Effect of CD19-CD28 and glofitamab treatments in vivo on the RNA-Seq profile in tumor tissue from humanized mice over time
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE260674 | GEO | 2024/03/03
REPOSITORIES: GEO
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Project description:Alternative splicing consists of exons that are selectively either included or excluded from the mature mRNA transcript. Previous studies have demonstrated that ~10-15% of alternatively spliced genes undergo signal-induced changes in isoform abundance in activated primary human CD4+ T cells. In the past, signal-induced alternative splicing changes in T cells have been characterized in the context of CD3 and CD28 activation. CD3 is a component of the T Cell Receptor (TCR) which is responsible for recognizing foreign peptides presented on antigen presenting cells. CD28 enhances various signaling events downstream of the TCR to boost the survival of T cells and is required for full T cell stimulation. The contribution of CD28 signaling to transcriptional changes has been well documented, but the impact on splicing has not been investigated. Here we test the hypothesis that CD28 exerts some of its functional impact through the enhancement of splicing changes in stimulated T cells. We utilized poly(A) RNA-seq and the MAJIQ alternative splicing algorithm to analyze splicing events of human CD4+ T cells stimulated with through CD3 in the presence and absence of co-stimulation with CD28. Consistent with previous studies, we identified approximately 400 and 1,000 significant splicing events induced by CD3/CD28 stimulation at 8 and 48 hours of culture, respectively. Alternative splicing changes induced by CD3 and CD3/CD28 stimuli are highly correlative, however, approximately 23% of alternative splicing changes are further enhanced with additional CD28 costimulation at 8 hours of culture. This enhancement drops to 8% of alternative splicing events by 48 hours. Therefore, we conclude that CD28 costimulation increases the magnitude of splicing during T cell activation, in a manner that is eventually compensated for over time with CD3 stimulation alone.
2020-06-13 | GSE135118 | GEO
Project description:The local mechanisms regulating exhaustion of tumor-infiltrating lymphocytes (TILs) and responsiveness to PD-1 blockade remain partly elucidated. In human ovarian cancer we show that tumor-reactive intraepithelial (ie)CD8+ TILs engaged by antigen are polyfunctional and upregulate PD-1, which restrains their effectiveness. PD-1+ TILs exhibit a continuum of TCR-engaged/exhausted states with variable effector fitness related to CD28 costimulation, which they receive in intraepithelial niches involving myeloid antigen-presenting cells (mAPC). Following PD-1 blockade, activation of TILs requires CD28 costimulation mediated in situ by tumor mAPCs, which is locally enhanced by CTLA-4 blockade. CD40 ligand also amplifies TIL responses in situ, especially in tumors in which mAPCs are not activated. Thus, dysfunctional and exhausted TILs, in a state of TCR engagement but without proper CD28 costimulation by mAPCs in situ, are unlikely to fully benefit from PD-1 blockade.
2021-10-12 | GSE178245 | GEO
Project description:The aim of the study was to compare the two different costimuli anti-CD28 (costimulus 2a) and IL-2 (costimulus 2b) – in the presence of a suboptimal anti-CD3 signal (signal 1) – on the de novo activation of freshly purified human naive T cells. To this end, purified human naive T cells were co-incubated for seven days with a tumor vaccine which consisted of gamma-irradiated and Newcastle Disease Virus (NDV)-infected MCF-7 cells (a well-defined mammacarcinoma cell line). The gamma-irradiation dose was 200 Gray (Gy) to suppress the proliferation capacity of the vaccine cells (although the vaccine cells are not killed by such a procedure but still survive for several days); NDV-infection was performed at a dose of 100 hemagglutination units (HU) per 10^7 vaccine cells. The latter led – among others – to the upregulation of the viral surface molecules hemagglutinin neuraminidase (HN) and the fusion protein (F), both of which can serve for the attachment of fusion proteins delivering the activation signals to the naive T cells. The bispecific (bs) fusion proteins used in this study were of the single chain (scFv) format, binding with one arm to the viral HN molecule (for the attachment to the vaccine cells), and with the other arm either to the T cell receptor (TCR)-associated CD3 complex [as a surrogate of a major histocompatibility complex (MHC)-presented peptide recognized by the TCR] (bsHN-CD3), or to the costimulatory molecule CD28 (bsHN-CD28). Furthermore, a bispecific fusion protein containing the human interleukin (IL)-2 (bsHN-IL-2, a so-called immunocytokine) was used. The gene expression analysis of the differentially activated naive T cells revealed that in the presence of a suboptimal dose of anti-CD3 the two costimuli anti-CD28 (sample d7-S2_280705) and IL-2 (sample d7-S3_280705) led to a highly redundant pattern of gene upregulation in comparison to control samples in which naive T cells received only anti-CD3 (sample d7-S4_280705), anti-CD28 (sample d7-S5_280705) or IL-2 (sample d7-S6_280705) signals alone, or no signal at all (i.e. only vaccine cells; sample d7-S7_280705). All signals