Unique Gene Expression Patterns Research Articles

Aged donor derived CAR-T exhibits enhanced effector functions but shorter persistence and less memory-like phenotypes

Abstract Background CD19 chimeric antigen receptor (CAR) T cell therapies have been successful in B cell malignancies. Recent reports about CD19 CAR T cell therapy in B-cell acute lymphoblastic leukemia suggest that the median event-free survival of children and young adult patients is longer than that of adult patients. Since the reason is unclear, we compared the functions of CAR-T derived from young or aged mice and also healthy human donors. Methods Young and aged B6 mice spleens (6-12 vs. ≥72 weeks) or young and aged human PBMCs (20-26 vs. 53-60 years) were used for mouse or human CAR-T preparation. 4 types of mouse CD19 CAR and 2 types of human CD19 CAR were evaluated in T cells. Results Aged mouse CAR-T predominates with CD8+ and effector-like phenotypes at the expense of CD4+ and memory-like phenotypes. Compared to young mouse CAR-T, aged mouse CAR-T exhibited superior cytotoxicity for mouse CD19+ artificial antigen presenting cell (aAPC). Using our immune competent in vivo murine model, aged mouse CAR-T was short-lived and expanded poorly despite superior in vitro cytotoxicity. RNA-Seq suggestes that young mouse CAR-T is advantageous for cell proliferation and regulation of cell differentiation whereas aged mouse CAR-T up-regulates gene expression pathways that regulate responses to stimulus and exocytosis. Furthermore, compared to mouse CAR-T, human CAR-T is complementary with immune phenotypes after human CD19+ aAPC stimulation. Conclusions Aged donor derived CAR-T exhibited enhanced effector functions but shorter persistence and less memory-like phenotypes. Our results suggest that the difference of clinical outcomes may be due to an age-dependent CAR-T cell phenotype that is reflected by its unique gene expression pattern, secretory profile, and/or transcription factor balance. In our future directions we are identifying potential methods to improve the function of aged donor derived CAR-T.

MRNA MPS tissue identification assay to aid in the investigation of traumatic injuries

Molecular analysis of the RNA transcriptome from a putative tissue fragment should permit assignment to a specific organ since each tissue will exhibit a unique pattern of gene expression. Determination of the organ source of tissues from crime scenes may aid in shooting and stabbing investigations. We have developed a new prototype massively parallel sequencing (MPS) mRNA profiling assay for organ tissue identification, designed to definitively identify 13 organ/tissue types using a targeted panel of 48 mRNA biomarkers. The identifiable organs and tissues include brain, spinal cord, lung, trachea, liver, skeletal muscle, heart, kidney, adipose, intestine, stomach, skin and spleen. The biomarkers were chosen after iterative specificity testing of numerous candidate genes in various tissue types. The assay is very specific with little cross reactivity with non-targeted tissue, and can detect RNA mixtures from different tissues, including two- to five-tissue admixtures. The sensitivity of the assay was evaluated as well as assay reproducibility between library preparations and sequencing runs. We also demonstrate the ability of the assay to successfully identify the tissue source of origin in cadaver samples, tissue samples with varying post mortem intervals (PMI) and mock and bona fide casework samples. We are using the data to train a multivariate statistical model that predicts the tissue type based on the mRNA profile. By considering co-expression of markers the model can recognize distinct expression patterns in each tissue.

Novel technique for the simultaneous isolation of cardiac fibroblasts and epicardial stromal cells from the infarcted murine heart.

