Gene Expression Profiles Of CD34 Research Articles

#1492 Metabolic switch in CD8+ T cells may influence immune response in chronic antibody-mediated rejection (CAMR)

Abstract Background and Aims CAMR is the main cause of chronic graft injury and subsequent graft loss, but its pathogenesis is still largely unclear. Our group demonstrated an increase in CD8+ T cells infiltrating biopsies from CAMR patients (PMID: 20595199), but their role remains to be defined. Recently, immunometabolism has emerged as a field connecting cell energy metabolism with the immune cell differentiation and functions. Particularly, the permanent aerobic glycolysis of CD8+ lymphocytes induces their transition from naïve to activated state and effector T cells (PMID: 37315709). Thus, the aim of the study was to investigate the molecular mechanisms underlying the development of CAMR by the analysis of gene expression profiles of CD8+ T lymphocytes in conjunction with their metabolic state. Method We enrolled 14 patients with biopsy-proven CAMR and 12 stable transplant recipients with normal graft histology and function (control group). CD8+ T cells were purified by CD8 MicroBeads (Miltenyi Biotec) then counted (TC20™ Automated Cell Counter). Gene expression profiles of CD8+ T lymphocytes isolated from both groups were assessed using Agilent microarrays. Data obtained were statistically and functionally evaluated (IPA software) and validated by qPCR. Oxygen consumption rate (OCR) in CD8+ and CD8- cells was measured by a Resipher oxygen sensing lid (Lucid Scientific Inc., USA). The contribution of mitochondrial respiration to OCR was investigated in isolated CD8+ T cells from CAMR and controls treated with rotenone/antimycin A (Rot/AA), oligomycin (Olygo) or carbonyl cyanide-p-trifluoromethoxyphenylhydrazone (FCCP) to evaluate spare respiratory capacity (SRC), ATP-linked respiration, proton leak and maximal respiration. Results Gene expression profiles of CD8+ T cells showed a characteristic alteration of lipid metabolism in CAMR patients with the triglyceride biosynthesis pathway (p = 2.69E-3) as the most altered pathway and several genes de-regulated all potentially involved in the altered metabolic state of CD8+ T cells. Among others, we validated the increased expression of Nicotinamide Phosphoribosyltransferase (NAMPT) (FC = +2.39), the rate-limiting enzyme of nicotinamide adenine dinucleotide (NAD+) salvage pathway involved in the glycolysis progression, mostly activated in effector T cells. We then decided to evaluate the OCR and the metabolic state of CD8+T cells. Basal OCR was higher in CD8+ rather than CD8- cells, but with different trends among cells isolated from control and CAMR patients. Indeed, CD8+ cells from CAMR patients showed higher OCR compared to control, while OCR was lower in CD8- from CAMR rather than control patients. CD8+ OCR from both CAMR and control patients was mostly dependent on mitochondrial respiration, since it was deeply reduced by Rot/AA treatment. Interestingly, inhibitory response to Oligo treatment by CD8+ cells from CAMR patients was modest, while OCR was noticeably stimulated by FCCP in these cells, suggesting that mitochondrial oxygen uptake was not ATP linked but rather associated with increased uncoupling. These data suggest that CD8+ T cells from CAMR patients are activated effector T cells primarily utilizing aerobic glycolysis. To confirm this hypothesis, we evaluated the gene expression levels of: i) HIF1a, which involves permanent dependence on glycolysis even in the presence of oxygen (Warburg effect); ii) fatty acid transporter CD36, whose levels mimic an energy dependence on the beta oxidation of fatty acids, a process activated in memory T cells. We confirmed an increased expression of HIF1a and a reduced expression of CD36 in CD8+T cells from CAMR patients compared to controls (p<0.05), that confirm the T effector phenotype. Conclusion Our data suggest that CD8+ T cell from CAMR patients showed permanent dependency on glycolysis leading to altered immune phenotype and response, thus indicating novel opportunities to modulate the immune system for therapeutic purposes in kidney transplanted patients and reduce graft rejection.

Digital spatial profiling of CD4+ T cells in classic Hodgkin lymphoma.

Classic Hodgkin lymphoma (CHL) harbors a small number of Hodgkin-Reed-Sternberg (HRS) cells scattered among numerous lymphocytes. HRS cells are surrounded by distinct CD4+ T cells in a rosette-like manner. These CD4+ T cell rosettes play an important role in the tumor microenvironment (TME) of CHL. To elucidate the interaction between HRS cells and CD4+ T cell rosettes, we completed digital spatial profiling to compare the gene expression profiles of CD4+ T cell rosettes and other CD4+ T cells separated from the HRS cells. Immune checkpoint molecules including OX40, programed cell death-1 (PD-1), and cytotoxic T lymphocyte associated protein 4 (CTLA-4) expression was higher in CD4+ T cell rosettes compared to other CD4+ T cells. Immunohistochemistry confirmed variable PD-1, CTLA-4, and OX40 expression in the CD4+ T cell rosettes. This study introduced a new pathological approach to study the CHL TME, and provided deeper insight into CD4+ T cells in CHL.

