical level, the actual role and importance of NMD in the mammalian organism has not been investigated. We therefore generated a conditional Upf2 knock-out mouse line (UPF2 being an essential NMD factor) which we crossed to different hematopoietic relevant Cre expressing lines. Full ablation of UPF2 (using the inducible Mx1-Cre deleter) led to complete loss of all nucleated cells in the bone marrow and death of the animals within 10 days. A similar phenotype was observed when Upf2fl/fl; Mx1Cre BM cells were transplanted into lethally irradiated WT recipients and induced with poly-IC, demonstrating the cell autonomous nature of the phenotype. Deletion of UPF2 in the myeloid lineage using the LysM-Cre deleter resulted in efficient ablation of UPF2 and the absence of NMD in reporter transfected bone marrow derived macrophages (BMDMs). However, the steady state levels of myeloid cells appeared unaltered. Finally, deletion of UPF2 in T cells using a Lck-Cre deleter led to a marked reduction of both CD4/CD8 double-positive and single-positive T cells and accumulation of PTC containing transcripts. Gene expression profiling experiments of BMDM and thymocytes from WT and UPF2-ablated animals identified a common core set of 27 up-regulated genes consistent with the role of NMD as a mRNA degrading system. The gene expression profiling data suggest that ablation of NMD leads to accumulation of unfolded proteins. In summary, these studies demonstrate the vital and cell-autonomous role of NMD in the hematopoietic system.

Gene Expression Profiling Implicates Attenuation of NFkB Signalling By Regulatory T Cells in Modulating Dendritic Cell Function

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3068-3068
Author(s):  
Lindsay Nicholson ◽  
Emily Mavin ◽  
Lynne Minto ◽  
Julie Irving ◽  
Anne Dickinson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Flow Cytometry ◽  
T Cells ◽  
Regulatory T Cells ◽  
Gene Expression Profiling ◽  
Pathway Analysis ◽  
Expression Profiling ◽  
Expression Profiles ◽  
Antigen Presenting ◽  
Unique Genes

Abstract Dendritic cells (DC) play a key role in the pathogenesis of Graft versus Host Disease (GvHD), a complication of haematopoietic stem cell transplantation and offer an attractive target for therapy. Regulatory T cells (Treg) have a potent immunoregulatory effect on the maturation and the antigen-presenting cell (APC) function of DC and adoptive transfer of Treg is highly efficacious in the induction of tolerance in an experimental model of GvHD and has entered Phase I clinical trials. Several mechanisms of suppression have been proposed, including Treg acting directly on DCs, attenuating their antigen-presenting and co-stimulatory functions by arresting their maturation. However, the molecular basis underpinning these effects in DCs remains ill-defined. We investigated the effect of Treg treatment on DCs by conducting gene expression profiling and confirmed the functional consequences using downstream assays. Immature, mature and Treg-treated DCs were generated from immuno-magnetic isolated monocytes (im-DC, mat-DC and Treg-DC, respectively) and moDC populations were generated using a well-established 6 day culture with GM-CSF and IL-4, followed by 24 hour LPS maturation. Treg were added on day 3 of culture at a 3:1 ratio. All cell populations were harvested on day 7 and sorted via FSC/SSC/CD3neg gating to remove Treg present in the co-culture and control for any changes in gene expression caused by shear stress. Gene expression profiling was carried out using the Illumina HumanHT12 microarray platform. Data was processed using R/Bioconductor workflows and the functional significance of differentially expressed genes was evaluated using Ingenuity Pathway Analysis software. Mat-DC and Treg-DC expression profiles were compared relative to the im-DC for data analysis. Upon LPS treatment, the levels of 1834 unique genes were differentially regulated in mat-DC by at least twofold (862 genes upregulated/972 downregulated) compared to the im-DC counterparts. In the Treg-DC, 1326 unique genes were differentially modulated (633 genes upregulated/693 genes downregulated). Microarray analysis of the CD markers identified a higher expression of the previously identified surface markers CD80, CD83 and CD86 in the mat-DC compared to the Treg-treated counterpart (validated by flow cytometry), confirming the semi-mature phenotype. Novel findings from the dataset include the reduction of the endocytotic-related genes, CD206 and CD209, in the Treg-DCs compared to the im-DC and this reduction manifested functionally in an impaired antigen uptake, as assessed by FITC-Dextran. Additionally, the surface marker, CD38, was downregulated in the Treg-DC compared to the mat-DC, confirmed by flow cytometry. CD38 has been shown to be NFκB-dependent and a marker of maturation in monocyte-derived DCs, further supporting the semi-mature phenotype. Furthermore, CD38 is functionally involved in CD83 expression and IL-12 induction. We assessed IL-12 cytokine secretion by Treg-treated DCs and showed a significantly reduced level of induction compared to mat-DC (p=0.0079). Pathway analysis revealed NFκB-related genes to be downregulated in the Treg-DC compared to the mat-DC. These differentially expressed genes included the TLR-adaptor protein, MYD88, the NFκB subunit, RELB and an inhibitor of NFκB, NFκB1A. This finding, coupled to the importance of NFκB signalling pathway in DC function, prompted us to investigate it at the functional level by measuring levels of phosphorylation of serine 536 of the RelA subunit as a marker of activity in response to LPS stimulation. DC cultured in the absence of Tregs (mat-DC) showed significantly higher levels of Ser536 phosphorylation when compared to those unstimulated cells (im-DC) (p= 0.0018). Concordant with the gene expression data, Treg-treated DCs (Treg-DC), showed a significantly attenuated NFκB activation when compared to their LPS-stimulated DCs counterparts (p = 0.0191), however, signalling was not completely abolished compared to those unstimulated DCs (p= 0.0003). In conclusion, gene expression profiles of Treg-treated DCs are significantly different to their mat-DC and im-DC counterparts. Here, we present the novel finding that Tregs modulate DC function, in part, by attenuation of the NFkB signalling pathway, arresting the DCs at a semi-mature phenotype, as evidenced by expression arrays and functional assays. Disclosures No relevant conflicts of interest to declare.

