Generated Gene Expression Profiles Research Articles

Identification of endophenotypes supporting outcome prediction in hemodialysis patients based on mechanistic markers of statin treatment

BackgroundStatins are widely used to reduce the risk of cardiovascular disease (CVD). Patients with end-stage renal disease (ESRD) on hemodialysis have significantly increased risk of developing CVD. Statin treatment in these patients however did not show a statistically significant benefit in large trials on a patient cohort level. MethodsWe generated gene expression profiles for statins to investigate the impact on cellular programs in human renal proximal tubular cells and mesangial cells in-vitro. We subsequently selected biomarkers from key statin-affected molecular pathways and assessed these biomarkers in plasma samples from the AURORA cohort, a double-blind, randomized, multi-center study of patients on hemodialysis or hemofiltration that have been treated with rosuvastatin. Patient clusters (phenotypes) were created based on the identified biomarkers using Latent Class Model clustering and the associations with outcome for the generated phenotypes were assessed using Cox proportional hazards regression models. The multivariable models were adjusted for clinical and biological covariates based on previously published data in AURORA. ResultsThe impact of statin treatment on mesangial cells was larger as compared with tubular cells with a large overlap of differentially expressed genes identified for atorvastatin and rosuvastatin indicating a predominant drug class effect. Affected molecular pathways included TGFB-, TNF-, and MAPK-signaling and focal adhesion among others. Four patient clusters were identified based on the baseline plasma concentrations of the eight biomarkers. Phenotype 1 was characterized by low to medium levels of the hepatocyte growth factor (HGF) and high levels of interleukin 6 (IL6) or matrix metalloproteinase 2 (MMP2) and it was significantly associated with outcome showing increased risk of developing major adverse cardiovascular events (MACE) or cardiovascular death. Phenotype 2 had high HGF but low Fas cell surface death receptor (FAS) levels and it was associated with significantly better outcome at 1 year. ConclusionsIn this translational study, we identified patient subgroups based on mechanistic markers of statin therapy that are associated with disease outcome in patients on hemodialysis.

Autonomous circadian rhythms in the human hepatocyte regulate hepatic drug metabolism and inflammatory responses.

Critical aspects of physiology and cell function exhibit self-sustained ~24-hour variations termed circadian rhythms. In the liver, circadian rhythms play fundamental roles in maintaining organ homeostasis. Here, we established and characterized an in vitro liver experimental system in which primary human hepatocytes display self-sustained oscillations. By generating gene expression profiles of these hepatocytes over time, we demonstrated that their transcriptional state is dynamic across 24 hours and identified a set of cycling genes with functions related to inflammation, drug metabolism, and energy homeostasis. We designed and tested a treatment protocol to minimize atorvastatin- and acetaminophen-induced hepatotoxicity. Last, we documented circadian-dependent induction of pro-inflammatory cytokines when triggered by LPS, IFN-β, or Plasmodium infection in human hepatocytes. Collectively, our findings emphasize that the phase of the circadian cycle has a robust impact on the efficacy and toxicity of drugs, and we provide a test bed to study the timing and magnitude of inflammatory responses over the course of infection in human liver.

Nuclear lamina component KAKU4 regulates chromatin states and transcriptional regulation in the Arabidopsis genome

BackgroundThe nuclear lamina links the nuclear membrane to chromosomes and plays a crucial role in regulating chromatin states and gene expression. However, current knowledge of nuclear lamina in plants is limited compared to animals and humans.ResultsThis study mainly focused on elucidating the mechanism through which the putative nuclear lamina component protein KAKU4 regulates chromatin states and gene expression in Arabidopsis leaves. Thus, we constructed a network using the association proteins of lamin-like proteins, revealing that KAKU4 is strongly associated with chromatin or epigenetic modifiers. Then, we conducted ChIP-seq technology to generate global epigenomic profiles of H3K4me3, H3K27me3, and H3K9me2 in Arabidopsis leaves for mutant (kaku4-2) and wild-type (WT) plants alongside RNA-seq method to generate gene expression profiles. The comprehensive chromatin state-based analyses indicate that the knockdown of KAKU4 has the strongest effect on H3K27me3, followed by H3K9me2, and the least impact on H3K4me3, leading to significant changes in chromatin states in the Arabidopsis genome. We discovered that the knockdown of the KAKU4 gene caused a transition between two types of repressive epigenetics marks, H3K9me2 and H3K27me3, in some specific PLAD regions. The combination analyses of epigenomic and transcriptomic data between the kaku4-2 mutant and WT suggested that KAKU4 may regulate key biological processes, such as programmed cell death and hormone signaling pathways, by affecting H3K27me3 modification in Arabidopsis leaves.ConclusionsIn summary, our results indicated that KAKU4 is directly and/or indirectly associated with chromatin/epigenetic modifiers and demonstrated the essential roles of KAKU4 in regulating chromatin states, transcriptional regulation, and diverse biological processes in Arabidopsis.