Myocardial infarction (MI) leads to activation of cardiac fibroblasts (aCFs) and at the same time induces the formation of epicardium-derived cells at the heart surface. To discriminate between the two cell populations, we elaborated a fast and efficient protocol for the simultaneous isolation and characterization of aCFs and epicardial stromal cells (EpiSCs) from the infarcted mouse heart. For the isolation of aCFs and EpiSCs, infarcted hearts (50 min ischaemia/reperfusion) were digested by perfusion with a collagenase-containing medium for only 8 min, while EpiSCs were enzymatically removed from the outside by applying mild shear forces via a motor driven device. Cardiac fibroblasts (CFs) isolated from unstressed hearts served as control. Viability of isolated cells was >90%. Purity of EpiSCs was confirmed by immunofluorescence staining and qPCR of various mesenchymal markers including Wilms-tumor-protein-1. Microarray analysis of CFs, aCFs, and EpiSCs on day 5 post-MI revealed a unique gene expression pattern in the EpiSC fraction, which was enriched for epithelial markers and epithelial to mesenchymal transition-related genes. Compared to aCFs, 336 significantly altered gene entities were identified in the EpiSC fraction. qPCR analysis showed high expression of Serpinb2, Cxcl13, Adora2b, and Il10 in EpiSCs relative to CFs and aCFs. Furthermore, microarray data identified Ddah1 and Cemip to be highly up-regulated in aCFs compared to CFs. Immunostaining of the infarcted heart revealed a unique distribution of Dermokine, Aquaporin-1, Cytokeratin, Lipocalin2, and Periostin within the epicardial cell layer. We describe the simultaneous isolation of viable, purified fractions of aCFs and EpiSCs from the infarcted mouse heart. In this study, several differentially expressed markers for aCFs and EpiSCs were identified, underlining the importance of cell separation to study heterogeneity of stromal cells in the healing process after MI.

Comparative identification, nutritional, and physiological regulation of chicken liver-enriched genes

The liver performs a number of vital functions in the chicken. In order to identify unique gene expression patterns and link them to potential functions in the chicken liver, genes enriched in the liver of chickens needed to be investigated in a comparative manner. In this study, 41 liver-enriched genes were identified through chicken microarray, and many of them were validated through comparative analysis of mice and humans. Thirteen of them were unique in chickens, and their liver enhancement was confirmed by reverse transcription PCR. Furthermore, the expression of those 13 chicken liver-enriched genes was investigated, in response to nutritional and physiological challenges. Real-time PCR revealed that expression of PIT54 (P < 0.01), phosphoribosyl pyrophosphate synthetase 2 (PRPS2) (P < 0.05), sulfotransferase (SULT) (P < 0.05), and cytochrome P450 family 2 subfamily C, polypeptide 18 (CYP2C18) (P < 0.05) were significantly decreased in the liver during fasting compared to ad libitum control. During the post-laying stage, expression of GAL8 was significantly increased (P < 0.01), but CYP2C18 expression was significantly reduced (P < 0.05). Liver-enriched genes that were identified in this study and their expression patterns under fasting and the post-laying stage will serve as future targets to gain a better understanding of liver physiology, function and development in poultry.

Competitive ability during mate competition relates to unique patterns of dopamine-related gene expression in the social decision-making network of male zebra finches

Aggressive interactions usually reveal individual differences in the competitive ability of contest participants. Individuals with higher competitive ability often gain priority access to resources such as food, territory, and/or mates. Individuals with lower competitive ability usually have reduced access to these resources and limited mating opportunities. Despite the importance of contest performance to the reproductive success of individuals, the neuroendocrine factors associated with individual differences in competitive ability have not been fully elucidated. Here, we investigate the relationship between dopamine (DA)-related gene expression and competitive ability during mate competition in male zebra finches. Males demonstrating high competitive ability (HCA) had higher tyrosine hydroxylase mRNA levels in the ventral tegmental area and higher D1 receptor (D1-R) mRNA levels in the preoptic area than low competitive ability (LCA) males. Additionally, HCA males had lower levels of D1-R mRNA in the anterior hypothalamus relative to LCA males. These data suggest that there are dynamic and region-specific changes in DA function that relate to variation in competitive ability during mate competition.

Integrative Analysis Reveals Subtype-Specific Regulatory Determinants in Triple Negative Breast Cancer.

Different breast cancer (BC) subtypes have unique gene expression patterns, but their regulatory mechanisms have yet to be fully elucidated. We hypothesized that the top upregulated (Yin) and downregulated (Yang) genes determine the fate of cancer cells. To reveal the regulatory determinants of these Yin and Yang genes in different BC subtypes, we developed a lasso regression model integrating DNA methylation (DM), copy number variation (CNV) and microRNA (miRNA) expression of 391 BC patients, coupled with miRNA–target interactions and transcription factor (TF) binding sites. A total of 25, 20, 15 and 24 key regulators were identified for luminal A, luminal B, Her2-enriched, and triple negative (TN) subtypes, respectively. Many of the 24 TN regulators were found to regulate the PPARA and FOXM1 pathways. The Yin Yang gene expression mean ratio (YMR) and combined risk score (CRS) signatures built with either the targets of or the TN regulators were associated with the BC patients’ survival. Previously, we identified FOXM1 and PPARA as the top Yin and Yang pathways in TN, respectively. These two pathways and their regulators could be further explored experimentally, which might help to identify potential therapeutic targets for TN.

