scholarly journals Extracting T Cell Function and Differentiation Characteristics from the Biomedical Literature

2019 ◽  
Author(s):  
Eric Czech ◽  
Jeff Hammerbacher
Keyword(s):  
T Cell ◽  
Cell Function ◽  
Relation Extraction ◽  
Biomedical Literature ◽  
Language Models ◽  
Molecular Signaling ◽  
Weak Supervision ◽  
Human T Cells ◽  
Molecular Signaling Network ◽  
Experimental Findings

AbstractThe role of many cytokines and transcription factors in the function and development of human T cells has been the subject of extensive research, however much of this work only demonstrates experimental findings for a relatively small portion of the molecular signaling network that enables the plasticity inherent to these cells. We apply recent advancements in methods for weak supervision and transfer learning for natural language models to aid in extracting these individual findings as 283k cell type, cytokine, and transcription factor relations from 64k relevant documents (53k full-text PMC articles and 11k PubMed abstracts). All data, results and source code available athttps://github.com/hammerlab/t-cell-relation-extraction.

scholarly journals Hypoxia is a dominant remodeler of the CD8+ T cell surface proteome relative to activation and regulatory T cell-mediated suppression

2021 ◽  
Author(s):  
James Robert Byrnes ◽  
Amy M Weeks ◽  
Julia Carnevale ◽  
Eric Shifrut ◽  
Lisa Kirkemo ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Cell Surface ◽  
T Cell Activation ◽  
Cell Activation ◽  
Cell Function ◽  
Metabolic Reprogramming ◽  
T Cell Function ◽  
Human T Cells ◽  
Surface Proteome

Immunosuppressive factors in the tumor microenvironment (TME) impair T cell function and limit the anti-tumor immune response. T cell surface receptors that influence interactions and function in the TME are already proven targets for cancer immunotherapy. However, surface proteome remodeling of primary human T cells in response to suppressive forces in the TME has never been characterized systematically. Using a reductionist cell culture approach with primary human T cells and SILAC-based quantitative cell surface capture glycoproteomics, we examined how two immunosuppressive TME factors, regulatory T cells (Tregs) and hypoxia, globally affect the activated CD8+ surface proteome (surfaceome). Surprisingly, the CD8+/Treg co-culture only modestly affected the CD8+ surfaceome, but did reverse several activation-induced surfaceomic changes. In contrast, hypoxia dramatically altered the CD8+ surfaceome in a manner consistent with both metabolic reprogramming and induction of an immunosuppressed state. The CD4+ T cell surfaceome similarly responded to hypoxia, revealing a novel hypoxia-induced surface receptor program. Our findings are consistent with the premise that hypoxic environments create a metabolic challenge for T cell activation, which may underlie the difficulty encountered in treating solid tumors with immunotherapies. Together, the data presented here provide insight into how suppressive TME factors remodel the T cell surfaceome and represent a valuable resource to inform future therapeutic efforts to enhance T cell function in the TME.

Novel Predictor Of Lenalidomide Response In Non-del5q MDS Reveals Linkage To Molecular Mechanism: First Characterization Of T-Cell Function In Cereblon Homozygous Deficient Mice

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 748-748
Author(s):  
Pearlie K Epling-Burnette ◽  
Ying Han ◽  
Adam W Mailloux ◽  
Ling Zhang ◽  
Jessica M. McDaniel ◽  
...  
Keyword(s):  
Bone Marrow ◽  
T Cells ◽  
T Cell ◽  
Peripheral Blood ◽  
Cell Function ◽  
Validation Cohort ◽  
Molecular Target ◽  
Bone Marrow Microenvironment ◽  
Training Cohort ◽  
Human T Cells