Common Markers of Muscle Damage Are Associated with Divergent Gene Expression Patterns after Eccentric Contractions.

Unaccustomed eccentric (ECC) exercise evokes exercise-induced muscle damage (EIMD). Soreness, strength loss, and serum creatine kinase (CK) are often used to quantify EIMD severity. However, changes in these markers are not fully understood mechanistically. To test the hypothesis that muscle damage markers are associated with unique molecular processes, we correlated gene expression responses with variation in each marker post-ECC. Vastus lateralis biopsies were collected from 35 young men 3 h post-ECC (10 sets of 10 maximal eccentric contractions; contralateral leg [CON] as control). Maximal isometric strength, soreness, and serum CK activity were assessed 24 h preexercise and every 24 h for 5 d post-ECC. Strength was also measured 10 min post-ECC. Over the 5 d after ECC, average peak strength loss was 51.5 ± 20%; average soreness increased from 0.9 ± 1.9 on a 100-mm visual analog scale to 39 ± 19; serum CK increased from 160 ± 130 to 1168 ± 3430 U·L -1 . Muscle RNA was used to generate gene expression profiles. Partek Genomics Suite correlated peak values of soreness, strength loss, and CK post-ECC with gene expression in ECC (relative to paired CON) using Pearson linear correlation ( P < 0.05) and repeated-measures ANOVA used to detect influence of ECC. After ECC, 2677 genes correlated with peak soreness, 3333 genes with peak strength loss, and 3077 genes with peak CK. Less than 1% overlap existed across all markers (16/9087). Unique genes included 2346 genes for peak soreness, 3032 genes for peak strength loss, and 2937 genes for peak CK. The largely unique molecular pathways associated with common indirect markers of EIMD indicate that each marker of "damage" represents unique mechanistic processes.

Abstract 2262: Spatial architecture and cellular interactions of tumor immune microenvironment to discover biomarkers and predict immune checkpoint inhibitor response in gastric cancer

Abstract Background: While immune checkpoint inhibitors (ICI) extend survival for patients suffering from a variety of cancers, most gastric cancer (GC) patients do not respond to ICI. There is a critical need to identify novel biomarkers that guide the use of ICI or strategies to improve outcomes for GC patients. We aim to gain a deeper understanding of the GC tumor microenvironment (TME) to refine the use of ICI using spatial transcriptomes from ICI-treated gastric tumors. Method: We collected 12 pre-ICI treatment gastric tumor samples from five responders and seven nonresponders and performed spatial profiling to investigate spatial heterogeneity, functions, and phenotypes of tumor and neighboring stromal and immune cells to identify features associated with ICI response. We used pan-cytokeratin (pan-CK) to mark epithelial cells, CD45 for immune cells, and smooth muscle actin (SMA) for fibroblasts. We generated gene expression profiles of each cell type within regions of interest (ROI) with a NanoString GeoMx Cancer Transcriptome Atlas panel, comprised of 1,800 genes. A total of 58 ROIs were analyzed from responders and 62 ROIs from nonresponders. Results: We measured the spatial heterogeneity of each cell type in ROIs within and across tumors. We found the tumor, immune, and fibroblasts from nonresponders are transcriptionally more heterogeneous, compared to those from responders. This might indicate a higher degree of intratumor transcriptional heterogeneity is linked to ICI resistance. We found that nonresponse was associated with higher expression of VEGFA and VEGFB in tumor cells and higher ACTA2 in fibroblasts, not in other cell types. These findings are intriguing when considering our other finding that increased endothelial cell and fibroblast proportions in the TME are associated with ICI nonresponse. We also found that the TME of nonresponders had fewer M1 and more M2 macrophages, and there were more T cells that overexpressed gene programs consistent with dysfunction and exhaustion. These findings indicate that ICI-resistant TMEs are densely surrounded by immune-suppressive cellular components which might reduce ICI efficacy and result in ICI resistance. Finally, we performed cell-cell interaction and identified ligand-receptor interactions that are stronger in nonresponders, including CXCL12-CXCR4, CD74-MIF, and LGALS9-LRP1 ligand-receptor interactions. The predicted ligand-receptor interactions are present in cell-type-specific manners, indicating the functional role of each cell type in facilitating ICI response. Conclusion: We investigated how tumor and neighboring stromal and immune cells interact within GC TME to mediate ICI response, which demonstrate that spatial analysis could be used to identify novel biomarkers that predict response to ICI, and new therapies to enhance ICI efficacy in GC patients. Citation Format: Sunho Park, Changjing Hong, Jae-Ho Cheong, Sam C. Wang, Matthew R. Porembka, In-Ho Kim, Sung Hak Lee, Tae Hyun Hwang. Spatial architecture and cellular interactions of tumor immune microenvironment to discover biomarkers and predict immune checkpoint inhibitor response in gastric cancer [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 2262.