Ventricular transcriptomic changes induced by cold‐acclimation in the painted turtle suggests epigenetic‐mediated transcriptional remodeling

Ectothermic vertebrates living at extreme latitudes are often forced to endure extended periods with their body temperatures at or just above the freezing point of water. Cold temperatures impose a number of physiological and biochemical challenges directly related to the thermodynamic effects on biological matter, including metabolic enzyme kinetics and even the physical properties of blood. The painted turtle, Chrysemys picta, is a pond turtle that can experience temperatures just above freezing for 3–5 months as adults and can tolerate freezing or even subzero temperatures as hatchlings. In the present study, we characterized how cold acclimation to 3°C affected the ventricular transcriptome in both adult and hatchling turtles. Because hatchlings must tolerate subzero temperatures when they overwinter in their nest, we sought to determine if they might also exhibit a unique gene expression pattern related to possible cryoprotective mechanisms. Despite differences in life history, adults and hatchlings responded similarly to cold acclimation at the transcriptomic level; out of the 1304 genes that were differentially expressed due to temperature, 1272 showed similar expression patterns in adults and hatchlings, the majority of which were upregulated. In adults and hatchlings combined, 776 genes were upregulated at 3°C, 550 genes were downregulated, of which 22 fell into both categories due to development‐specific expression patterns. Of these upregulated genes, 51 encoded for transcription factors, 27 for histone modification proteins, and 26 for mRNA processing and translational regulation enzymes. These results suggest that the ventricle actively remodels chromatin structure and modulates both gene expression and mRNA processing in response to cold acclimation.Support or Funding InformationThis work was supported by NSF CAREER grant 1253939 awarded to DEWThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Distinct Patterns of Gene Expression Identified Longitudinally and within AlloMap Score Ranges are Associated with Clinical Outcomes

Summary of Objectives Gene expression profiling (GEP, AlloMap) has become the standard of care in heart transplant patient management with over 120,000 performed. The large size of the dataset enables identification of distinct patterns of longitudinal and component gene expression. OAR is a prospective observational heart transplant registry with integrated GEP testing to elucidate factors that contribute to long term outcomes. Samples with GEP scores and individual gene data but not included in OAR have been examined by unsupervised methods to identify patterns of gene expression. These patterns can then be correlated with outcomes collected in OAR to identify specific signals that are indicative of different outcomes. Methods Latent class mixed models were used to estimate profiles of GEP score over time with 62,833 samples from 8,066 patients with at least two GEP score measures. Distinct patterns were identified in a 3-class model; with 69% of the 8,066 patients in a class with a gradual increase in GEP score over time; 23% with a stable GEP score, and 8% with a rapid increase in GEP score. The full dataset of 19,761 patients and 104,827 samples was used to identify patterns of gene expression among the 7 gene terms and the principle components contributing to the GEP Scores. PDCD1, ITGA4, RHOU, and SEMA7A were correlated more closely than the remaining terms. Additionally, the 7 terms were used in an archetypal analysis that identified eight unique archetype patterns of gene expression. For example, two archetypes, #4 and #8 have median GEP scores of 29.4 and 29.9, but different gene patterns. Archetype #4 has high RHOU and PF4/G6B1, but low SEMA7A. Archetype #8 has high IL1R2/FLT3/ITGAM and low PF4/G6B1. Endpoints The principal components analysis identified correlations that match the known and hypothesized biological mechanisms of the genes; the highest correlation was among four genes known or hypothesized to be indicators of T cell activation. The identified archetypal patterns will be assigned to patients in the OAR registry to identify clinical correlates with each archetype group. Among the clinical factors that will be investigated are malignancies, infections, cellular rejection, and cardiac allograft vasculopathy.

Identification of the molecular subgroups in coronary artery disease by gene expression profiles.