Abstract Background Durable responses to lenalidomide (LEN, an immunomodulatory drug, IMiDTM) occur in both non-del5q and del5q Myelodysplastic Syndrome (MDS). In non-del5q MDS and multiple myeloma, modulation of the bone marrow microenvironment by an unknown mechanism has been theorized. IMiDs initiate numerous effects on the immune system, some of which may induce an anti-leukemic and anti-inflammatory response. The connection between the drug's immune modulating activity and its hematopoietic stimulatory activity in MDS is currently untested. We and others have shown that LEN expands T-cells and increases IL-2 (p<0.001) by substituting for CD28 co-stimulation. In support of this, we found that LEN activates a CD28-specfic transcription factor pCREB in the absence of extracellular ligation of the CD28 receptor suggesting that it is acting to suppress a pharmacologic target that is involved specifically in costimulatory signaling. Normally, several negative regulators provide immunotolerance to T-cells to limit self-reactivity and protect against autoimmune disease. Anti-cancer immunosurveillance is often circumvented through acquired resistance to costimulation. Methods The critical role of immune modulation in LEN-induced hematologic response was examined by testing the performance of a predictive biomarker in patients stratified by del5q status in a training cohort and in a blinded validation cohort. Molecular analyses were performed on sorted populations of cells and knock-down of genes in normal human T-cells. Finally, we demonstrate the relevance of cereblon, a molecular target of LEN, in the negative regulation of costimulatory CD28 signaling using a homozygous germline knockout mouse. Results Comparison of sorted CD28+CD8+ and CD28-CD8+ human T-cells illustrates the importance of the expression of this receptor in LEN-induced T-cell activation. CD28- T-cells were found to be resistant to LEN. Accumulation of CD28- cells is a form of accelerated immunosenescence that is often associated with cancer and has been reported in MDS. To determine if CD28- T-cell accumulation is associated with LEN hematopoietic outcome in patients, we performed T-cell profiling before treatment in a training cohort (n=21) and a blinded validation cohort (n=35). Of the T-cell markers studied, a higher percentage of CD28- T-cells was associated with LEN hematopoietic failure in the training cohort (p=0.001). Using a R-Part-defined cutoff of CD28+ vs CD28- T-cells, the biomarker sensitivity was found to be 86%, specificity 82%, positive predictive value (PPV) 67%, and negative PV (NPV) 93% in non-del5q MDS patients, but did not improve response discrimination in del5q MDS. The association between CD28 and LEN response led us to hypothesize that the molecular target of LEN is involved in signaling by the CD28 receptor. A landmark study identified cereblon (CRBL), a RING-domain E3-Ubiquitin Ligase (UbL) to be the primary target of thalidomide and LEN. To examine the effect of CRBL on CD28 signaling, germ-line crbl knock-out mice (crbl-/-) were examined compared to wild-type (WT) C57BL6 mice. We found that crbl deficiency augments T-cell proliferation (Fig. 1A) and contextual activation of IL2 in the absence of CD28 co-stimulation similar to LEN. Examination of the bone marrow, thymus, and peripheral blood shows that crbl is a negative regulator of lymphopoiesis in the spleen and thymocyte with increased peripheral blood lymphocyte counts (Fig. 1B) and increased double negative (DN)-1 (P=0.01), DN3 (p=0.03), and reduced DN4 (p=0.005) thymocytes in crbl-/- compared to WT mice. Conclusions Our results indicate that immune reconstitution mediated by T-cell CD28 signaling is important for hematologic response in non-del5q MDS, but not del5q MDS, and is consistent with different molecular mechanisms of action in these two groups of patients. LEN may improve T-cell function by directly suppressing CRBL a novel E3-UbL regulator involved in lymphopoiesis, thymocyte development and CD28 co-stimulation. Our data suggests that CRBL acts similarly to the E3 UbL proteins Cbl-b, GRAIL, and ITCH that mechanistically induce immunotolerance. In response to LEN, T-cell functional activation may sustain anti-leukemic immunosurveillance or act to remove suppressive immature cell populations from the bone marrow microenvironment allowing hematologic improvement in non-del5q MDS. Disclosures: Epling-Burnette: Celgene: Research Funding. McDaniel:Celgene: Employment. List:Celgene: Membership on an entity’s Board of Directors or advisory committees.

scholarly journals Reprogramming human T cell function and specificity with non-viral genome targeting