Enhancing Cytotoxicity of Autologous T Cells in AML By Blockade of CTLA-4 and PD-1

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4057-4057 ◽  
Author(s):  
Kirsten Marie Boughan ◽  
Xiaohua Chen ◽  
Paul Szabolcs
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
T Cell ◽  
T Cell Activation ◽  
Cell Response ◽  
Conflicts Of Interest ◽  
Expression Profiles ◽  
T Cell Response ◽  
Inhibitory Receptors

Abstract Background: AML remains a disease diagnosed in the aging population with chemotherapy followed by bone marrow transplant in some cases being the standard of care. Although response rates remain around 50-60%, treatment related mortality and disease relapse remain high. Adoptive immunotherapy, especially those targeting T cell co-inhibitory receptors, has proven successful in solid malignancies however, AML remains less explored. Our laboratory has previously demonstrated the feasibility to generate autologous AML reactive T cells in vitro (Mehta/Szabolcs; Immunotherapy 2016). It was noted that "resistant" AML blasts over expressed a number of genes associated with immunosuppressive characteristics. Over expression of these genes may induce T cell functional exhaustion. Therefore, we hypothesized that blocking PD-1 and/or CTLA-4 during co-culture with IFNg activated AML blasts, may enhance T cell activation and cytotoxicity. To test this hypothesis, we tested CTL responses against AML blasts and IFNg ELISpot formation after blocking with PD-1, CTLA-4 or both receptors, and compared the response in untreated T cells. Gene expression profiles of co-stimulatory/co-inhibitory receptors were also monitored to test for correlation. Methods: We evaluated 12 patients with newly diagnosed AML under an IRB approved protocol with written informed consent of patients. Mononuclear cell preparation was generated from fresh marrow samples or drawn from a biorepository of previously cryopreserved leukophereses. T cells were then purified using immunomagnetic CD3/CD28 beads (Life technologies) and cultivated in media with IL-2 and IL-7 for 2 weeks. AML blasts were cultured over a supporting layer of mesenchymal stromal cells (MSCs) derived from healthy BM donors for 1 week and then cryopreserved. T cells were then co-cultured with restored and irradiated autologous AML cells at an effector: target (E: T) ratio of 5:1 to 40:1. AML and T cells were co-cultured in the presence of Ipilimumab (anti-CTLA-4), or Nivolumab (anti-PD-1), or a combination of both drugs. T cells and AML were re stimulated in X-vivo 15 with IL-12, IL-15 and IL-2 weekly x 3weeks. T cell response to AML was quantitated by IFNg ELISpot assay and Europium TDA (EuTDA) CTL assays independently. Co-stimulatory/co-inhibitory expression on T cells was examined with RT-q PCR assay. Paired-sample student t test was used for statistical analysis with p<0.05. Results and Discussion: Out of 12 samples, 10 (83%) yielded viable AML cells available for cytotoxicity assay. One third (33%) of co-cultures exhibited a positive T cell response in CTL assays ("killers"). There was no difference in CTL activity by blockade of either PD-1 or CTL-4 (Fig 1). IFN-ɣ spot formation in ELISpot was observed in 4/10 samples (40%) with statistical significance noted in cells blocked with PD-1 as compared to all other blockade types (Fig 2). The results indicated that in vitro priming with autologous AML blasts or together with blocking PD-1 can enhance T cell response in 33-40%. By gene expression analysis, the ratio of co-stimulatory to co-inhibitory genes was calculated. In PD-1 blocked cells, the ratio of activation/inhibition was not impacted in T cells from "killers" (0.9; p=0.1), however, T cells from "non-killer cells" had a diminished ratio due to higher expression of co-inhibitory molecules (0.4; p=0.04) (Fig 3). This trend was also present in CTLA-4 blocked cells (0.85; p=0.4 in killers vs 0.54; p=0.03 in non-killers) (data not shown). Interestingly, dual blockage failed to influence gene expression ratio, data not shown. Conclusion: The above studies demonstrate that cytotoxicity can be achieved in T cells when primed against autologous AML. PD-1 blockade can enhance IFNg production and cytotoxic responses, but CTLA-4 and dual blockade failed to enhance T cell function. The upregulation of an inhibitory pattern of genes in T cells that did not express cytotoxicity (non-killers) could allude to an "inhibitory phenotype" that may be resistant to immunotherapy drug blockade and requires further study. Disclosures No relevant conflicts of interest to declare.

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