Coronary artery disease (CAD) is the most common type of cardiovascular disease and becomes a leading cause of death worldwide. Aiming to uncover the underlying molecular features for different types of CAD, we classified 352 CAD cases into three subgroups based on gene expression profiles, which were retrieved from the Gene Expression Omnibus database. Also, these subgroups present different expression patterns and clinical characteristics. To uncover the transcriptomic differences between the subgroups, weighted gene co-expression analysis (WGCNA) was used and identified six subgroup-specific WGCNA modules. Characterization of the WCGNA modules revealed that lipid metabolism pathways, specifically upregulated in subgroup I, might be an indicator of increased severity. Moreover, subgroup II was considered as an early-stage of CAD because of normal-like gene expression patterns. In contrast, the mammalian target of rapamycin signaling pathway was significantly upregulated in subgroup III. Although subgroups II and III did not have a significant prognostic difference, their intrinsic biological characteristics were highly different, suggesting that the transcriptome classification may represent risk factors of both age and the intrinsic biological characteristics. In conclusion, the transcriptome classification of CAD cases revealed that cases from different subgroups may have their unique gene expression patterns, indicating that patients in each subgroup should receive more personalized treatment.

Abstract # 3200 IL-6 production during repeated social defeat stress primes monocytes to induce anxiety-like behavior

Interleukin (IL)-6 is elevated in circulation with chronic stress and may contribute to the neurobehavioral complications. We have reported that repeated social defeat (RSD) stress in mice caused recruitment of proinflammatory monocytes to the brain and triggered the onset of anxiety-like behavior. The purpose of this study was to determine the role of IL-6 signaling in the peripheral immune response, neuroinflammation, and anxiety following stress. WT and IL-6KO mice were subjected to RSD. Although monocyte recruitment to the brain following stress was maintained in the IL-6KO mice, anxiety and social avoidance were completely prevented. Nanostring profiling of sorted monocytes from blood (CD11b + Ly6Chi) and brain (CD11b + CD45hi) revealed a unique pattern of immune-related gene expression that was dependent on stress and IL-6. For instance, blood monocytes had a transcriptional signature consistent with priming and glucocorticoid resistance, which was absent in the monocytes from IL-6KO mice after stress. Brain monocytes from WT mice had increased levels of Il-1b, Mmp9, Stat3, Myd88 and Cd14 following stress. This phenotype was absent in brain monocytes from IL-6KO mice. Here, we show the effects of IL-6 on the transcriptional signature of monocytes in circulation and in the brain after stress. Overall, robust increases in circulating IL-6 after stress induced a primed profile in the monocytes, which were recruited to the brain and functioned to augment IL-1-mediated inflammation and anxiety.

Sleeping Beauty Screen Identifies RREB1 and Other Genetic Drivers in Human B-cell Lymphoma.

Follicular lymphoma and diffuse large B-cell lymphoma (DLBCL) are the most common non-Hodgkin lymphomas distinguishable by unique mutations, chromosomal rearrangements, and gene expression patterns. Here, it is demonstrated that early B-cell progenitors express 2',3'-cyclic-nucleotide 3' phosphodiesterase (CNP) and that when targeted with Sleeping Beauty (SB) mutagenesis, Trp53R270H mutation or Pten loss gave rise to highly penetrant lymphoid diseases, predominantly follicular lymphoma and DLBCL. In efforts to identify the genetic drivers and signaling pathways that are functionally important in lymphomagenesis, SB transposon insertions were analyzed from splenomegaly specimens of SB-mutagenized mice (n = 23) and SB-mutagenized mice on a Trp53R270H background (n = 7) and identified 48 and 12 sites with statistically recurrent transposon insertion events, respectively. Comparison with human data sets revealed novel and known driver genes for B-cell development, disease, and signaling pathways: PI3K-AKT-mTOR, MAPK, NFκB, and B-cell receptor (BCR). Finally, functional data indicate that modulating Ras-responsive element-binding protein 1 (RREB1) expression in human DLBCL cell lines in vitro alters KRAS expression, signaling, and proliferation; thus, suggesting that this proto-oncogene is a common mechanism of RAS/MAPK hyperactivation in human DLBCL. IMPLICATIONS: A forward genetic screen identified new genetic drivers of human B-cell lymphoma and uncovered a RAS/MAPK-activating mechanism not previously appreciated in human lymphoid disease. Overall, these data support targeting the RAS/MAPK pathway as a viable therapeutic target in a subset of human patients with DLBCL.