2017 ◽  
Author(s):  
Theodore L. Roth ◽  
Cristina Puig-Saus ◽  
Ruby Yu ◽  
Eric Shifrut ◽  
Julia Carnevale ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Dna Sequences ◽  
Viral Genome ◽  
Viral Vectors ◽  
Cell Function ◽  
Experimental Manipulation ◽  
Target Cells ◽  
Human T Cell ◽  
Human T Cells

Human T cells are central to physiological immune homeostasis, which protects us from pathogens without collateral autoimmune inflammation. They are also the main effectors in most current cancer immunotherapy strategies1. Several decades of work have aimed to genetically reprogram T cells for therapeutic purposes2–5, but as human T cells are resistant to most standard methods of large DNA insertion these approaches have relied on recombinant viral vectors, which do not target transgenes to specific genomic sites6, 7. In addition, the need for viral vectors has slowed down research and clinical use as their manufacturing and testing is lengthy and expensive. Genome editing brought the promise of specific and efficient insertion of large transgenes into target cells through homology-directed repair (HDR), but to date in human T cells this still requires viral transduction8, 9. Here, we developed a non-viral, CRISPR-Cas9 genome targeting system that permits the rapid and efficient insertion of individual or multiplexed large (>1 kilobase) DNA sequences at specific sites in the genomes of primary human T cells while preserving cell viability and function. We successfully tested the potential therapeutic use of this approach in two settings. First, we corrected a pathogenic IL2RA mutation in primary T cells from multiple family members with monogenic autoimmune disease and demonstrated enhanced signalling function. Second, we replaced the endogenous T cell receptor (TCR) locus with a new TCR redirecting T cells to a cancer antigen. The resulting TCR-engineered T cells specifically recognized the tumour antigen, with concomitant cytokine release and tumour cell killing. Taken together, these studies provide preclinical evidence that non-viral genome targeting will enable rapid and flexible experimental manipulation and therapeutic engineering of primary human immune cells.

scholarly journals Zinc Aspartate Induces IL-16 Secretion and Apoptosis in Human T Cells

Biomedicines ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 246
Author(s):  
Dirk Reinhold ◽  
Karina Guttek ◽  
Annika Reddig ◽  
Linda Voss ◽  
Claudia Schubert ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Autoimmune Diseases ◽  
T Cell Activation ◽  
Cell Activation ◽  
Caspase 3 ◽  
Cell Function ◽  
Human T Cell ◽  
Human T Cells ◽  
Zinc Aspartate

T cell activation mediates immunity to pathogens. On the flipside, T cells are also involved in pathological immune responses during chronic autoimmune diseases. We recently reported that zinc aspartate, a registered drug with high bioavailability, dose-dependently inhibits T cell activation and Th1/Th2/Th17 cytokine production of stimulated human and mouse T cells. To understand the suppressive effect of zinc on T cell function, we here investigated the influence of zinc aspartate on human T cells focusing on the secretion of immunosuppressive cytokines, induction of apoptosis, and caspase 3/7 activity. To this end, we monitored either freshly stimulated or pre-activated human T cells in the presence of zinc aspartate from 40–140 µM over a period of 72 h. Under both experimental conditions, we observed a dose-dependent suppression of human T cell proliferation. While IL-1ra, latent TGF-β1, and IL-10 were dose-dependently reduced, we, unexpectedly, detected elevated levels of IL-16 upon zinc supplementation. In addition, the number of cells with active caspase 3/7 and, consecutively, the amount of cells undergoing apoptosis, steadily increased at zinc aspartate concentrations exceeding 100 µM. Taken together, our findings suggest that zinc aspartate impairs T cell fitness and might be beneficial for the treatment of T cell-mediated autoimmune diseases.

scholarly journals Neoplastic human T-cells capable of responding to multiple human alloantigens

Blood ◽  
1980 ◽  
Vol 55 (3) ◽  
pp. 470-473
Author(s):  
MR Rubenfeld ◽  
RL Edelson ◽  
LM Lofstrom ◽  
CL Berger ◽  
D Warburton
Keyword(s):  
T Cells ◽  
T Cell ◽  
Cell Function ◽  
Cell Lymphoma ◽  
Mixed Lymphocyte Culture ◽  
Lymphocyte Culture ◽  
T Cell Lymphoma ◽  
Cutaneous T Cell Lymphoma ◽  
T Cell Function ◽  
Human T Cells