Abstract 4843: Characterization of T-cell metabolic defects in chronic lymphocytic leukemia preclinical model

Abstract Chronic lymphocytic leukemia (CLL) is the most predominant leukemia affecting elderly population in western countries. T-cell dysfunction is a CLL hallmark contributing to the low success rates of adoptive cell therapy in patients. Generally, exhausted states of tumor infiltrating lymphocytes are associated with defects in metabolic and mitochondrial adaptation, preventing normal cytotoxic functions. A handful of recent reports have demonstrated metabolic defects in CLL patients’ T-cells. Nevertheless, the field is still lacking sufficient studies to validate these metabolic changes in the preclinical Eµ-TCL1 murine model which is the most established model for CLL. Our aim is to uncover T-cell mitochondrial and metabolic defects in the Eµ-TCL1 splenic microenvironment. In this study, CLL was induced in mice via the adoptive transfer of leukemic splenocytes from transgenic Eµ-TCL1 mice into wild type (WT) recipients. Multiparameter flow cytometry was used to investigate mitochondrial properties and cellular glucose uptake of splenic CLL CD8+ T-cells. Moreover, we measured the expression levels of PGC-1α, a master regulator of mitochondrial function, and exhaustion-related markers in CD8+ T-cells. T-cell mitochondrial function was measured using mitochondrial stress test following in vitro CD3/CD28 stimulation for 72 hours. Nanostring gene expression analysis was done to compare metabolic gene expression profiles of CD8+ T-cells from either WT or Eµ-TCL1 mice. Probing Eµ-TCL1 splenocytes with mitotracker green and tetramethylrhodamine methyl ester revealed accumulation of depolarized mitochondria in CD8+ T-cells compared to WT counterparts. Our results also showed significant changes in mitochondrial and cellular reactive oxygen species levels as indicated by mitosox and H2DCFDA staining, respectively. Additionally, marked reduction of glucose uptake by Eµ-TCL1 CD8+ T-cells was noted following incubation with 2-NBDG glucose analog. Observed mitochondrial abnormalities in the Eµ-TCL1 CD8+ T-cells were associated with a significant downregulation of PGC-1α expression. Flow cytometry analysis demonstrated a significant increase in the expression of exhaustion markers in Eµ-TCL1 CD8+ T-cells and reduction in self-renewal marker, TCF-1. Interestingly, the abnormal mitochondrial properties were directly correlated with PD-1 expression in Eµ-TCL1 T-cells. Nanostring significance score analysis of Eµ-TCL1 versus WT CD8+ T-cell RNA revealed upregulation of glycolysis, mitochondrial respiration, T-cell receptor and costimulatory pathways. On the other hand, there was a downregulation in autophagy, AMPK and amino acid transporter pathways. In conclusion, our work characterizes for the first time the metabolic and mitochondrial defects of CD8+ T-cells from Eµ-TCL1 murine model and outlines the correlation of these defects with T-cell exhaustion in CLL. Citation Format: Wael Gamal, Melanie Mediavilla-Varela, Kamira Maharaj, Angimar Uriepero, Vishaal Kunta, Eva Sahakian, Javier Pinilla-Ibarz. Characterization of T-cell metabolic defects in chronic lymphocytic leukemia preclinical model. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4843.

Early and late stage MPN patients show distinct gene expression profiles in CD34+ cells

Myeloproliferative neoplasms (MPN), comprising essential thrombocythemia (ET), polycythemia vera (PV), and primary myelofibrosis (PMF), are hematological disorders of the myeloid lineage characterized by hyperproliferation of mature blood cells. The prediction of the clinical course and progression remains difficult and new therapeutic modalities are required. We conducted a CD34+ gene expression study to identify signatures and potential biomarkers in the different MPN subtypes with the aim to improve treatment and prevent the transformation from the rather benign chronic state to a more malignant aggressive state. We report here on a systematic gene expression analysis (GEA) of CD34+ peripheral blood or bone marrow cells derived from 30 patients with MPN including all subtypes (ET (n = 6), PV (n = 11), PMF (n = 9), secondary MF (SMF; post-ET-/post-PV-MF; n = 4)) and six healthy donors. GEA revealed a variety of differentially regulated genes in the different MPN subtypes vs. controls, with a higher number in PMF/SMF (200/272 genes) than in ET/PV (132/121). PROGENγ analysis revealed significant induction of TNFα/NF-κB signaling (particularly in SMF) and reduction of estrogen signaling (PMF and SMF). Consistently, inflammatory GO terms were enriched in PMF/SMF, whereas RNA splicing–associated biological processes were downregulated in PMF. Differentially regulated genes that might be utilized as diagnostic/prognostic markers were identified, such as AREG, CYBB, DNTT, TIMD4, VCAM1, and S100 family members (S100A4/8/9/10/12). Additionally, 98 genes (including CLEC1B, CMTM5, CXCL8, DACH1, and RADX) were deregulated solely in SMF and may be used to predict progression from early to late stage MPN.Graphical abstract

Gene expression profiling of CD34(+) cells from patients with myeloproliferative neoplasms.

Myeloproliferative neoplasms (MPN) are clonal disorders characterized by the increased proliferation of hematopoietic stem cell precursors and mature blood cells. Mutations of Janus kinase 2 (JAK2), Calreticulin (CALR) and MPL (myeloproliferative leukemia virus) are key driver mutations in MPN. However, the molecular profile of triple negative MPN has been a subject of ambiguity over the past few years. Mutations of, methylcytosine dioxygenase TET2, polycomb group protein ASXL1 and histone-lysine N-methyltransferase EZH2 genes have accounted for certain subsets of triple negative MPNs but the driving cause for majority of cases is still unexplored. The present study performed a microarray-based transcriptomic profile analysis of bone marrow-derived CD34(+) cells from seven MPN samples. A total of 21,448 gene signatures were obtained, which were further filtered into 472 upregulated and 202 downregulated genes. Gene ontology and protein-protein interaction (PPI) network analysis highlighted an upregulation of genes involved in cell cycle and chromatin modification in JAK2V617F negative vs. positive MPN samples. Out of the upregulated genes, seven were associated with the hematopoietic stem cell signature, while forty-seven were associated with the embryonic stem cell signature. The majority of the genes identified were under the control of NANOG and E2F4 transcription factors. The PPI network indicated a strong interaction between chromatin modifiers and cell cycle genes, such as histone-lysine N-methyltransferase SUV39H1, SWI/SNF complex subunit SMARCC2, SMARCE2, chromatin remodeling complex subunit SS18, tubulin β (TUBB) and cyclin dependent kinase CDK1. Among the upregulated epigenetic markers, there was a ~10-fold increase in MYB expression in JAK2V617F negative samples. A significant increase in total CD34 counts in JAK2V617F negative vs. positive samples (P<0.05) was also observed. Overall, the present data showed a distinct pattern of expression in JAK2V617F negative vs. positive samples with upregulated genes involved in epigenetic modification.

