Characterization of the transcriptome profiles related to globin gene switching during in vitro erythroid maturation

<p>Abstract</p> <p>Background</p> <p>The fetal and adult globin genes in the human β-globin cluster on chromosome 11 are sequentially expressed to achieve normal hemoglobin switching during human development. The pharmacological induction of fetal γ-globin (<it>HBG</it>) to replace abnormal adult sickle β^S-globin is a successful strategy to treat sickle cell disease; however the molecular mechanism of γ-gene silencing after birth is not fully understood. Therefore, we performed global gene expression profiling using primary erythroid progenitors grown from human peripheral blood mononuclear cells to characterize gene expression patterns during the γ-globin to β-globin (γ/β) switch observed throughout <it>in vitro </it>erythroid differentiation.</p> <p>Results</p> <p>We confirmed erythroid maturation in our culture system using cell morphologic features defined by Giemsa staining and the γ/β-globin switch by reverse transcription-quantitative PCR (RT-qPCR) analysis. We observed maximal γ-globin expression at day 7 with a switch to a predominance of β-globin expression by day 28 and the γ/β-globin switch occurred around day 21. Expression patterns for transcription factors including <it>GATA1, GATA2, KLF1 </it>and <it>NFE2 </it>confirmed our system produced the expected pattern of expression based on the known function of these factors in globin gene regulation. Subsequent gene expression profiling was performed with RNA isolated from progenitors harvested at day 7, 14, 21, and 28 in culture. Three major gene profiles were generated by Principal Component Analysis (PCA). For profile-1 genes, where expression decreased from day 7 to day 28, we identified 2,102 genes down-regulated > 1.5-fold. Ingenuity pathway analysis (IPA) for profile-1 genes demonstrated involvement of the Cdc42, phospholipase C, NF-Kβ, Interleukin-4, and p38 mitogen activated protein kinase (MAPK) signaling pathways. Transcription factors known to be involved in γ-and β-globin regulation were identified.</p> <p>The same approach was used to generate profile-2 genes where expression was up-regulated over 28 days in culture. IPA for the 2,437 genes with > 1.5-fold induction identified the mitotic roles of polo-like kinase, aryl hydrocarbon receptor, cell cycle control, and <it>ATM </it>(Ataxia Telangiectasia Mutated Protein) signaling pathways; transcription factors identified included <it>KLF1, GATA1 </it>and <it>NFE2 </it>among others. Finally, profile-3 was generated from 1,579 genes with maximal expression at day 21, around the time of the γ/β-globin switch. IPA identified associations with cell cycle control, ATM, and aryl hydrocarbon receptor signaling pathways.</p> <p>Conclusions</p> <p>The transcriptome analysis completed with erythroid progenitors grown <it>in vitro </it>identified groups of genes with distinct expression profiles, which function in metabolic pathways associated with cell survival, hematopoiesis, blood cells activation, and inflammatory responses. This study represents the first report of a transcriptome analysis in human primary erythroid progenitors to identify transcription factors involved in hemoglobin switching. Our results also demonstrate that the <it>in vitro </it>liquid culture system is an excellent model to define mechanisms of global gene expression and the DNA-binding protein and signaling pathways involved in globin gene regulation.</p

Strain background determines lymphoma incidence in Atm knockout mice

About 10% to 30% of patients with ataxia-telangiectasia (A-T) develop leukemias or lymphomas. There is considerable interpatient variation in the age of onset and leukemia/lymphoma type. The incomplete penetrance and variable age of onset may be attributable to several factors. These include competing mortality from other A-T-associated pathologies, particularly neurodegeneration and interstitial lung disease, and allele-specific effects of ataxia-telangiectasia mutated (ATM) gene mutations. There is also limited evidence from clinical observations and studies using Atm knockout mice that modifier genes may account for some variation in leukemia/lymphoma susceptibility. We have introgressed the Atm knockout allele (Atm) onto several inbred murine strains and observed differences in thymic lymphoma incidence and latency between Atm mice on the different strain backgrounds and between their F1 hybrids. The lymphomas that arose in these mice had a pattern of sequence gains and losses that were similar to those previously described by others. These results provide further evidence for the existence of modifier genes controlling lymphomagenesis in individuals carrying defective copies of Atm, at least in mice, and the characterized Atm- congenic strain set provides a resource with which to identify these genes. In addition, we found that fewer than expected Atm pups were weaned on two strain backgrounds and that there was no correlation between body weight of young Atm mice and lymphoma incidence or latency