Monoclonally-derived neoplastic T-cells from a patient with cutaneous T- cell lymphoma respond to multiple human HLA-D antigens in mixed lymphocyte culture. The implications of this phenomenon relevant to normal T-cell function and to malignancy are discussed.

scholarly journals Generation of knock-in primary human T cells using Cas9 ribonucleoproteins

2015 ◽  
Vol 112 (33) ◽  
pp. 10437-10442 ◽  
Author(s):  
Kathrin Schumann ◽  
Steven Lin ◽  
Eric Boyer ◽  
Dimitre R. Simeonov ◽  
Meena Subramaniam ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Genome Engineering ◽  
Cell Function ◽  
Genetic Manipulation ◽  
Cell Surface Expression ◽  
Great Promise ◽  
Knock Out ◽  
Human T Cells ◽  
Genome Modifications

T-cell genome engineering holds great promise for cell-based therapies for cancer, HIV, primary immune deficiencies, and autoimmune diseases, but genetic manipulation of human T cells has been challenging. Improved tools are needed to efficiently “knock out” genes and “knock in” targeted genome modifications to modulate T-cell function and correct disease-associated mutations. CRISPR/Cas9 technology is facilitating genome engineering in many cell types, but in human T cells its efficiency has been limited and it has not yet proven useful for targeted nucleotide replacements. Here we report efficient genome engineering in human CD4+T cells using Cas9:single-guide RNA ribonucleoproteins (Cas9 RNPs). Cas9 RNPs allowed ablation of CXCR4, a coreceptor for HIV entry. Cas9 RNP electroporation caused up to ∼40% of cells to lose high-level cell-surface expression of CXCR4, and edited cells could be enriched by sorting based on low CXCR4 expression. Importantly, Cas9 RNPs paired with homology-directed repair template oligonucleotides generated a high frequency of targeted genome modifications in primary T cells. Targeted nucleotide replacement was achieved inCXCR4andPD-1(PDCD1), a regulator of T-cell exhaustion that is a validated target for tumor immunotherapy. Deep sequencing of a target site confirmed that Cas9 RNPs generated knock-in genome modifications with up to ∼20% efficiency, which accounted for up to approximately one-third of total editing events. These results establish Cas9 RNP technology for diverse experimental and therapeutic genome engineering applications in primary human T cells.

scholarly journals Neoplastic human T-cells capable of responding to multiple human alloantigens

Blood ◽  
1980 ◽  
Vol 55 (3) ◽  
pp. 470-473 ◽  
Author(s):  
MR Rubenfeld ◽  
RL Edelson ◽  
LM Lofstrom ◽  
CL Berger ◽  
D Warburton
Keyword(s):  
T Cells ◽  
T Cell ◽  
Cell Function ◽  
Cell Lymphoma ◽  
Mixed Lymphocyte Culture ◽  
Lymphocyte Culture ◽  
T Cell Lymphoma ◽  
Cutaneous T Cell Lymphoma ◽  
T Cell Function ◽  
Human T Cells

Abstract Monoclonally-derived neoplastic T-cells from a patient with cutaneous T- cell lymphoma respond to multiple human HLA-D antigens in mixed lymphocyte culture. The implications of this phenomenon relevant to normal T-cell function and to malignancy are discussed.

scholarly journals RNAi Screening with Self-Delivering, Synthetic siRNAs for Identification of Genes That Regulate Primary Human T Cell Migration

2015 ◽  
Vol 20 (8) ◽  
pp. 943-956 ◽  
Author(s):  
Michael Freeley ◽  
Emily Derrick ◽  
Eugene Dempsey ◽  
Antje Hoff ◽  
Anthony Davies ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Cell Function ◽  
Cell Polarization ◽  
Small Gtpase ◽  
Lymphocyte Function ◽  
Rnai Screening ◽  
Chemically Modified ◽  
Human T Cell ◽  
Human T Cells