Deficient Radiation Transcription Response in COVID-19 Patients

The ongoing SARS-CoV-2 pandemic has resulted in over 6.3 million deaths and 560 million COVID-19 cases worldwide. Clinical management of hospitalized patients is complex due to the heterogeneous course of COVID-19. Low-dose radiation therapy is known to dampen localized chronic inflammation and has been suggested to be used to reduce lung inflammation in patients with COVID-19. However, it is unknown whether SARS-CoV-2 alters the radiation response and associated radiation exposure related risk. We generated gene expression profiles from circulating leukocytes of hospitalized patients with COVID-19 and healthy donors. The p53 signaling pathway was found to be dysregulated, with mRNA levels of p53, ATM, and CHK2 being lower in patients with COVID-19. Several key p53 target genes involved in cell cycle arrest, apoptosis, and p53 feedback inhibition were upregulated in patients with COVID-19 while other p53 target genes were downregulated. This dysregulation has functional consequences as the transcription of p53-dependant genes (CCNG1, GADD45A, DDB2, SESN1, FDXR, APOBEC) was reduced 24 hours after x-ray exposure ex vivo to both low (100 mGy) or high (2 Gy) doses. SARS-CoV-2 infection affects a DNA damage response that may modify radiation-induced health risks in exposed patients with COVID-19.

Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST

Spatial transcriptomics technologies generate gene expression profiles with spatial context, requiring spatially informed analysis tools for three key tasks, spatial clustering, multisample integration, and cell-type deconvolution. We present GraphST, a graph self-supervised contrastive learning method that fully exploits spatial transcriptomics data to outperform existing methods. It combines graph neural networks with self-supervised contrastive learning to learn informative and discriminative spot representations by minimizing the embedding distance between spatially adjacent spots and vice versa. We demonstrated GraphST on multiple tissue types and technology platforms. GraphST achieved 10% higher clustering accuracy and better delineated fine-grained tissue structures in brain and embryo tissues. GraphST is also the only method that can jointly analyze multiple tissue slices in vertical or horizontal integration while correcting batch effects. Lastly, GraphST demonstrated superior cell-type deconvolution to capture spatial niches like lymph node germinal centers and exhausted tumor infiltrating T cells in breast tumor tissue.

Transcriptome profiles associated with human periodontal ligament differentiation

ObjectivesTissue differentiation is regulated by transcription factors. This study aimed to identify candidate transcription factors that induce periodontal ligament (PDL) cell differentiation in human pluripotent stem cells (hPSCs). MethodsHuman PDL tissues were scraped from the root surfaces of extracted teeth for orthodontic treatment and cultured using the explant culture method. We used RNA-seq to generate gene expression profiles of third-passage PDL cells and compared them with those of undifferentiated human induced pluripotent stem cells (hiPSCs) and human embryonic stem cell (hESC)-derived neural crest (NC) cells (publicly available data). ResultsPrimary cultured PDL cells exhibited a spindle-shaped fibroblast-like appearance and the gene expression of several PDL cell-specific markers. The gene expression profiles of PDL cells were relatively similar to those of hESC-derived NC cells but not those of undifferentiated hiPSCs. Thirty-seven transcription factors were identified as upregulated genes in PDL cells. Pathway analysis showed that differentially expressed genes were enriched in several functional groups and pathways, including the SMAD 2/3 nuclear pathway. ConclusionsWe identified 37 upregulated transcription genes in primary cultured PDL cells compared with hESC-derived NC cells. Regulating these genes and the SMAD signaling pathway may be promising ways to induce PDL cells from hPSC-derived NC cells.