Reanalysis of Gene Expression Profiles of CD4+ T Cells Treated with HIV-1 Latency Reversal Agents.

The human immunodeficiency virus (HIV-1) causes a progressive depletion of CD4+ T cells, hampering immune function. Current experimental strategies to fight the virus focus on the reactivation of latent HIV-1 in the viral reservoir to make the virus detectable by the immune system, by searching for latency reversal agents (LRAs). We hypothesize that if common molecular pathways elicited by the presence of LRAs are known, perhaps new, more efficient, “shock-and-kill” strategies can be found. Thus, the objective of the present study is to re-evaluate RNA-Seq assays to find differentially expressed genes (DEGs) during latency reversal via transcriptome analysis. We selected six studies (45 samples altogether: 16 negative controls and 29 LRA-treated CD4+ T cells) and 11 LRA strategies through a systematic search in Gene Expression Omnibus (GEO) and PubMed databases. The raw reads were trimmed, counted, and normalized. Next, we detected consistent DEGs in these independent experiments. AZD5582, romidepsin, and suberanilohydroxamic acid (SAHA) were the LRAs that modulated most genes. We detected 948 DEGs shared by those three LRAs. Gene ontology analysis and cross-referencing with other sources of the literature showed enrichment of cell activation, differentiation and signaling, especially mitogen-activated protein kinase (MAPK) and Rho-GTPases pathways.

Decidual CD8+T cells exhibit both residency and tolerance signatures modulated by decidual stromal cells

BackgroundDuring early pregnancy, tolerance of the semi-allogeneic fetus necessitates comprehensive modifications of the maternal immune system. How decidual CD8+T (CD8+dT) cells balance maternal tolerance of the fetus with defense from invading pathogens remains undefined.MethodsWe investigated the distribution patterns of CD8+T cells and their heterogeneity in paired peripheral blood and decidual tissue in the first trimester of pregnancy using flow cytometry and mRNA-Seq. Gene Set Enrichment Analysis was utilized to determine the transcriptional features of CD8+dT cells. Moreover, we examined activation of T cells when they were cocultured with trophoblasts, in addition to the effect of the fetal–maternal environment on peripheral CD8+T (CD8+pT) cells.ResultsWe found that, compared with CD8+pT cells, CD8+dT cells consisted mainly of effector memory cells (TEM) and terminally differentiated effector memory cells (TEMRA). Both TEM and TEMRA subsets contained increased numbers of CD27+CD28− cells, which have been shown to possess only partial effector functions. In-depth analysis of the gene-expression profiles of CD8+dT cells revealed significant enrichment in T cell exhaustion-related genes and core tissue residency signature genes that have been found recently to be shared by tissue resident memory cells and tumor−infiltrating lymphocytes (TILs). In accordance with gene expression, protein levels of the exhaustion-related molecules PD-1 and CD39 and the tissue resident molecules CD103 and CXCR3 were increased significantly with almost no perforin secretion in CD8+dT cells compared with CD8+pT cells. However, the levels of granzyme B, IFN-γ, and IL-4 in CD8+dT cells were increased significantly compared with those in CD8+pT cells. Both CD8+dT and CD8+pT cells were not activated after being cocultured with autologous trophoblast cells. Moreover, the production of granzyme B in CD103+CD8+dT cells decreased significantly compared with that in their CD103− counterparts. Coculture with decidual stromal cells and trophoblasts upregulated CD103 expression significantly in CD8+pT cells.ConclusionsOur findings indicate that the selective silencing of effector functions of resident CD8+dT cells may favor maternal–fetal tolerance and that the decidual microenvironment plays an important role in promoting the residency of CD8+T cells and their tolerance–defense balance.

Robust Sampling of Defective Pathways in Multiple Myeloma.

We present the analysis of defective pathways in multiple myeloma (MM) using two recently developed sampling algorithms of the biological pathways: The Fisher’s ratio sampler, and the holdout sampler. We performed the retrospective analyses of different gene expression datasets concerning different aspects of the disease, such as the existing difference between bone marrow stromal cells in MM and healthy controls (HC), the gene expression profiling of CD34+ cells in MM and HC, the difference between hyperdiploid and non-hyperdiploid myelomas, and the prediction of the chromosome 13 deletion, to provide a deeper insight into the molecular mechanisms involved in the disease. Our analysis has shown the importance of different altered pathways related to glycosylation, infectious disease, immune system response, different aspects of metabolism, DNA repair, protein recycling and regulation of the transcription of genes involved in the differentiation of myeloid cells. The main difference in genetic pathways between hyperdiploid and non-hyperdiploid myelomas are related to infectious disease, immune system response and protein recycling. Our work provides new insights on the genetic pathways involved in this complex disease and proposes novel targets for future therapies.

Inhibition of Lysine-Specific Demethylase 1A (LSD1) Supports Human HSCs in Culture By Preserving Their Immature State