Multi-Domain Active Learning for Recommendation

Recently, active learning has been applied to recommendation to deal with data sparsity on a single domain. In this paper, we propose an active learning strategy for recommendation to alleviate the data sparsity in a multi-domain scenario. Specifically, our proposed active learning strategy simultaneously consider both specific and independent knowledge over all domains. We use the expected entropy to measure the generalization error of the domain-specific knowledge and propose a variance-based strategy to measure the generalization error of the domain-independent knowledge. The proposed active learning strategy use a unified function to effectively combine these two measurements. We compare our strategy with five state-of-the-art baselines on five different multi-domain recommendation tasks, which are constituted by three real-world data sets. The experimental results show that our strategy performs significantly better than all the baselines and reduces human labeling efforts by at least 5.6%, 8.3%, 11.8%, 12.5% and 15.4% on the five tasks, respectively

Characterization of transcription factor networks involved in umbilical cord blood CD34+ stem cells-derived erythropoiesis.

Fetal stem cells isolated from umbilical cord blood (UCB) possess a great capacity for proliferation and differentiation and serve as a valuable model system to study gene regulation. Expanded knowledge of the molecular control of hemoglobin synthesis will provide a basis for rational design of therapies for β-hemoglobinopathies. Transcriptome data are available for erythroid progenitors derived from adult stem cells, however studies to define molecular mechanisms controlling globin gene regulation during fetal erythropoiesis are limited. Here, we utilize UCB-CD34+ stem cells induced to undergo erythroid differentiation to characterize the transcriptome and transcription factor networks (TFNs) associated with the γ/β-globin switch during fetal erythropoiesis. UCB-CD34+ stem cells grown in the one-phase liquid culture system displayed a higher proliferative capacity than adult CD34+ stem cells. The γ/β-globin switch was observed after day 42 during fetal erythropoiesis in contrast to adult progenitors where the switch occurred around day 21. To gain insights into transcription factors involved in globin gene regulation, microarray analysis was performed on RNA isolated from UCB-CD34+ cell-derived erythroid progenitors harvested on day 21, 42, 49 and 56 using the HumanHT-12 Expression BeadChip. After data normalization, Gene Set Enrichment Analysis identified transcription factors (TFs) with significant changes in expression during the γ/β-globin switch. Forty-five TFs were silenced by day 56 (Profile-1) and 30 TFs were activated by day 56 (Profile-2). Both GSEA datasets were analyzed using the MIMI Cytoscape platform, which discovered TFNs centered on KLF4 and GATA2 (Profile-1) and KLF1 and GATA1 for Profile-2 genes. Subsequent shRNA studies in KU812 leukemia cells and human erythroid progenitors generated from UCB-CD34+ cells supported a negative role of MAFB in γ-globin regulation. The characteristics of erythroblasts derived from UCB-CD34+ stem cells including prolonged γ-globin expression combined with unique TFNs support novel mechanisms controlling the γ/β-globin switch during UCB-derived erythropoiesis