Interferon-alpha2 Favorably Impacts Deregulated Atherosclerosis Genes in Polycythemia Vera and Related Neoplasms

Introduction: Chronic inflammation has been suggested to be the driving force for clonal evolution and disease progression in the Philadelphia-chromosome negative myeloproliferative neoplasms (MPNs) but also potentially having an impact upon the development of accelerated (premature) atherosclerosis, which is recorded in several other chronic inflammatory diseases. Using whole blood gene expression profiling, we have previously shown massive deregulation of genes involved in oxidative stress. Importantly, we have also reported these genes to be favorably regulated during treatment with interferon-alpha2 (IFN). Herein, we report the favorable regulation of deregulated atherosclerosis genes by IFN as well. Objectives: By whole blood gene expression profiling to investigate the regulation of atherosclerosis-promoting genes during treatment with IFN. Methods: Global gene expression profiling was performed at baseline and after 3 months of treatment with IFN in 8 patients with ET, 21 patients with PV, and 4 patients with PMF. Hydroxyurea (n = 18) or anagrelide (n = 6) were discontinued 1 week prior to enrollment. The Affymetrix HG-U133 2.0 Plus microarray was used to generate gene expression profiles. Total RNA was purified from whole blood, amplified to biotin-labeled aRNA, and hybridized to microarray chips. Data preprocessing and statistical analysis of microarray data were done in R. Results: Single gene analysis was performed on 84 genes represented on the Qiagen Human Atherosclerosis gene panel. In response to treatment with IFN in all three patient categories, 10 genes became upregulated in ET including ABCA1, BCL2, CCL2, CCR1, KLF2, LIF, SELL, TGFB1, RXRA, and VEGFA, and 8 genes became downregulated including APOE, BCL2L1, CD44, IL1A, IL1R1, IL1R2, LPA and SPP1. In PV patients, ABCA1, ADFP, BAX, BCL2, CCL1, CCR2, CCR2, CSF1, HBEGF, LIF, NR1H3, RXRA, SELL, TGFB1, TNFAIP3, TNF, and VEGFA were among the 17 upregulated genes, and CD44, CFLAR, IL1A, IL1R1, IL1R2, ITGAX, MMP1, and SPP1 among the 8 downregulated genes. In PMF, 5 genes became upregulated including ABCA1, BAX, CCL2, CCR1, and TNFAIP3, and 5 genes became downregulated including BCL2L1, IL1R1, IL1R2, ITGAX, and SPP1 (all P<0.05) (Table 1 and 2). In a previous microarray study comparing another cohort of patients with ET, PV, or PMF with healthy controls, we have shown significant downregulation of the atherosclerosis genes BCL2, CCR2, CFLAR, FAS, IL1A, ITGA5, KLF2, NFKB1, PPARA, and SELPLG, and significant upregulation of BCL2L1, COL3A1, ELN, FGA, FGF2, IL4, IL5, KDR, LIF, MMP1, PDGFA, PDGFB, PDGFRB, PTGS1, SERPINE1, TGFB2, and THBS4 in all three disease entities (FDR<0.05). Comparing 3 months IFN treatment with baseline in ET, PV and PMF, COL3A1, ELN, FAS, FGA, FGF2, IL4, IL5, ITGA5, KDR, NFKB1, PDGFA, PDGFB, PDGFRB, PPARA, PTSG1, SELPLG, SERPINE1, TGFB2 and THBS4 were not significantly deregulated in any of the disease entities. Furthermore, IFN upregulated downregulated atherosclerosis genes including BCL2 (ET, PV), CCR2 (PV), and KLF2 (ET) and downregulates upregulated atherosclerosis genes including BCL2L1 (ET, PMF) and MMP1 (PV). Discussion and conclusions: Atherosclerosis is a chronic inflammatory disease, which involves several circulating blood cells, including both leukocytes and platelets, which all are variably elevated in MPNs and normalized during IFN-treatment. Therefore, we speculated, if IFN might favorably impact deregulated atherosclerosis genes in patients with MPNs. Indeed, for the first time, we herein report that IFN impacts several atherosclerosis-promoting genes, including both significant upregulation and downregulation of key genes of importance during atherosclerosis development, plaque formation and rupture. Our results add novel important information in regard to the beneficial impact of IFN in regulating deregulated atherosclerosis-promoting genes of potential importance for the development of premature atherosclerosis and accordingly the heavy cardiovascular disease burden in MPNs. The significance of our observations in MPNs should be further explored and confirmed in other MPN-cohorts, including comparative studies of atherosclerosis gene signatures in atherosclerotic plaques from patients with and without MPNs being operated for occlusive vascular diseases and aneurysms. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Gene-expression profiles of pretreatment biopsies predict complete response of rectal cancer patients to preoperative chemoradiotherapy