The molecular mechanisms that govern hematopoietic stem cell (HSC) fate decisions remain incompletely defined. It has been a long-standing goal in the field to gain a better understanding of the genes and pathways that regulate the self-renewal ability of HSCs in order to develop optimal culture conditions in which HSCs can be expanded for clinical benefit.Lysine-specific histone demethylase 1A (LSD1), also known as lysine (K)-specific demethylase 1A (KDM1A), regulates gene expression by specifically eliminating di- and mono-methyl groups on H3 lysine K4 and K9 residues. Studies in mice have shown that, conditional knockdown of LSD1 results in an expansion of bone marrow hematopoietic stem and progenitor cells (HSPCs). However, a complete knockout of LSD1 results in pancytopenia and a dramatic reduction of HSPCs.In this study, we asked whether inhibition of LSD1 would improve the maintenance or expansion of cultured human HSCs derived from umbilical cord blood (UCB). To evaluate the effect of LSD1 inhibition we treated UCB CD34+ cells with three different LSD1 inhibitors (2-PCPA, GSK-LSD1 and RN1) at their respective IC50 values (20µM, 16nM and 70nM) and expanded the cultures for 6 days in serum free medium supplemented with stem cell factor (SCF), thrombopoietin (TPO) and FMS-like tyrosine kinase 3 ligand (FLT3L). Since we (Subramaniam et. al. Haematologica 2018) and others recently have shown that EPCR is a reliable cell surface marker to track UCB derived HSCs during in vitro culture, we quantified the numbers of CD34+EPCR+ cells using flow cytometry and compared to DMSO treated control cultures. Remarkably, treatment with either 2-PCPA or GSK-LSD1 resulted in a more than 10-fold increase of CD34+EPCR+ cells, compared to controls. Further, from dose response experiments we found that 2-PCPA at 1.25 µM expanded the total CD34+ cell population more efficiently than GSK-LSD1, and we therefore used 2-PCPA at this concentration for the subsequent experiments.Using carboxyfluorescein succinimidyl ester (CFSE) labeling to monitor cell division, we found that 2-PCPA did not significantly alter the cell division rate of the cultured CD34+ cells compared to DMSO controls, suggesting that the expansion of CD34+EPCR+ cells is not due to increased proliferation, and that LSD1 inhibition rather may prevent differentiation of the immature HSPCs. To further explore this, we mapped the early transcriptional changes triggered by 2-PCPA in HSCs using gene expression profiling of CD34+CD38-CD45RA-CD90+ cells following 24 hours of culture with or without 2-PCPA treatment. We found that gene sets corresponding to UCB and fetal liver HSCs were significantly enriched upon 2-PCPA treatment compared to DMSO control (Normalized Enrichment Score (NES)=1.49, q=0.05). This suggest that 2-PCPA indeed restricts differentiation and preserves the HSC state upon ex vivo culture. Strikingly, the gene signature induced by LSD1 inhibition was highly similar to that induced by the known HSC expanding compound UM171 (NES=1.43, q=0.11). UM171 is a molecule with unknown target and has also been shown to dramatically expand the EPCR+ population in culture.Finally, the frequency of functional HSCs in DMSO and 2-PCPA treated cultures were measured using limiting dilution analysis (LDA). LDA was performed by transplanting 4 doses (day 0 equivalents of 20000, 1000, 300 and 100 CD34+ cells) of DMSO and 2-PCPA treated cultures into sub lethally irradiated (300cGy) NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice. Human CD45+ cell engraftment in the bone marrow was analyzed 18 weeks' post transplantation. Cultures treated with 2-PCPA showed a 5-fold higher content of long-term repopulating cells per day 0 CD34+ cell equivalent compared to the DMSO control (1 in 615 vs 1 in 3041, p=0.03). Thus, the 2-PCPA treated cultures had significantly enhanced HSCs numbers. To determine the absolute expansion rate, we are currently performing LDA using uncultured cells as well. Altogether our data suggest that LSD1 inhibition supports both phenotypic and functional HSCs in culture by preserving the immature state. Currently we are exploring the possibilities of using LSD1 inhibitors in combination with other known modifiers of HSC expansion. DisclosuresNo relevant conflicts of interest to declare.

Role of TGF-β1/miR-382-5p/SOD2 axis in the induction of oxidative stress in CD34+ cells from primary myelofibrosis.

Primary myelofibrosis (PMF) is a myeloproliferative neoplasm characterized by an excessive production of pro‐inflammatory cytokines resulting in chronic inflammation and genomic instability. Besides the driver mutations in JAK2,MPL, and CALR genes, the deregulation of miRNA expression may also contribute to the pathogenesis of PMF. To this end, we recently reported the upregulation of miR‐382‐5p in PMF CD34+ cells. In order to unveil the mechanistic details of the role of miR‐382‐5p in pathogenesis of PMF, we performed gene expression profiling of CD34+ cells overexpressing miR‐382‐5p. Among the downregulated genes, we identified superoxide dismutase 2 (SOD2), which is a predicted target of miR‐382‐5p. Subsequently, we confirmed miR‐382‐5p/SOD2 interaction by luciferase assay and we showed that miR‐382‐5p overexpression in CD34+ cells causes the decrease in SOD2 activity leading to reactive oxygen species (ROS) accumulation and oxidative DNA damage. In addition, our data indicate that inhibition of miR‐382‐5p in PMF CD34+ cells restores SOD2 function, induces ROS disposal, and reduces DNA oxidation. Since the pro‐inflammatory cytokine transforming growth factor‐β1 (TGF‐β1) is a key player in PMF pathogenesis, we further investigated the effect of TGF‐β1 on ROS and miR‐382‐5p levels. Our data showed that TGF‐β1 treatment enhances miR‐382‐5p expression and reduces SOD2 activity leading to ROS accumulation. Finally, inhibition of TGF‐β1 signaling in PMF CD34+ cells by galunisertib significantly reduced miR‐382‐5p expression and ROS accumulation and restored SOD2 activity. As a whole, this study reports that TGF‐β1/miR‐382‐5p/SOD2 axis deregulation in PMF cells is linked to ROS overproduction that may contribute to enhanced oxidative stress and inflammation. Our results suggest that galunisertib may represent an effective drug reducing abnormal oxidative stress induced by TGF‐β1 in PMF patients.Database linkingGEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103464.

Genome-wide expression profiling analysis to identify key genes in the anti-HIV mechanism of CD4+ and CD8+ T cells.