Comparative transcriptome analysis reveals unique genetic adaptations conferring salt tolerance in a xerohalophyte.

Most studies on salt tolerance in plants have been conducted using glycophytes like Arabidopsis thaliana (L.) Heynh., with limited resistance to salinity. The xerohalophyte Zygophyllum xanthoxylum (Bunge) Engl. is a salt-accumulating desert plant that efficiently transports Na+ into vacuoles to manage salt and exhibits increased growth under salinity conditions, suggesting a unique transcriptional response compared with glycophytes. We used transcriptome profiling by RNA-seq to compare gene expression in roots of Z. xanthoxylum and A. thaliana under 50 mM NaCl treatments. Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis suggested that 50 mM NaCl was perceived as a stimulus for Z. xanthoxylum whereas a stress for A. thaliana. Exposure to 50 mM NaCl caused metabolic shifts towards gluconeogenesis to stimulate growth of Z. xanthoxylum, but triggered defensive systems in A. thaliana. Compared with A. thaliana, a vast array of ion transporter genes was induced in Z. xanthoxylum, revealing an active strategy to uptake Na+ and nutrients from the environment. An ascorbate-glutathione scavenging system for reactive oxygen species was also crucial in Z. xanthoxylum, based on high expression of key enzyme genes. Finally, key regulatory genes for the biosynthesis pathways of abscisic acid and gibberellin showed distinct expression patterns between the two species and auxin response genes were more active in Z. xanthoxylum compared with A. thaliana. Our results provide an important framework for understanding unique patterns of gene expression conferring salt resistance in Z. xanthoxylum.

EGFR-Mutant SCLC Exhibits Heterogeneous Phenotypes and Resistance to Common Antineoplastic Drugs

IntroductionApproximately 5% of patients with EGFR-activating mutations acquire EGFR tyrosine kinase inhibitor (TKI) resistance through SCLC transformation. However, the reason for the poor outcome and the molecular basis of EGFR-mutant SCLC that has transformed from adenocarcinoma remain unclear. MethodsIn this study, we established two EGFR-mutant SCLC cell lines from lung adenocarcinoma patients after failed EGFR-TKI treatment to investigate their molecular basis and potential therapeutic strategies in the hope of improving patient outcome. ResultsThese two EGFR-mutant SCLC cell lines displayed two different phenotypes: suspensive and adherent. Both phenotypes shared the same genomic alterations analyzed by array-based comparative genomic hybridization assay. Increased expression of EGFR and mesenchymal markers and decreased expression of neuroendocrine markers were observed in adherent cells. Principal component analysis and hierarchical clustering analysis of RNA microarray revealed that these two cell lines displayed a unique gene expression pattern that was distinctly different from that in NSCLC and classical SCLC cells. Combined treatment using an EGFR-TKI and an AKT inhibitor attenuated cell viabilities in our two cell lines. Moreover, the use of a histone deacetylase inhibitor significantly inhibited the cell viabilities of both cell lines in vitro and in vivo. ConclusionOur findings suggest that EGFR-mutant SCLC may be a distinct subclass of SCLC that exhibits epithelial-mesenchymal transition phenotypes, and adding an AKT or histone deacetylase inhibitor to pre-existing therapies may be one of the therapeutic choices for transformed EGFR-mutant SCLC.

Aged CAR T Cells Exhibit Enhanced Cytotoxicity and Effector Function but Shorter Persistence and Less Memory-like Phenotypes