PurposePreoperative (neoadjuvant) chemoradiotherapy (CRT) and total mesorectal excision is the standard treatment for rectal cancer patients (UICC stage II/III). Up to one-third of patients treated with CRT achieve a pathological complete response (pCR). These patients could be spared from surgery and its associated morbidity and mortality, and assigned to a “watch and wait” strategy. However, reliably identifying pCR based on clinical or imaging parameters remains challenging.Experimental designWe generated gene-expression profiles of 175 patients with locally advanced rectal cancer enrolled in the CAO/ARO/AIO-94 and -04 trials. One hundred and sixty-one samples were used for building, training and validating a predictor of pCR using a machine learning algorithm. The performance of the classifier was validated in three independent cohorts, comprising 76 patients from (i) the CAO/ARO/AIO-94 and -04 trials (n = 14), (ii) a publicly available dataset (n = 38) and (iii) in 24 prospectively collected samples from the TransValid A trial.ResultsA 21-transcript signature yielded the best classification of pCR in 161 patients (Sensitivity: 0.31; AUC: 0.81), when not allowing misclassification of non-complete-responders (False-positive rate = 0). The classifier remained robust when applied to three independent datasets (n = 76).ConclusionThe classifier can identify >1/3 of rectal cancer patients with a pCR while never classifying patients with an incomplete response as having pCR. Importantly, we could validate this finding in three independent datasets, including a prospectively collected cohort. Therefore, this classifier could help select rectal cancer patients for a “watch and wait” strategy.Translational relevanceForgoing surgery with its associated side effects could be an option for rectal cancer patients if the prediction of a pathological complete response (pCR) after preoperative chemoradiotherapy would be possible. Based on gene-expression profiles of 161 patients a classifier was developed and validated in three independent datasets (n = 76), identifying over 1/3 of patients with pCR, while never misclassifying a non-complete-responder. Therefore, the classifier can identify patients suited for “watch and wait”.

Neurodegeneration and neuroinflammation are linked, but independent of alpha-synuclein inclusions, in a seeding/spreading mouse model of Parkinson's disease.

A key pathological process in Parkinson's disease (PD) is the transneuronal spreading of α‐synuclein. Alpha‐synuclein (α‐syn) is a presynaptic protein that, in PD, forms pathological inclusions. Other hallmarks of PD include neurodegeneration and microgliosis in susceptible brain regions. Whether it is primarily transneuronal spreading of α‐syn particles, inclusion formation, or other mechanisms, such as inflammation, that cause neurodegeneration in PD is unclear. We used a model of spreading of α‐syn induced by striatal injection of α‐syn preformed fibrils into the mouse striatum to address this question. We performed quantitative analysis for α‐syn inclusions, neurodegeneration, and microgliosis in different brain regions, and generated gene expression profiles of the ventral midbrain, at two different timepoints after disease induction. We observed significant neurodegeneration and microgliosis in brain regions not only with, but also without α‐syn inclusions. We also observed prominent microgliosis in injured brain regions that did not correlate with neurodegeneration nor with inclusion load. Using longitudinal gene expression profiling, we observed early gene expression changes, linked to neuroinflammation, that preceded neurodegeneration, indicating an active role of microglia in this process. Altered gene pathways overlapped with those typical of PD. Our observations indicate that α‐syn inclusion formation is not the major driver in the early phases of PD‐like neurodegeneration, but that microglia, activated by diffusible, oligomeric α‐syn, may play a key role in this process. Our findings uncover new features of α‐syn induced pathologies, in particular microgliosis, and point to the necessity for a broader view of the process of α‐syn spreading.

Characterization of hormone-producing cell types in the teleost pituitary gland using single-cell RNA-seq

The pituitary is the vertebrate endocrine gland responsible for the production and secretion of several essential peptide hormones. These, in turn, control many aspects of an animal’s physiology and development, including growth, reproduction, homeostasis, metabolism, and stress responses. In teleost fish, each hormone is presumably produced by a specific cell type. However, key details on the regulation of, and communication between these cell types remain to be resolved. We have therefore used single-cell sequencing to generate gene expression profiles for 2592 and 3804 individual cells from the pituitaries of female and male adult medaka (Oryzias latipes), respectively. Based on expression profile clustering, we define 15 and 16 distinct cell types in the female and male pituitary, respectively, of which ten are involved in the production of a single peptide hormone. Collectively, our data provide a high-quality reference for studies on pituitary biology and the regulation of hormone production, both in fish and in vertebrates in general.

The role of stem cell antigen-1/Lymphocyte antigen 6A-2/6E-1 knock out in murine epidermis.