Comprehensive bioinformatics analyses were performed to explore the key biomarkers in response to HIV infection of CD4+ and CD8+ T cells. The numbers of CD4+ and CD8+ T cells of HIV infected individuals were analyzed and the GEO database (GSE6740) was screened for differentially expressed genes (DEGs) in HIV infected CD4+ and CD8+ T cells. Gene Ontology enrichment, KEGG pathway analyses, and protein-protein interaction (PPI) network were performed to identify the key pathway and core proteins in anti-HIV virus process of CD4+ and CD8+ T cells. Finally, we analyzed the expressions of key proteins in HIV-infected T cells (GSE6740 dataset) and peripheral blood mononuclear cells(PBMCs) (GSE511 dataset). 1) CD4+ T cells counts and ratio of CD4+ /CD8+ T cells decreased while CD8+ T cells counts increased in HIV positive individuals; 2) 517 DEGs were found in HIV infected CD4+ and CD8+ T cells at acute and chronic stage with the criterial of P-value <0.05 and fold change (FC) ≥2; 3) In acute HIV infection, type 1 interferon (IFN-1) pathway might played a critical role in response to HIV infection of T cells. The main biological processes of the DEGs were response to virus and defense response to virus. At chronic stage, ISG15 protein, in conjunction with IFN-1 pathway might play key roles in anti-HIV responses of CD4+ T cells; and 4) The expression of ISG15 increased in both T cells and PBMCs after HIV infection. Gene expression profile of CD4+ and CD8+ T cells changed significantly in HIV infection, in which ISG15 gene may play a central role in activating the natural antiviral process of immune cells.

TRAIL-Mediated Suppression of T Cell Receptor Signaling Inhibits T Cell Activation and Inflammation in Experimental Autoimmune Encephalomyelitis.

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induces cell apoptosis by transducing apoptosis signals after interacting with its receptor (TRAIL-R). Although the actual biological role of TRAIL remains to be elucidated, recent accumulating evidence implies that TRAIL regulates immune responses and immune cell homeostasis via an apoptosis-independent pathway, suggesting a novel immune-regulatory role of TRAIL in autoimmune diseases. The purpose of this study is to address the immune-regulatory role and molecular mechanism of TRAIL in regulating T cell activation in autoimmune diseases. TRAIL was administered to mice to induce experimental autoimmune encephalomyelitis (EAE), and to evaluate its impact on neuroinflammation and disease activity. The effects of TRAIL on neuroantigen [myelin oligodendrocyte glycoprotein (MOG)35-55]-activated T cell proliferation and cytokine production were investigated. TRAIL-treated MOG35-55-activated splenic Th17 cells were further adoptively transferred into Rag1 KO mice to induce passive EAE. Gene expression profiles of CD4+ T cells from EAE mice treated with TRAIL were analyzed by RNA sequencing and transcriptome analysis. TRAIL suppressed autoimmune encephalomyelitis and inhibited T cell reactivity to neuro-antigen in murine EAE, and the effects were dependent on TRAIL-R signaling. Moreover, TRAIL directly inhibited activation of MOG35-55-activated CD4+ T cells, resulting in suppression of neuroinflammation and reduced disease activity in adoptive transfer-induced EAE. Furthermore, TRAIL-R signaling inhibited phosphorylation of proximal T cell receptor (TCR)-associated tyrosine kinases in activated CD4+ T cells. Importantly, TRAIL/TRAIL-R interaction downregulated TCR downstream signaling genes in RNA sequencing and transcriptome analysis. TRAIL/TRAIL-R interaction regulates CD4+ T cell activation in autoimmune inflammation and directly suppresses T cell activation via inhibiting TCR signaling, suggesting that TRAIL-R serves as a novel immune checkpoint in T cell responses.

Transcriptome analysis of CD34+ cells from myelodysplastic syndrome patients

The myelodysplastic syndrome (MDS) represents a heterogeneous group of clonal hematologic stem cell disorders with the characteristic of ineffective hematopoiesis leading to low blood counts, and a risk of progression to acute myeloid leukemia (AML). To understand specific molecular characteristics of different MDS subtypes with del(5q), we analyzed the gene expression profiles of CD34+ cells from MDS patients of different databases and its enriched pathways. 44 genes, such as MME and RAG1, and eight related pathways were identified to be commonly changed, indicating their conserved roles in MDS development. Additionally, U43604 was identified to be specifically changed in three subtypes with del(5q), including refractory anemia (RA), refractory anemia with ringed sideroblasts (RARS) and refractory anemia with excess blasts (RAEB). C10orf10 and CD79B were specifically changed in RA patients with del(5q), while POU2AF1 were in RARS patients with del(5q). We also analyzed specific pathways of MDS subtypes, such as “Glycosaminoglycan biosynthesis-chondroitin sulfate” which was specific identified in RARS patients. Importantly, those findings can be validated well using another MDS database. Taken together, our analysis identified specific genes and pathways associated with different MDS subtypes with del(5q).

PWE-025 Serum Calprotectin – A Novel Diagnostic and Prognostic Marker in Inflammatory Bowel Diseases