▪[Introduction]CD19 chimeric antigen receptor (CAR) T cell therapies have been approved by the FDA for children and young adults with relapsed/refractory (r/r) B-cell acute lymphoblastic leukemia (B-ALL) and adults with r/r large B-cell lymphoma. Recent reports about long-term follow-up of CD19 CAR T cell therapy in B-ALL (Maude et. al. NEJM 2018, Park et. al. NEJM 2018) suggest that the median event-free survival of children and young adult patients is longer than that of adult patients (Over 11 months versus 6.1 months). The reason for the difference between survival of pediatric and adult patient is unclear, but we hypothesize it is due to age-related changes in the T cells collected from patients. Therefore, we compared the function of CAR T cells derived from young or aged mice.[Methods]Young C57BL/6J (B6) mice (6-12 weeks) and aged B6 mice (³ 72 weeks) were used as donors for CAR T cell preparation. Four types of mouse specific CD19 CAR encoded GFP fusion proteins were evaluated with all having the same anti-CD19 scFv and CD8 hinge and transmembrane domains but differing in their intracellular domain (m19Δz: lacks the CD3ξ signaling domain, m19z: CD3ξ signaling domain only, m1928z: CD28 and CD3ξ signaling domains, m19-humBBz: 4-1BB and CD3ξ signaling domains).[Results]T cells isolated from the spleen of aged B6 mice were significantly fewer than those of young B6 mice. However, CAR transduction efficiency, viability and yield were similar between young and aged CAR T cells for each CAR group. All groups of aged CAR T cells predominate with CD8+ and effector-like phenotypes at the expense of CD4+ and memory-like phenotypes after CD19+ artificial antigen presenting cell (aAPC) stimulation (Fig. 1A-1B). Furthermore, compared to CAR T cells derived from young mice, aged CAR T cells (m19z, m1928z and m19BBz) exhibited superior cytotoxicity in a real-time cell analysis for CD19+ aAPC killing (Fig. 1C). Using our immune competent in vivo murine model, aged CAR T cells were short-lived and expanded poorly despite their superior in vitro cytotoxicity. To evaluate for potential mechanisms involving preferential production of effector-like CAR T cells from aged mice we performed gene-expression, as well as single cell secretory polyfunctional analyses. While the polyfunctional strength index (PSI) of CD8+ aged CAR T cells was higher for aged CAR T cells, the increased score was due mostly to abundant secretion of a chemokine (Fig. 1D). Furthermore, the RNA-DESeq analysis demonstrated increased expression of chemokines and perturbation of the EOMES/TBET transcription factor axis. RNA-DESeq also suggested that young CAR T cells were highly active in cell proliferation and cell differentiation whereas aged CAR T cells upregulated gene expression pathways that regulated responses to stimulus and exocytosis.[Conclusions]CAR T cells derived from aged mice exhibited enhanced cytotoxicity but shorter persistence and less memory-like phenotypes. Our results suggest that the difference of clinical outcome between younger patients and older patients may be due to an age-dependent CAR T cell phenotype that is reflected by its unique gene expression pattern, secretory profile, and/or transcription factor balance. In our future directions we are extending these observations to human CAR T cells and identifying potential methods to improve the function of aged CAR T cells. [Display omitted] DisclosuresDavila:Celyad: Consultancy, Membership on an entity's Board of Directors or advisory committees.

Transcriptomic insights into the early host-pathogen interaction of cat intestine with Toxoplasma gondii

BackgroundAlthough sexual reproduction of the parasite Toxoplasma gondii exclusively occurs in the cat intestine, knowledge about the alteration of gene expression in the intestine of cats infected with T. gondii is still limited. Here, we investigated the temporal transcriptional changes that occur in the cat intestine during T. gondii infection.MethodsCats were infected with 100 T. gondii cysts and their intestines were collected at 6, 12, 18, 24, 72 and 96 hours post-infection (hpi). RNA sequencing (RNA-Seq) Illumina technology was used to gain insight into the spectrum of genes that are differentially expressed due to infection. Quantitative RT-PCR (qRT-PCR) was also used to validate the level of expression of a set of differentially expressed genes (DEGs) obtained by sequencing.ResultsOur transcriptome analysis revealed 2363 DEGs that were clustered into six unique patterns of gene expression across all the time points after infection. Our analysis revealed 56, 184, 404, 508, 400 and 811 DEGs in infected intestines compared to uninfected controls at 6, 12, 18, 24, 72 and 96 hpi, respectively. RNA-Seq results were confirmed by qRT-PCR. DEGs were mainly enriched in catalytic activity and metabolic process based on gene ontology enrichment analysis. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that transcriptional changes in the intestine of infected cats evolve over the course of infection, and the largest difference in the enriched pathways was observed at 96 hpi. The anti-T. gondii defense response of the feline host was mediated by Major Histocompatibility Complex class I, proteasomes, heat-shock proteins and fatty acid binding proteins.ConclusionsThis study revealed novel host factors, which may be critical for the successful establishment of an intracellular niche during T. gondii infection in the definitive feline host.