Screening of RNA interference (RNAi) libraries in primary T cells is labor-intensive and technically challenging because these cells are hard to transfect. Chemically modified, self-delivering small interfering RNAs (siRNAs) offer a solution to this problem, because they enter hard-to-transfect cell types without needing a delivery reagent and are available in library format for RNAi screening. In this study, we have screened a library of chemically modified, self-delivering siRNAs targeting the expression of 72 distinct genes in conjunction with an image-based high-content-analysis platform as a proof-of-principle strategy to identify genes involved in lymphocyte function-associated antigen-1 (LFA-1)-mediated migration in primary human T cells. Our library-screening strategy identified the small GTPase RhoA as being crucial for T cell polarization and migration in response to LFA-1 stimulation and other migratory ligands. We also demonstrate that multiple downstream assays can be performed within an individual RNAi screen and have used the remainder of the cells for additional assays, including cell viability and adhesion to ICAM-1 (the physiological ligand for LFA-1) in the absence or presence of the chemokine SDF-1α. This study therefore demonstrates the ease and benefits of conducting siRNA library screens in primary human T cells using self-delivering, chemically modified siRNAs, and it emphasizes the feasibility and potential of this approach for elucidating the signaling pathways that regulate T cell function.

Deltex1 suppresses T cell function and is a biomarker for diagnosis and disease activity of systemic lupus erythematosus

Rheumatology ◽  
2019 ◽  
Vol 58 (4) ◽  
pp. 719-728 ◽  
Author(s):  
Chuen-Miin Leu ◽  
Tzu-Sheng Hsu ◽  
Yu-Ping Kuo ◽  
Ming-Zong Lai ◽  
Po-Chun Liu ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Disease Activity ◽  
Cell Function ◽  
Healthy Controls ◽  
Cell Functions ◽  
T Cell Function ◽  
Human T Cell ◽  
Human T Cells ◽  
Ifn Γ

Abstract Objective Deletion of Deltex1 (DTX1) in mice caused hyperactivation of T cells and lupus-like autoimmune syndromes, however, the association of DTX1 with human autoimmune diseases is totally unknown. This study investigated the role of DTX1 in human T cell functions and its correlation with disease activity in patients with SLE. Methods The influence of DTX1 on T cell function was evaluated using human primary cells. DTX1 expression in peripheral blood mononuclear cells (PBMCs) from healthy controls and SLE patients was measured by quantitative real-time PCR and the SLEDAI was used to assess disease activity. Results After stimulation with anti-CD3 and anti-CD28, silencing of DTX1 expression enhanced IFN-γ secretion by human T cells. The expression of DTX1 in PBMCs was significantly lower in 100 SLE patients than in 50 age- and sex-matched healthy controls (DTX1/glyceraldehyde 3-phosphate dehydrogenase, 0.452 vs 1.269, P < 0.001). The area under the receiver operator characteristics curve of the model was 0.737 (95% CI 0.658, 0.815). Intriguingly, a low DTX1 level in T cells led to high IFN-γ production in SLE patients and had a correlation with severe disease activity. In addition, low DTX1 expression in SLE patients was associated with active LN, lung involvement or hypocomplementaemia. Conclusion Knockdown DTX1 expression in human T cells reduced IFN-γ secretion. DTX1 expression in the PBMCs was significantly lower in SLE patients and had an inverse correlation with disease activity, indicating that the DTX1 level may be a good disease marker of SLE.

scholarly journals 35 Targeted non-viral integration of large cargo in primary human T cells by CRISPR/Cas9 guided homology mediated end joining

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A36-A36
Author(s):  
Beau Webber ◽  
Matthew Johnson ◽  
Nicholas Slipek ◽  
Walker Lahr ◽  
Xiaohong Qiu ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
T Cells ◽  
T Cell ◽  
Cell Function ◽  
Nucleic Acid Delivery ◽  
End Joining ◽  
Car T Cells ◽  
Human T Cells ◽  
Car T ◽  
Culture Protocol