Introduction There is an unmet need for novel blood based biomarkers that offer timely and accurate diagnostic and prognostic testing in Inflammatory Bowel Diseases (IBD). We aimed to investigate the diagnostic and prognostic utility of serum calprotectin (SC) in IBD Methods A total of 156 patients (82 IBD and 74 non-IBD) were sampled within 90 days from diagnosis (median 0 days; IQR 0–7). A multibiomarker diagnostic and prognostic model was derived using multivariable logistic regression analysis. Treatment escalation was defined as the need for escalation and establishment of 2 or more immunomodulatory therapies and/or surgery for disease flare after initial induction of disease remission (criteria previously used by Lee et al) (1). Cox proportional hazards model was derived to assess the contribution of each variable to disease outcomes Results SC correlated strongly with current biomarkers including CRP (rho = 0.60, p = 1.4x10−16) faecal calprotectin (FC) (rho = 0.51, p = 1.6x10−4). Paired FC was available within 30 days (median 0 days, IQR: -4 to5 days) of SC in 50 patients (IBD n = 30, non-IBD n = 20).The area under receiver operating characteristic discriminating IBD from controls was similar for FC and SC(0.95, 95% CI 0.87–1.00 and 0.89, 95%CI 0.81–0.98 respectively;p = 0.36). SC was the strongest individual predictor of IBD diagnosis (odds ratio (OR): 12.33 (95% CI 4.48–38.33, p = 3.5×10−6) compared with other markers (CRP: OR 4.44, CI 1.58–12.90; albumin: OR 5.65, CI 1.98–17.16). At follow up (median 342 days; IQR: 88–563),a total of 1 (2%), 16 (47%),23 (51%) patients required treatment escalation in the IBDU, CD and UC group respectively.SC predicted treatment escalation and/or surgery in IBD (HR 2.4, 95% CI: 1.1–4.9), in particular CD (HR 4.1, 95% CI 1.1–14.7). A model incorporating SC, CRP and albumin has a positive likelihood ratio of 20.03 for IBD.At 1 year, our prognostic model can predict treatment escalation in IBD in 65% of cases (95% CI: 43–79%) and 80% (95% CI: 31–94%) in CD if 2 or more blood marker criteria are met. Conclusion Sampling faeces can be a hurdle for patients and some individuals can decline FC testing. These factors impact on the practical utility of FC.SC shows promise as a diagnostic and prognostic biomarker in IBD. Our findings warrant further exploration and validation within large multicentre cohorts. Reference 1 Lee JC, et al. Gene expression profiling of CD8+ T cells predicts prognosis in patients with Crohn disease and ulcerative colitis. J Clin Invest 2011;121:4170–9. Disclosure of Interest None Declared

Gene expression profiling of asthma phenotypes demonstrates molecular signatures of atopy and asthma control

Recent studies have used cluster analysis to identify phenotypic clusters of asthma with differences in clinical traits, as well as differences in response to therapy with anti-inflammatory medications. However, the correspondence between different phenotypic clusters and differences in the underlying molecular mechanisms of asthma pathogenesis remains unclear. We sought to determine whether clinical differences among children with asthma in different phenotypic clusters corresponded to differences in levels of gene expression. We explored differences in gene expression profiles of CD4(+) lymphocytes isolated from the peripheral blood of 299 young adult participants in the Childhood Asthma Management Program study. We obtained gene expression profiles from study subjects between 9 and 14years of age after they participated in a randomized, controlled longitudinal study examining the effects of inhaled anti-inflammatory medications over a 48-month study period, and we evaluated the correspondence between our earlier phenotypic cluster analysis and subsequent follow-up clinical and molecular profiles. We found that differences in clinical characteristics observed between subjects assigned to different phenotypic clusters persisted into young adulthood and that these clinical differences were associated with differences in gene expression patterns between subjects in different clusters. We identified a subset of genes associated with atopic status, validated the presence of an atopic signature among these genes in an independent cohort of asthmatic subjects, and identified the presence of common transcription factor binding sites corresponding to glucocorticoid receptor binding. These findings suggest that phenotypic clusters are associated with differences in the underlying pathobiology of asthma. Further experiments are necessary to confirm these findings.

Distinct Properties of Leukemia Stem Cells in Primary Refractory Acute Myeloid Leukemia

Introduction: Acute Myeloid Leukemia (AML) patients who are refractory to induction chemotherapy (RF) have a dismal prognosis. Properties of AML cell populations that cause the refractory phenotype are poorly understood. It is postulated that the leukemia stem cell (LSC) pool promotes chemotherapy resistance in AML; yet whether differences exist in this pool as a function of eventual remission status, and thus may account for induction failure, is unknown. Our group has recently found that in AML patients who initially achieve complete remission (CR) and then relapse, the LSC pool evolves to become larger and more immunophenotypically diverse at the time of relapse [Blood 2013; 122(21): abstract #883]. Since relapsed AML patients are often refractory to salvage chemotherapy, we postulated that diagnostic specimens from RF AML patients would have enlarged, immunophenotypically-diverse LSC pools relative to AML patients achieving CR, implicating these properties in the refractory phenotype. Defining unique properties of LSCs in RF AML might provide greater insight into the mechanisms responsible for the treatment-resistant phenotype.Methods: RF AML patients were defined by having ≥ 6% leukemic blasts in their bone marrow or peripheral blood after 1 or 2 cycles of anthracycline/cytarabine-based induction chemotherapy. All studies were conducted with pre-treatment AML specimens on approved IRB protocols at the University of Rochester Medical Center. LSC frequency was determined by limiting dilution analysis and xenotransplantation into sublethally irradiated NOD scid gamma (NSG) mice. To determine immunophenotypically-defined cell populations harboring functional LSC activity, AML specimens were sorted into four distinct populations defined by CD34 and CD38 staining. The presence of LSC activity in the four resultant populations (CD34+/CD38-, CD34+/CD38+, CD34-/CD38+, and CD34-/CD38-) was determined by the ability of each sorted population to engraft NSG mice in primary and secondary transplantation experiments. RNA-seq analysis was conducted on LSC-enriched cell populations.Results: Specimens from RF AML patients were more likely to engraft NSG mice relative to those from AML patients achieving CR (6/6 vs. 13/29 in RF vs. CR patients, respectively; P=0.02). The LSC pool from six RF AML patients was studied in detail. LSC frequency ranged from 1/19 to 1/326,123. Four of the 6 RF specimens harbored LSC frequencies 6- to 7,700-fold higher than those previously reported in primary AML [Sarry et al. J Clin Invest 2011; 121(1384-395]. In 5/6 RF specimens, LSCs were present in more than one immunophenotypically-defined cell population. Relative to specimens from AML patients achieving CR, specimens from RF patients were more likely to harbor LSCs in both CD34+ and CD34- populations (P=0.04). Treatment of NSG mice xenografted with specimens from RF patients with anthracycline/cytarabine-based chemotherapy failed to eradicate disease from engrafted mice; thus, therapeutic outcome of NSG mice engrafted with specimens from RF patients resembles that seen in patients. To identify genes potentially driving the refractory LSC phenotype, we compared gene expression profiles of CD34+ cells from RF patients to those from AML patients achieving long-term remission and to those from normal donors. Ninety-nine genes were uniquely deregulated in RF LSCs, including numerous Homeobox transcription factors and components of the Wnt and Hedgehog signaling pathways, all implicated in the maintenance of stemness. Pathway analysis revealed that amino acid metabolic pathways critical to other treatment-resistant cancers and molecules involved in IL-1 signaling and implicated in metastasis of solid tumors are dysregulated in primary refractory LSCs.Conclusions: This study is the first to systematically analyze the LSC pool in primary refractory AML. Similar to our findings in relapsed AML, RF AML patients harbor enlarged, phenotypically diverse LSC pools relative to AML patients achieving CR. Challenge of leukemic mice with an anthracycline/cytarabine treatment regimen mimics the effect seen in patients, facilitating the development of patient-derived xenograft models of RF AML. We identify a refractory LSC gene signature, opening the door to future mechanistic investigations and novel therapeutic approaches for this AML patient population in great need. DisclosuresCalvi:Fate Therapeutics: Patents & Royalties. Becker:Millenium: Research Funding.