Interleukin-6 Induced by Social Stress Promotes a Unique Transcriptional Signature in the Monocytes That Facilitate Anxiety

BackgroundInterleukin-6 (IL-6) is elevated in circulation with chronic stress and may contribute to neurobehavioral complications. We have reported that repeated social defeat stress in mice caused recruitment of proinflammatory monocytes to the brain and triggered the onset of anxiety-like behavior. Therefore, the purpose of this study was to determine the role of IL-6 signaling in the peripheral immune response, neuroinflammation, and anxiety following stress. MethodsWild-type and IL-6 knockout mice were subjected to repeated social defeat, and immune and behavioral parameters were determined 14 hours later. ResultsAlthough monocyte release and recruitment to the brain during stress were maintained in the IL-6 knockout mice, anxiety and social avoidance were prevented. NanoString analysis of fluorescence-activated cell–sorted blood monocytes (CD11b+/Ly6Chi) and brain monocytes (CD11b+/CD45hi) revealed a unique pattern of immune-related gene expression that was dependent on stress and IL-6. For instance, blood monocytes after stress had a transcriptional signature and immune profile consistent with priming, which was attenuated in monocytes from IL-6 knockout stress mice. Moreover, the monocytes recruited to the brain and associated with the development of anxiety had a transcriptional signature (enhanced IL-1β, CD14, Mmp9, Myd88, Ager, and Stat3) that was dependent on IL-6. ConclusionsHere, we show the effects of IL-6 on the transcriptional signature of monocytes in circulation and brain after stress. Overall, robust increases in IL-6 after stress induced a primed profile in monocytes that were recruited to the brain and propagated IL-1-mediated inflammation and anxiety.

Microglia-Specific Expression of Olfml3 Is Directly Regulated by Transforming Growth Factor β1-Induced Smad2 Signaling.

Microglia maturation takes place during the postnatal weeks and is characterized by the establishment of a unique microglia-specific gene expression pattern. Tmem119, Fcrls, Hexb, and Olfml3 have been identified among these microglia-specific genes. Transforming growth factor β1 (TGFβ1) has been reported as a critical factor for microglia maturation and maintenance and active TGFβ signaling precedes the inductions of microglial gene expression. In this study, we demonstrate Olfml3 expression in adult microglia and further provide evidence that TGFβ1 induces upregulation of Olfml3 expression in postnatal microglia. Using chromatin immunoprecipitation and microglia-specific silencing of TGFβ signaling in vitro and in vivo, we in clearly show that Olfml3 is a direct TGFβ1/Smad2 target gene. Together, our data underline the importance of TGFβ1 as a critical regulator of microglia functions and microglia maturation and further broaden our understanding of TGFβ1-mediated effects on the resident immune cells of the central nervous system.

Genetic profiles of transcriptomic clusters of childhood asthma determine specific severe subtype.

Previous studies have defined transcriptomic subtypes of adult asthma using samples of induced sputum and bronchial epithelium; however, those procedures are not readily applicable in the clinic, especially for childhood asthma. We aim to dissect the transcriptomic clusters of childhood asthma using highly variably expressed genes of peripheral blood mononuclear cells (PBMC) among patients. Gene expression of PBMC from 133 asthmatic children and 11 healthy controls was measured with Illumina microarrays. We applied the k-means clustering algorithm of 2048 genes to assign asthmatic children into clusters. Genes with differential expression between asthma clusters and healthy controls were used to investigate whether they could identify severe asthma of children and adults. We identified 3 asthma clusters with distinct inflammatory profiles in peripheral blood. Cluster 1 had the highest eosinophil count. Cluster 2 showed lower counts of both eosinophils and neutrophils. Cluster 3 had the highest neutrophil count and the poorest treatment control. Compared with other patients, Cluster 3 exhibited a unique gene expression pattern which was associated with changes in the glucocorticoid signalling and activation of the T helper 1/T helper 17 (TH 1/TH 17) immune pathways. In the validation studies, an 84-gene signature could identify severe asthma in children on leucocytes, as well as severe asthma in adults on CD8+ T cells. Gene expression profiling of PBMC is useful for the identification of TH 1/TH 17-mediated asthma with poor treatment control. PBMC and CD8+ T cells could be important targets for the investigation and identification of severe asthma.