Stem Cell Antigen-1 (SCA-1) is a central positive marker for isolating stem cells in several tissues in the mouse. However, for the epidermis, this appears to be the opposite since lack of SCA-1 has been shown to identify keratinocyte populations with progenitor characteristics. This study investigates the effect of SCA-1 knockout in murine keratinocytes. We compared Sca-1EGFP/EGFP knockout and wildtype mice with respect to the three-dimensional morphology of the epidermis, performed functional assays, and generated gene expression profiles on FACS sorted cells. There were no morphological abnormalities on skin, fur, or hair follicles in transgenic knockout mice compared to wild type mice. SCA-1 knockout keratinocytes showed significantly reduced colony-forming efficiency, colony size and proliferation rate in vitro, however, SCA-1 knockout did not alter wound healing efficiency or keratinocyte proliferation rate in vivo. Moreover, gene expression profiling shows that the effect from knockout of SCA-1 in keratinocytes is dissimilar from what has been observed in other tissues. Additionally, tumor assay indicated that SCA-1 knockout decreases the number of formed papillomas. The results indicate a more complex role for SCA-1, which might differ between epidermal keratinocytes during homeostasis and activated conditions.

Abstract B46: Targeting pancreatic cancer organoids with dual BET and CBP/P300 inhibitor NEO2734

Abstract Pancreatic ductal adenocarcinoma (PDA) has a dismal prognosis due to largely ineffective therapeutics available for this disease. Recently, inhibitors of bromodomain and extraterminal domain (BET) inhibitors have been shown to have therapeutic efficacy against various malignancies, including PDA. Here we present data on sensitivity of PDA patient-derived organoids (PDO) to a novel dual BET and CBP/P300 inhibitor, NEO2734 (Epigene Therapeutics Inc.). Our cell viability screen on a panel of 30 PDOs derived from PDA patient and xenograft tumor tissue revealed differential drug sensitivities to NEO2734 inhibitor. Antitumor effect of NEO2734 on the most sensitive PPTO.2 model was further confirmed in vivo using patient-derived xenograft PPTO.2 model. To identify potential biomarkers associated with differential sensitivities of PDA PDOs to NEO2734 inhibitor, we generated gene expression profiles from 13 PDOs derived from primary patient tumors. Using the probabilistic concordance index (C-index), 13 genes (Bonferroni corrected P&amp;lt;1.0E-10) were identified as potential therapeutic targets. Among the biomarkers identified, we found three associations with known BET inhibitor target genes, including CA9 (C-index= 0.38, PBonferroni= 2.7E-19), which is known to be downregulated by BET inhibitor and coexpressed with the target gene BRDT. Furthermore, the biomarker SLC7A2 (0.28, 3.4E-37) has a known genetic interaction with BRD4, and ABCB6 (0.31, 1.5E-27) is predicted to be coexpressed with CREBBP. Overall, this work reveals that dual BET and CBP/P300 inhibitor, NEO2734, could be a novel therapeutic option for a subset of PDA patients. Citation Format: Nikolina Radulovich, Laura Tamblyn, Heewon Seo, Benjamin Haibe-Kains, Mathieu Lupien, Francis Gilles, Ming S. Tsao. Targeting pancreatic cancer organoids with dual BET and CBP/P300 inhibitor NEO2734 [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr B46.

Highly Deregulated Fibulins in Patients with Philadelphia-Negative Chronic Myeloproliferative Neoplasms