BackgroundEngineered immune cells hold tremendous promise for the treatment of advanced cancers. As the scale and complexity of engineered cell therapies increase, reliance on viral vectors for clinical production limits translation of promising new therapies. Here, we present an optimized platform for CRISPR/Cas9-targeted, non-viral engineering of primary human T cells that overcomes key limitations of previous approaches, namely DNA-induced toxicity and low efficiency integration of large genetic cargos.MethodsA systematic optimization of nucleic acid delivery, editing reagent composition, and culture protocol was performed to overcome DNA toxicity. Targeted knockin (KI) at AAVS1 and TRAC was compared across multiple vector configurations with genetic cargos ranging from 1 to 3 kilobases (kb) in size. Integration efficiency was measured by flow cytometry and sequencing. Off-target editing and integration were evaluated using GUIDE-seq and targeted locus amplification (TLA), respectively. Phenotype and function of non-virally and lentivirus engineered CAR-T cells was compared using flow cytometry, cytokine profiling and cytotoxicity assays.ResultsWe identified a temporal window following T cell activation where transfection efficiency, cell-cycle-status, and cytosolic DNA sensor expression were optimal for targeted DNA integration and reduced toxicity. Within this window, we targeted a 1kb GFP reporter to the AAVS1 locus with an efficiency of ~45% using homologous recombination (HR). Efficiency was reduced to ~11% with a larger ~3kb TCR cassette targeted to the TRAC locus, consistent with previous reports.1–3 To improve large cargo integration we employed homology mediated end-joining (HMEJ) and short homology design (48bp vs. ~1kb for traditional HR).4 Using HMEJ, knockin of the 1kb GFP cassette at AAVS1 reached ~70%. Strikingly, integration of the 3kb TCR at TRAC reached ~50% using HMEJ. Additional optimization of the culture protocol doubled post-engineering survival and proliferation (up to ~35-fold expansion in 7 days). Non-virally engineered TRAC KI CAR-T cells were phenotypically and functionally equivalent to lentivirally engineered T cells in vitro. In vivo assays in xenograft models are underway and results will be presented.ConclusionsComprehensive, orthogonal optimization of parameters impacting nucleic acid delivery and DNA-toxicity in combination with novel modalities for integration achieved knockin of TCR and CAR cargo at efficiencies equivalent to that of current viral vector platforms without compromising expansion or function. Our protocol is suitable for clinical scale production under GMP conditions and offers an improved methodology over previous methods for non-viral engineering of human T cells.ReferencesRoth TL, Puig-Saus C, Yu R, Shifrut E, Carnevale J, Li PJ, Hiatt J, Saco J, Krystofinski P, Li H, Tobin V, Nguyen DN, Lee MR, Putnam AL, Ferris AL, Chen JW, Schickel J-N, Pellerin L, Carmody D, Alkorta-Aranburu G, Del Gaudio D, Matsumoto H, Morell M, Mao Y, Cho M, Quadros M, Gurumurthy CB, Smith, B, Haugwitz M, Hughes SH, Weissman JS, Schumann K., Esensten JH., May AP, Ashworth A., Kupfer G. M., Atma S., Greeley W. & Marson A. Reprogramming human T cell function and specificity with non-viral genome targeting. Naturedoi:10.1038/s41586-018-0326-5Parker Autoimmune SN, Zuckerberg Biohub C, Francisco S. & Helen U. Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency. Nat. Biotechnol. doi:10.1038/s41587-019-0325-6Schober K, Müller TR, Gökmen F, Grassmann S, Effenberger M, Poltorak M, Stemberger C, Schumann K, Roth TL, Marson A. & Busch DH. Orthotopic replacement of T-cell receptor α- and β-chains with preservation of near-physiological T-cell function. Nature Biomedical Engineering 3, 974–984 ( 2019).Wierson WA, Welker JM, Almeida MP, Mann CM, Webster DA, Torrie ME, Weiss TJ, Kambakam S, Vollbrecht MK, Lan M, McKeighan KC, Levey J, Ming Z, Wehmeier A, Mikelson CS, Haltom JA, Kwan KM, Chien C-B, Balciunas D, Ekker SC, Clark KJ, Webber, BR, Moriarity BS, Solin SL, Carlson DF, Dobbs DL, McGrail M & Essner J. Efficient targeted integration directed by short homology in zebrafish and mammalian cells. Elife9, ( 2020).

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