were compared to the reference sample which consisited of freshly isolated, non-activated naive T cells (sample d0-S1_280705). Global analysis of the gene expression showed that full naive T cell activation by anti-CD3/anti-CD28 and anti-CD3/IL-2 led to a significant upregulation of 76 and 71 genes, respectively (upregulation was considered to be significant if the relative gene expression was more than 5-fold than in the reference sample). However, the suboptimal anti-CD3 stimulus alone upregulated only 31 genes, the anti-CD28 stimulus alone only 6 genes, and the IL-2 stimulus alone only 22 genes. Naive T cells that reveived virus-modified vaccine cells alone upregulated 18 genes. Equally upregulated genes in anti-CD3/anti-CD28 and anti-CD3/IL-2 activated naive T cells comprised genes coding for both (i) signalling and (ii) effector molecules. Concerning signalling molecules, both costimuli induced the nuclear factor (NF)-kappa B and nuclear factor of activated T cells (NF-AT) pathway via the key enzymes protein kinase C (PKC)-theta and phospholipase C (PLC)-gamma 1, respectively. Of special note was that signalling molecules of the CD28-mediated stress-activated protein kinase (Sapk) pathway, namely Vav-1, Rac-1 and Jnk-2, were also upregulated by IL-2 costimulation. Upregulated genes coding for effector molecules could be classified into different functional groups: namely regulators of apoptosis, cell adhesion, receptors/ligands and cytokines/chemokines. Some examples of effector molecule-coding genes similarly upregulated in anti-CD3/anti-CD28 and anti-CD3/IL-2 stimulated naive T cells, respectively, were for instance the cell adhesion molecules LFA-1 and CD2, or members of the TNF and TNF receptor superfamilies such as CD27, CD70, CD40 ligand, Fas ligand, as well as TNF-alpha and TNF-beta (and their corresponding receptors). Among apoptosis-related genes, the anti-apoptotic gene bcl-XL as well as the pro-apoptotic gene caspase 9 were upregulated. The latter – together with the observed upregulation of cytotoxic T lymphocytes-associated protein (CTLA)-4 – might be interpreted as an indication of cellular events occurring seven days after stimulation which are aiming at termination of the response. Furthermore, the microarray analysis also revealed and upregulation of the receptor for interferon (IFN)-gamma inducible protein of 10 kDa (IP-10), namely CXCR3, of the IL-12 receptor beta-chain and of the IL-15 receptor alpha-chain; these are often seen in close association with T cell activation in general, with T cell proliferation and with generation of memory T cells. It is also of interest to mention the upregulation of beta-actin which is required for a re-organization of the cytoskeleton and the 40-fold upregulation of the metabolic enzyme glyceraldehye-3-phosphate dehydrogenase (GAPDH) which provides ATP necessary for the increased metabolism of the activated cells. A summary of the interesting gene subset is attached as a supplementary table (including the pairwise compared normalized data). In summary, these data suggest a synergism and cross-talk between the two costimulatory pathways mediated by anti-CD28/CD28 and IL-2/IL-2 receptor, respectively. Keywords: Human naive T cells, activation, costimulation, anti-CD28, IL-2, signal transduction, tumor vaccine, immunocytokine
2009-12-17 | GSE6888 | GEO
Project description:TC-510 is a novel cell therapy that consists of autologous genetically engineered T cells expressing two synthetic constructs: first, a single-domain antibody that recognizes human Mesothelin, fused to the CD3-epsilon subunit which, upon expression, is incorporated into the endogenous T cell receptor (TCR) complex and second, a PD-1:CD28 switch receptor, which is expressed on the surface of the T cell, independently from the TCR. The PD-1:CD28 switch receptor comprises the PD-1 extracellular domain fused to the CD28 intracellular domain via a transmembrane domain. Thus, the switch is designed to produce a costimulatory signal upon engagement with PD-L1 on cancer cells.
| 2740481 | ecrin-mdr-crc
Project description:We observed self-activation of SKM-CAR-T cells which target novel mesothelioma antigen. CAR-T with CD28 costimulatory domain showed signs of exhaustion while those with 4-1BB costimulatory domain did not. To elucidate molecules responsible for self-activation-induced exhaustion, we performed RNA-seq analysis of SKM-CAR-T cells with CD28 or 4-1BB and CD19-CAR-T cells with CD28 or 4-1BB.
2022-08-19 | GSE211352 | GEO
Project description:We report the differential gene expression between anti-CD3/CD28 stimulated WT and LRCH1-deficient CD8+ T cells. Improving cytotoxicity, proliferation and infiltration ability of CD8+ T cells is critical in T cell immunotherapies against tumors. This study has identified LRCH1 as a negative regulator of LAT-mediated TCR signal transduction, as LRCH1 inhibits LAT signalosome formation and facilitates the endocytosis of LAT on the plasma membrane. LRCH1-deficient CD8+ T cells are more proliferative and effective at pathogen control and tumor elimination. Importantly, CRISPR/Cas9-mediated knockout of LRCH1 in human T cells also increases IFN-γ production, cell proliferation and migration ability in vitro. These data suggest LRCH1 as a potential target to improve CD8+ T cell responses against tumor and pathogens.