PAM: Pyramid Attention Mechanism Based on Contextual Reasoning

Recent work has shown that self-attention modules improve the performance of convolutional neural networks (CNNs), in which global operations are conventionally used to generate descriptors from feature context for attention calculation and characteristics recalibration. However, the performance gain is compromised due to sharing the same descriptor for different feature context. In this paper, we propose Pyramid Attention Mechanism (PAM) that incorporates contextual reasoning into self-attention module for enhancing the discriminative ability of descriptors. PAM is lightweight yet efficient and can be integrated with most self-attention modules. It consists of two operators: aggregation and distribution, which are used for assembling and synthesizing contextual information at different levels. Extensive experiments on different benchmarks (including CIFAR-100, ImageNet-1K, MS COCO, and VOC 2007) indicate that PAM can produce competitive performance gains. In classification tasks, by plugging PAM into self-attention modules, at most 2.18% accuracy improvement over various network structures can be obtained

miR-551a and miR-551b-3p target GLIPR2 and promote tumor growth in high-risk head and neck cancer by modulating autophagy

The potential role for microRNA (miRNA) in the metastatic process that occurs in head and neck squamous cell carcinoma (HNSCC) was examined. miRNA was extracted from surgically excised tumor samples from 41 HNSCC cancer patients diagnosed with distant metastasis (DM) and from 53 patients who displayed no evidence of disease (NED) for a minimum of two years a minimum of two years after treatment with post-operative radiotherapy (PORT). A comparative two-way ANOVA of miRNA expression between DM and NED specimens identified 28 differentially expressed miRNAs with a false discovery rate (FDR)  1.5. Two miRNA, miR-551a and miR-551b-3p, which share the same seed sequence, were associated with the DM group and with poor survival. Cell proliferation, migration, and invasion assays using the HN5 and UMSCC-17B HNSCC cell lines were performed after transfecting mimics or inhibitors of these miRNA uncovered an oncogenic role for miR-551a and miR-551b-3p. Furthermore, it was determined that miR-551a and miR-551b-3p directly target GLIPR2 mRNA, a negative regulator of autophagy. Overexpression of GLIPR2 reduced proliferation, migration and invasion of HNSCC cells. In addition, overexpression of miR-551a and miR-551b-3p increased radioresistance while GLIPR2 overexpression increased the radiosensitivity of HNSCC cell lines. These results propose that the miR-551a, miR-551b-3p and GLIPR2 axis plays an important role in tumor growth, invasion and metastasis, at least in part by modulating autophagy and that the proliferative and pro-survival roles of miR-551a and miR-551b-3p may represent potential therapeutic targets by inhibiting autophagy through the regulation of GLIPR2 expression in HNSCC

Hypoxia-Inducible mir-210 Regulates Normoxic Gene Expression Involved in Tumor Initiation

Previous studies have suggested that the HIF transcription factors can both activate and inhibit gene expression. Here we show that HIF1 regulates the expression of mir-210 in a variety of tumor types through a hypoxia-responsive element. Expression analysis in primary head and neck tumor samples indicates that mir-210 may serve as an in vivo marker for tumor hypoxia. By Argonaute protein immunoprecipitation, we identified 50 potential mir-210 targets and validated randomly selected ones. The majority of these 50 genes are not classical hypoxia-inducible genes, suggesting mir-210 represses genes expressed under normoxia that are no longer necessary to adapt and survive in a hypoxic environment. When human head and neck or pancreatic tumor cells ectopically expressing mir-210 were implanted into immunodeficient mice, mir-210 repressed initiation of tumor growth. Taken together, these data implicate an important role for mir-210 in regulating the hypoxic response of tumor cells and tumor growth

UCB-stem cell Class A (Profile-1) transcription factors.

1<p>ES, enrichment score of TFs identified by GSEA using three TF gene sets (TF activity, TF complex and DNA binding). A positive ES indicates the gene expression correlated with a Profile-1 pattern (decreased expression from day 21 to day 56).</p>2<p>Gene Rank, gene rank list generated by GSEA using 3786 TFs with >1.5-fold changes in expression from day 21 to day 56 in culture.</p><p>UCB-stem cell Class A (Profile-1) transcription factors.</p