Cardiomyocytes have mosaic patterns of protein expression.

Skeletal myocytes have well-established fast and slow twitch fibers with unique gene and protein specific expression patterns. By immunohistochemical staining, these show a mosaic pattern across myocytes. We hypothesized cardiac myocytes may behave similarly where some proteins are differentially expressed between mature cardiomyocytes. We utilized the tool HPASubC on over 52,000 cardiac images of the Human Protein Atlas to identify differential protein expression patterns by immunohistochemistry across the cardiomyocytes. We matched identified proteins to open chromatin and gene expression data. We identified 143 putative proteins with mosaic patterns of expression across the cardiomyocytes. We validated four of these proteins (MYL3, MYL4, PAM, and MYOM1) and demonstrated unique atrial or ventricular patterns of expression for each. Acetylation of histone H3K27 at the promoters of these four genes were consistent with the atrial/ventricular expression patterns. Despite the generally accepted homogeneity of cardiomyocytes, a small subset of proteins varies between cardiomyocytes in a mosaic pattern. This fundamental process has been previously uncharacterized. These changes may inform on different functional and disease-related activities of proteins in individual cardiomyocytes.

Abstract PD8-02: Mechanisms of recurrence: Paired analysis of primary and metastatic triple negative breast cancer

Abstract Background: Triple negative breast cancer (TNBC) is the most aggressive subtype of invasive breast cancer that lacks ER, PR, and HER2 expression. It is a heterogeneous disease with several molecular subtypes: basal-like1 (BL-1), basal-like 2 (BL-2), mesenchymal (M), and luminal androgen receptor (LAR). Treatment for TNBC is normally limited to chemotherapy, and relapse is common. Here we report molecular alterations associated with TNBC metastasis by analyzing the genomic profiles of paired primary and metastatic TNBCs. Methods:50 paired TNBCs were identified through an IRB-approved protocol via the City of Hope (COH) Biospecimen Repository. DNA mutation and mRNA expression profiles of 10 paired primary and metastatic TNBCs were analyzed. DNA mutations were identified using exome sequencing by FoundationOne®. Affymetrix Human Genechip 2.0 was used for mRNA expression profiling. Raw data were normalized and processed using Expression Console, and linear regression was performed using Limma to identify the differentially expressed genes between primary and metastatic TNBCs. Results: DNA mutation profiling showed that multiple mutations occurred within genes covering pathways of PI3K/AKT/mTOR, DNA repair, RAS/MAPK, cell cycle, and growth factor receptor signaling, reconfirming genomic heterogeneity of TNBCs. Gene expression profiles were analyzed for Lehmann's TNBC molecular subtypes (BL-1, BL-2, M, and LAR). Six of ten TNBCs showed phenotype shift between the primary and metastatic TNBCs. Several unique gene expression patterns were identified by comparing the paired TNBCs. CCNE1 and TPX2 were co-overexpressed in metastatic TNBCs compared to paired primaries. This mirrored prior studies in ovarian cancer, where co-overexpression of CCNE1 and TPX2 were found related to clonal resistance against chemotherapy. Splicing factors TRA2B and SRSF7 were also over-expressed in metastatic TNBCs compared with primaries. The analysis studying the association of CCNE1 and TPX2 with overall survival is ongoing using TCGA. Conclusion: Overall, these results show the comparative changes between primary and relapsed TNBCs and indicate the heterogeneity of molecular mechanisms of recurrence. CNNE1 and TPX2 may represent important genes involved in TNBC metastasis. Further analyses including a total of 50 paired TNBCs are currently underway. Study Contact: Yuan Yuan MD PhD, City of Hope Comprehensive Cancer Center; Duarte, CA 91030; Email: yuyuan@coh.org Citation Format: Zhao Z-M, Yost S, Yuan Y-C, Warden C, Chuang J, Yuan Y. Mechanisms of recurrence: Paired analysis of primary and metastatic triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD8-02.