2020-07-29 | GSE150634 | GEO
Project description:This analysis reveals the different gene expression profiles between human melanoma tumor infiltrating lymphocytes subsets CD8+CD28+ and CD8+CD28-. Adoptive cell therapy (ACT) is an effective approach that removes tumor-infiltrating lymphocytes (TILs) from this suppressive tumor microenvironment and expands and activates CD8+ and CD4+ T cells in vitro, differentiating them into potent anti-tumor effector cells that can be re-introduced back into patients. One of the key problems that may limit tumor regression and long-term durable clinical responses in ACT is the persistence of TILs following infusion. Our study has indicated that ex vivo expanded TILs to be hypo-responsive to peptide re-stimulation, manifested in slow entry into cell cycle and increased apoptosis. Phenotypic and functional analysis using a number of different T-cell differentiation markers found that CD28 was markedly down-modulated in post-REP cells, while CD27 and CD57 levels showed no statistically-relevant changes in expression. Here on a global gene expression level, microarray gene chip analysis of sorted CD8+CD28+ and CD8+CD28- post-REP TILs revealed a number of key differences in their gene expression profiles; notably, an increase in KIR family member expression, loss of p53-binding proteins, and lower CD127/IL-7Ra gene expression found in the CD28- population. On top of advancing T cell phenotype, reactivation and memory, this set of data may also provide insight for ACT clinical protocol optimization to improve TIL response in vivo.
2009-06-10 | GSE16517 | GEO
Project description:Adoptive transfer of anti-CD19 chimeric antigen receptor (CAR)-engineered T cells has shown impressive clinical responses in patients with refractory B-cell malignancies. However, therapeutic effects of CAR-T cells targeting other hematologic malignancies and solid tumors are not yet satisfactory. Although inefficient tumor trafficking and multiple immunosuppressive molecules impede CAR-T cell effector responses, signals delivered by the current CAR constructs may still be insufficient to fully activate antitumor T cell functions. Optimal T cell activation and proliferation requires multiple signals including T cell receptor (TCR) engagement (signal 1), costimulation (signal 2), and cytokine engagement (signal 3). CAR genes developed to date contain a CD3z domain and costimulatory domain(s), but not a domain to transmit signal 3. In this study, we have developed a novel CAR construct capable of inducing cytokine signaling in an antigen-dependent manner. The new generation CD19 CAR encodes a cytoplasmic domain of IL-2RB and STAT3-binding YXXQ motif together with CD3z and CD28 domains (28-DIL2RB-z (YXXQ)). The 28-DIL2RB-z (YXXQ) CAR-T cells showed antigen-dependent JAK-STAT, especially the STAT3-mediated pathway activation, which promoted their proliferation and prevented terminal differentiation. The 28-DIL2RB-z (YXXQ) CAR-T cells demonstrated superior in vivo persistence and antileukemia effects compared with the currently used CARs in multiple tumor models.
2018-01-21 | GSE103906 | GEO
Project description:Adoptive transfer of anti-CD19 chimeric antigen receptor (CAR)-engineered T cells has shown impressive clinical responses in patients with refractory B-cell malignancies. However, therapeutic effects of CAR-T cells targeting other hematologic malignancies and solid tumors are not yet satisfactory. Although inefficient tumor trafficking and multiple immunosuppressive molecules impede CAR-T cell effector responses, signals delivered by the current CAR constructs may still be insufficient to fully activate antitumor T cell functions. Optimal T cell activation and proliferation requires multiple signals including T cell receptor (TCR) engagement (signal 1), costimulation (signal 2), and cytokine engagement (signal 3). CAR genes developed to date contain a CD3z domain and costimulatory domain(s), but not a domain to transmit signal 3. In this study, we have developed a novel CAR construct capable of inducing cytokine signaling in an antigen-dependent manner. The new generation CD19 CAR encodes a cytoplasmic domain of IL-2RB and STAT3-binding YXXQ motif together with CD3z and CD28 domains (28-IL2RB-z (YXXQ)). The 28-IL2RB-z (YXXQ) CAR-T cells showed antigen-dependent JAK-STAT, especially the STAT3-mediated pathway activation, which promoted their proliferation and prevented terminal differentiation. The 28-IL2RB-z (YXXQ) CAR-T cells demonstrated superior in vivo persistence and antileukemia effects compared with the currently used CARs in multiple tumor models.
2020-02-15 | GSE95037 | GEO
Project description:Profiling of Naïve (CD45RA+CD28+), EM (CD45RA-CD28-) and TEMRA (CD45RA+CD28-) CD8+ T cells
| PRJNA530997 | ENA