Introduction The Philadelphia-negative chronic myeloproliferative neoplasms (MPNs) develop in a biological continuum from the early cancer stages (ET/PV) to the advanced myelofibrosis stage characterized by huge splenomegaly, bone marrow failure and -fibrosis. Importantly, bone marrow fibrosis also increases from the early stages with reticulin fibrosis only and later deposition of mature collagen as well. Fibulins are glycoproteins that are important constituents of the extracellular matrix (ECM). Thus, fibulins have been shown to modulate cell morphology, growth, adhesion and motility. Dysregulation of fibulins has been reported in several cancers. In addition, upregulation of fibulins and elevated circulating fibulins have been reported in diseases - other than cancers -, in which chronic inflammation is an important pathogenetic factor, such as cardiovascular diseases. Thus, deregulated fibulins have been described in patients with type 2 diabetes mellitus. Herein, using whole blood gene expression profiling, we for the first time report deregulated fibulins in patients with MPNs. Aim To detect if genes associated with pre-atherosclerotic changes in type II diabetes are deregulated in patients with MPNs. Material and methods Gene expression microarrays were applied to generate gene expression profiles of whole blood from control subjects (n=21) and patients with ET (n=19), PV (n=41), and PMF (n=9). Total RNA was purified, amplified to biotin-labeled aRNA and hybridized to microarray chips. The statistical software R was applied to perform initial data processing and statistical analysis of gene expression changes between patients and control subjects. An FDR &lt;0.05 was considered significant. Results We identified 23,657, 25,567, and 17,417 probe sets which were significantly differentially expressed between controls and patients with ET, PV, and PMF, respectively (FDR &lt; 0.05). We focused upon the top 15 upregulated genes from a previous gene expression microarray study performed on arterial tissue from patients with type 2 diabetes compared to non-diabetic patients undergoing artery bypass graft surgery. Several of these genes were significantly deregulated in patients with MPNs (Table 1). In patients with ET, FBLN1, FBLN2,FAM107A, IGF2, MEG3, and ELN were significantly upregulated and ZFP36L2 were significantly downregulated. In patients with PV, FBLN1, FBLN2, ELN, LEPR, FAM107A, IGF2, CRISPLD2, and MEG3 were significantly upregulated and ZFP36L2 and SERPINF1 were significantly downregulated. In patients with PMF, MEG3, LEPR, FBLN1, FAM107A, ELN, IGF2, and VWF were significantly upregulated and ZFP36L2 and SERPINF1 were significantly downregulated. Discussion and conclusions Fibulins regulate several cellular functions including tissue homeostasis and remodeling after injury, angiogenesis, and tumorigenesis. Thus, fibulins have been reported to be upregulated in several cancer types, in which deregulated fibulins have been associated with cancer invasiveness and disease progression. We have for the first time shown that fibulins are also highly deregulated in patients with MPNs. The significance of our findings is presently unknown but since interactions between fibulins and transforming growth factor (TGFbeta) have been demonstrated, upregulated fibulins may enhance the capacities of TGFbeta, which shares several of the regulatory functions excerted by fibulins. In the context of chronic inflammation being a driving force for MPN development during the biological continuum from early cancer stages to the advanced myelofibrosis stage and chronic inflammation likely also accelerates the development of atherosclerosis in MPNs, it is highly intriguing to note that fibulins are also elevated in arteries from patients with type 2 diabetes mellitus. Thus, upregulated fibulins in blood cells may actually indirectly reflect ongoing matrix modelling during atherosclerosis development, including remodeling and turnover of basement membranes in the inflamed endothelium. In conclusion, highly deregulated fibulins have been demonstrated in circulating blood cells by whole blood gene expression profiling. Further studies are needed to assess the significance of our findings in terms of potential associations to modelling of ECM in the bone marrow and during development of atherosclerosis in MPNs. Disclosures Hasselbalch: Novartis: Research Funding; AOP Orphan Pharmaceuticals: Other: Data monitoring board.

A simple in silico approach to generate gene-expression profiles from subsets of cancer genomics data.

In biomedical research, large-scale profiling of gene expression has become routine and offers a valuable means to evaluate changes in onset and progression of diseases, in particular cancer. An overwhelming amount of cancer genomics data has become publicly available, and the complexity of these data makes it a challenge to perform in silico data exploration, integration and analysis, in particular for scientists lacking a background in computational programming or informatics. Many web interface tools make these large datasets accessible but are limited to process large datasets. To accelerate the translation of genomic data into new insights, we provide a simple method to explore and select data from cancer genomic datasets to generate gene-expression profiles of subsets that are of specific genetic, biological or clinical interest.

Diapause within the Context of Life-History Strategies in Calanid Copepods (Calanoida: Crustacea).

Post-embryonic diapause in copepods is an adaptation that allows species in the copepod family Calanidae to thrive in high-latitude environments by transforming a short spring phytoplankton bloom into large numbers of lipid-rich individuals capable of surviving a long period of starvation. The copepods, with their high-energy lipid reservoirs, are a critical food source for higher trophic levels, making the Calanidae a key component of high-latitude marine ecosystems. The physiological ecology of the developmental program remains poorly understood. However, new studies using high-throughput RNA sequencing approaches are giving detailed access to physiological status by generating gene expression profiles for both field-collected and laboratory-incubated individuals. These are beginning to characterize the diapause phenotype, elucidate the transcriptional and physiological progression through the diapause program, and illustrate the effects of organism-environment interactions. This paper reviews gene expression profiling studies on the life cycle and diapause program of Neocalanus flemingeri Miller (1988) that were conducted as part of a long-term observation program in the northern Gulf of Alaska. It summarizes recent findings and relates them to the ecology of this species and to that of other calanids.