Transcription profiling of CD4⁺ T cells in rhesus macaques that infected with simian-human immunodeficiency virus and re-challenged with SIVmac251.

Insights into the host factors that contribute to an effective antiviral immune response may be obtained by examining global gene expression in simian-human immunodeficiency virus (SHIV)-infected non-human primates that exhibit different virological outcomes. Six chronically SHIV-infected macaques were rectally challenged with SIVmac251. Viral RNA and proviral DNA load in blood were measured. Gene expression profiles in CD4+ T cells were examined and compared between animals with different levels of infection following challenge. Viral RNA was markedly controlled in four challenged animals, whereas two animals had persistent high viremia. Analysis of the gene expression profiles at early infection revealed gene expression signatures between protectors and non-protectors and identified potential protective biomarkers. Pathway analyses revealed that IFN pathway genes are down-regulated in protectors compared to unprotectors. This study suggests that high levels of expression of type 1 IFN-related genes may paradoxically promote virus replication.

Microarray and Proteomic Analyses of Myeloproliferative Neoplasms with a Highlight on the mTOR Signaling Pathway.

The gene and protein expression profiles in myeloproliferative neoplasms (MPNs) may reveal gene and protein markers of a potential clinical relevance in diagnosis, treatment and prediction of response to therapy. Using cDNA microarray analysis of 25,100 unique genes, we studied the gene expression profile of CD34+ cells and granulocytes obtained from peripheral blood of subjects with essential thrombocythemia (ET), polycythemia vera (PV) and primary myelofibrosis (PMF). The microarray analyses of the CD34+ cells and granulocytes were performed from 20 de novo MPN subjects: JAK2 positive ET, PV, PMF subjects, and JAK2 negative ET/PMF subjects. The granulocytes for proteomic studies were pooled in 4 groups: PV with JAK2 mutant allele burden above 80%, ET with JAK2 mutation, PMF with JAK2 mutation and ET/PMF with no JAK2 mutation. The number of differentially regulated genes was about two fold larger in CD34+ cells compared to granulocytes. Thirty-six genes (including RUNX1, TNFRSF19) were persistently highly expressed, while 42 genes (including FOXD4, PDE4A) were underexpressed both in CD34+ cells and granulocytes. Using proteomic studies, significant up-regulation was observed for MAPK and PI3K/AKT signaling regulators that control myeloid cell apoptosis and proliferation: RAC2, MNDA, S100A8/9, CORO1A, and GNAI2. When the status of the mTOR signaling pathway related genes was analyzed, PI3K/AKT regulators were preferentially up-regulated in CD34+ cells of MPNs, with down-regulated major components of the protein complex EIF4F. Molecular profiling of CD34+ cells and granulocytes of MPN determined gene expression patterns beyond their recognized function in disease pathogenesis that included dominant up-regulation of PI3K/AKT signaling.

Knockdown of HSPA9 Induces Apoptosis and Increases TP53 Levels in Human CD34+ Hematopoietic Progenitor Cells

HSPA9, a gene located on chromosome 5q31.2, is commonly deleted in patients with myelodysplastic syndromes (MDS). MDS patients with a deletion of the long arm of chromosome 5 [del(5q)] typically present with cytopenias, including anemia, and have increased levels of apoptosis in their bone marrow contributing to ineffective hematopoiesis. Recent evidence suggests that upregulation of TP53 in MDS bone marrow cells may contribute to the cytopenias and accererated apoptosis observed in patients. While the mechanisms of TP53 activation in MDS are likely to be multifactorial, gene haploinsufficiency has been shown to contribute. Previous reports have shown that knockdown of RPS14, a chromosome 5q33.1 gene, in human CD34+ cells (or heterozygous knockout in mouse bone marrow cells) results in upregulation of TP53 and an increase in apoptosis. It is not known whether additional del(5q) candidate genes contribute to TP53 activation in del(5q)-associated MDS. In order to determine whether HSPA9 gene deletion also results in TP53 activation, we used lentiviral shRNA vectors to knockdown the expression of HSPA9 in primary human CD34+ hematopoietic progenitor cells. The HSPA9 protein level was reduced to ~20% (sh960) and ~50% (sh433) compared to the control lentiviral shRNA (shGFP). Knockdown of HSPA9 significantly inhibited the growth (fold change sh960 compared to shGFP = 0.16, p<0.01; sh433 compared to shGFP = 0.39, p=0.06, N=3) and erythroid differentiation (CD71+ expression fold change sh960 compared to shGFP =0.26, p<0.001; sh433 compared to shGFP = 0.52, p<0.01, N=3) of human CD34+ cells grown in media promoting erythroid differentiation after 7 days in culture. In addition, knockdown of HSPA9 by sh960 significantly increased apoptosis (AnnexinV+ cells) in CD34+ cells compared to shGFP (fold change = 2, p<0.01, N=3). The increased apoptosis observed following HSPA9 knockdown was associated with increased TP53 expression (fold change sh960 compared to shGFP = 2 by intracellular flow cytometry, p<0.05, N=3), TP53 activity (sh960 compared to shGFP, p<0.05; sh433 compared to shGFP, p=0.06 by TP53 luciferase reporter assay), and increased mRNA expression of the pro-apoptotic TP53 target gene BAX (fold change sh960 compared to shGFP = 1.8 by Q-RT-PCR, p<0.05). Gene expression profiling of CD34+ cells transduced with sh433 vs. control knockdown revealed that 26 well-annotated TP53-induced genes are also expressed higher in HSPA9 knockdown cells compared to controls by gene set enrichment (FWER p=0.01), further implicating TP53 activation in HSPA9 knockdown cells. We show that treatment of primary human CD34+ cells with MKT-077, a rhodacyanine dye with inhibitory effects on HSPA9 protein by binding to its nucleotide binding domain, also results in dose-dependent growth inhibition, enhanced apoptosis, and reduced erythroid differentiation, similar to that observed following HSPA9 knockdown. HSPA9 has been shown to physically interact with TP53 in the cytoplasm, and knockdown of HSPA9 changes localization of TP53 from the cytoplasm to the nucleus in non-hematopoietic cells. The loss of cytoplasmic sequestration of TP53 by HSPA9 following HSPA9 knockdown is thought to contribute to many of the cellular phenotypes induced by HSPA9 knockdown. We show by immunoprecipitation that HSPA9 also interacts with TP53 in primary human CD34+ cells, providing a possible mechanism for regulation of TP53 by HSPA9 in hematopoietic cells. These findings indicate that HSPA9 knockdown may contribute to TP53 activation and increased apoptosis observed in del(5q)-associated MDS. The data also suggest that genetic (i.e., mutation or deletion) or functional inactivation of TP53 may be necessary for disease progression to occur in MDS patients with del(5q). DisclosuresNo relevant conflicts of interest to declare.

Identification of microRNA-Regulated Pathways through a Integration of Mcrorna-mRNA Microarray and Bioinformatics Analysis in CD34+ Cells of Myelodysplastic Syndromes

BackgroundMicroRNAs (miRNAs) are considered to play a key role in the pathogenesis of myelodysplastic syndromes (MDS). However, the effect of miRNA and targeted mRNA on signal transduction is not fully understood in MDS.ObjectiveThe objective of this study is to identify the miRNAs-regulated pathways.MethodsAffymetrix GeneChip microRNA and PrimeView Array were used to analyze miRNAs and gene expression profile of CD34+ cells in 12 MDS patients and 6 healthy controls. Comprehensive bioinformatics analysis of the coordinate expression of miRNAs and mRNAs including Difference, Go, Pathway, Pathway-network, miRNA-Gene-Network and miRNA-Go-Network analysis was performed to identify the miRNAs-regulated networks.Results1. 34 differentially expressed miRNAs (5 up- and 29 down-regulated miRNAs) and 1783 mRNAs (405 up- and 1378 down-regulated mRNAs) in CD34+ cells from MDS and Healthy controls were identified by miRNA and mRNA microarray, respectively (Fig.1).2. 25 dysregulated miRNAs and 234 targeted mRNAs were identified by a combination of Pearson’s correlation analysis and prediction by TargetScan; 394 target relationship of miRNAs was established (Fig.2).3. Go analysis revealed that these miRNA-mRNAs pairs were involved in signal transduction, apoptotic process, DNA-dependent transcription regulation, protein phosphophoration, etc. Pathway analysis showed that MAPK, JAK/STAT and PI3K/Akt signaling pathways might be regulated by these miRNA-mRNAs pairs (Fig.3).4. The pathway-network analysis revealed that MAPK signaling pathway, Jak-Stat signaling pathway and apoptosis signaling pathway (displayed by red cycle) located in the downstream of signal networks (Fig. 3E). Dysregulation of These pathways may be more meaningful for explaining the pathogenesis of MDS.5. Through a combination of Pathway, miRNA-Gene-Network and miRNA-Go- Network analysis, 29 miRNA-mRNA-regulated pathways were identified such as miR-148a/TEK/PI3K-Akt signaling pathway, miR-195/BDNF/MAPK signaling pathway, miR-195/DLL1/Notch signaling pathway, miR-145/CCND2/ JAK-STAT signaling pathway, etc. (Table 1).ConclusionAlteration expression of several miRNAs and targeted mRNAs might have an important impact on cancer-related cellular pathways including MAPK, PI3K/Akt, JAK/STAT, etc. The role of these miRNAs-mediated pathways in pathogenesis of MDS merit further investigation. [Display omitted] [Display omitted] Table 1.Parts of dysregulated miRNAs, genes and targeted pathway in MDSMicroRNAStyleGene_synbolPathwaymiR-148aDownTEKPI3K-Akt signaling pathwayITGA9PI3K-Akt signaling pathwayKITPI3K-Akt signaling pathwayHMGA2Transcriptional misregulation in cancermiR-145DownHHEXTranscriptional misregulation in cancerMEIS1Transcriptional misregulation in cancermiR-200cDownEFNA1PI3K-Akt signaling pathwayKLF3Transcriptional misregulation in cancermiR-195UpBDNFMAPK signaling pathwayCDC25BMAPK signaling pathwayDLL1Notch signaling pathwayMRASMAPK signaling pathwaymiR-17UpCAMK2DCalcium signaling pathwaymiR-19aUpMAML1Notch signaling pathwaySLC8A1Calcium signaling pathwayTHBS1Proteoglycans in cancerTNFMAPK signaling pathwayTNFRSF1BAdipocytokine signaling pathwayACSL1Adipocytokine signaling pathwayEDNRBCalcium signaling pathwaymiR-19bUpCALM1Calcium signaling pathwayTNFProteoglycans in cancer [Display omitted] DisclosuresNo relevant conflicts of interest to declare.