Generation of gene expression profiles for AD model mice by GAN deep learning

Generation of gene expression profiles for AD model mice by GAN deep learning

PF661 MOLECULAR PROFILING REVEALS HIGHLY DEREGULATED INSULIN GROWTH FACTOR BINDING PROTEINS IN PATIENTS WITH MYELOFIBROSIS AND RELATED NEOPLASMS

Background:The Insulin Growth Factor (IGF) system has been extensively studied in polycythemia vera (PV) showing erythroid progenitors to be hypersensitive to IGF1, levels of the IGF1‐binding protein – IGFBP‐1 to be fourfold increased but normal levels of IGF1 and IGFBP3. Furthermore, the stimulatory effect of IGFBP1 on erythroid progenitors in vitro provided a connection to overproduction of red blood cells in PV through IGF1. Most lately, increased IGF‐1R expression of mononuclear cells was found in patients with Philadelphia‐negative myeloproliferative neoplasms (MPN). In addition, the JAK2V617F mutation has been shown to result in IGF1 hypersensitivity in Ba/F3 cells providing a molecular basis for significance of IGF1 signaling in MPNs.Dysregulation of the IGF system is important in cancer development. We herein for the first time demonstrate several genes of IGF system to be markedly deregulated in MPNsAims:To study whole blood gene expression profiling in patients with MPNs.Methods:Gene expression microarrays were applied to whole blood from control subjects (n = 21) and patients with ET (n = 19), PV (n = 41), and PMF (n = 9). Affymetrix HG‐U133 2.0 Plus microarrays were used to generate gene expression profiles of 54.675 probe sets (38.500 genes). Total RNA was purified from whole‐blood, amplified to biotin‐labeled aRNA and hybridized to microarray chips. The statistical software R was applied to perform initial data processing and statistical analysis of microarray data.Results:20,439, 25,307, and 17,417 probe sets were significantly differentially expressed between control subjects and patients with ET, PV and PMF, respectively (FDR&lt;0.05). Several of the insulin‐like growth factor (IGF) and insulin‐like growth factor binding protein (IGFBP) genes were significantly deregulated (Table 1). IGF1, IGF2, IGFALS, IGFBP2, and IGF2BP1 were significantly upregulated in all three disease entities of which IGFBP2 was progressively and significantly upregulated from ET over PV to PMF (FDR&lt;0.05).Summary/Conclusion:In the present study we found several IGF‐related genes to be significantly deregulated in MPNs. Of note, IGF‐1 was significantly upregulated in all three subgroups of patients (ET, PV and PMF) and IGFBP1 was significantly downregulated in ET and PV patients. These observations are not in line with previous findings of normal IGF‐1 and highly elevated IGFBP1 levels in patients with PV. IGF‐1 has been shown to stimulate cell growth and up‐and down‐regulate the expression of anti‐ and pro‐apoptotic molecules, respectively, thereby protecting cancer cells from apoptosis. Enhanced IGF‐I gene expression might contribute to the chronic inflammatory state in MPN through enhancement of IL‐6 activity. It is intriguing to consider if IGF‐1 might also promote angiogenesis in MPN by stimulating VEGF secretion by e.g. megakaryocytes and monocytes similar to stimulation of VEGF‐secretion by e.g. myeloma cells. In conclusion, we have shown a number of genes in the IGF‐1 system to be deregulated in MPN, which altogether might contribute in driving clonal myeloproliferation, decreased apoptosis, bone marrow angiogenesis, immune evasion and inflammation as well. Future studies on the interplay between the transcriptome, IGF‐related proteins and IGF‐R expression levels might deliver new insight into the role of IGF‐system in the pathogenesis of MPNs and ultimately give the impetus to studies on the efficacy of inhibitors of IGF1 or IGF1R, which prohibit development of MPN‐phenotype in JAK2V617F mice.image

Multi-species transcriptome analyses for the regulation of crocins biosynthesis in Crocus

BackgroundCrocins are soluble apocarotenoids that mainly accumulate in the stigma tissue of Crocus sativus and provide the characteristic red color to saffron spice, in addition to being responsible for many of the medicinal properties of saffron. Crocin biosynthesis and accumulation in saffron is developmentally controlled, and the concentration of crocins increases as the stigma develops. Until now, little has been known about the molecular mechanisms governing crocin biosynthesis and accumulation. This study aimed to identify the first set of gene regulatory processes implicated in apocarotenoid biosynthesis and accumulation.ResultsA large-scale crocin-mediated RNA-seq analysis was performed on saffron and two other Crocus species at two early developmental stages coincident with the initiation of crocin biosynthesis and accumulation. Pairwise comparison of unigene abundance among the samples identified potential regulatory transcription factors (TFs) involved in crocin biosynthesis and accumulation. We found a total of 131 (up- and downregulated) TFs representing a broad range of TF families in the analyzed transcriptomes; by comparison with the transcriptomes from the same developmental stages from other Crocus species, a total of 11 TF were selected as candidate regulators controlling crocin biosynthesis and accumulation.ConclusionsOur study generated gene expression profiles of stigmas at two key developmental stages for apocarotenoid accumulation in three different Crocus species. Differential gene expression analyses allowed the identification of transcription factors that provide evidence of environmental and developmental control of the apocarotenoid biosynthetic pathway at the molecular level.