RESUMO
BACKGROUND: This study aimed to assess the expression level of upstream stimulator 1 (USF1) in the bone marrow of newly diagnosed acute myeloid leukemia (AML) patients and investigate its clinical and prognostic significance. METHODS: Bone marrow samples from 60 newly diagnosed AML patients constituted the observation group, while 20 samples from healthy individuals formed the control group. Real-time quantitative PCR (qRT-PCR) was used to measure the USF1 expression in both groups and to analyze its correlation with clinicopathological features and prognosis in AML patients. Kaplan-Meier curves were utilized to assess the impact of USF1 on the overall survival (OS) in AML patients. The prognostic factors of AML were examined by using Cox regression analysis. RESULTS: A univariate analysis revealed a significantly higher USF1 expression in the AML patients compared to the control group (p < 0.001), with no difference in the clinicopathological features between the low-expression group and the control group. However, there was a significant difference between the high-expression group and the control group (p < 0.01). Moreover, the OS of the high USF1 expression group was notably shorter than of the low USF1 expression group (p < 0.0001). A multivariate analysis identified high USF1 expression and age ≥ 60 years as independent risk factors for a poor AML prognosis. CONCLUSIONS: High expression of USF1 is linked to a worse prognosis and shorter survival time in AML patients. USF1 may serve as an indicator of prognosis and survival in AML patients and could be a potential target for AML treatment.
Assuntos
Leucemia Mieloide Aguda , Fatores Estimuladores Upstream , Humanos , Leucemia Mieloide Aguda/genética , Leucemia Mieloide Aguda/diagnóstico , Leucemia Mieloide Aguda/mortalidade , Feminino , Masculino , Pessoa de Meia-Idade , Fatores Estimuladores Upstream/genética , Fatores Estimuladores Upstream/metabolismo , Adulto , Idoso , Prognóstico , Adulto Jovem , Estimativa de Kaplan-Meier , Estudos de Casos e Controles , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Adolescente , Modelos de Riscos Proporcionais , Medula Óssea/patologia , Medula Óssea/metabolismo , Análise Multivariada , Relevância ClínicaRESUMO
Autophagy, a highly conserved self-digestion process crucial for cellular homeostasis, is triggered by various environmental signals, including nutrient scarcity. The regulation of lysosomal and autophagy-related processes is pivotal to maintaining cellular homeostasis and basal metabolism. The consequences of disrupting or diminishing lysosomal and autophagy systems have been investigated; however, information on the implications of hyperactivating lysosomal and autophagy genes on homeostasis is limited. Here, we present a mechanism of transcriptional repression involving upstream stimulatory factor 2 (USF2), which inhibits lysosomal and autophagy genes under nutrient-rich conditions. We find that USF2, together with HDAC1, binds to the CLEAR motif within lysosomal genes, thereby diminishing histone H3K27 acetylation, restricting chromatin accessibility, and downregulating lysosomal gene expression. Under starvation, USF2 competes with transcription factor EB (TFEB), a master transcriptional activator of lysosomal and autophagy genes, to bind to target gene promoters in a phosphorylation-dependent manner. The GSK3ß-mediated phosphorylation of the USF2 S155 site governs USF2 DNA-binding activity, which is involved in lysosomal gene repression. These findings have potential applications in the treatment of protein aggregation-associated diseases, including α1-antitrypsin deficiency. Notably, USF2 repression is a promising therapeutic strategy for lysosomal and autophagy-related diseases.
Assuntos
Autofagia , Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos , Lisossomos , Fatores Estimuladores Upstream , Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/metabolismo , Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/genética , Lisossomos/metabolismo , Autofagia/genética , Humanos , Fatores Estimuladores Upstream/metabolismo , Fatores Estimuladores Upstream/genética , Fosforilação , Histona Desacetilase 1/metabolismo , Histona Desacetilase 1/genética , Glicogênio Sintase Quinase 3 beta/metabolismo , Glicogênio Sintase Quinase 3 beta/genética , Regulação da Expressão Gênica , Regiões Promotoras Genéticas , Células HEK293 , Animais , Histonas/metabolismo , Células HeLa , Camundongos , AcetilaçãoRESUMO
Macrophages are central innate immune cells whose function declines with age. The molecular mechanisms underlying age-related changes remain poorly understood, particularly in human macrophages. We report a substantial reduction in phagocytosis, migration, and chemotaxis in human monocyte-derived macrophages (MDMs) from older (>50 years old) compared with younger (18-30 years old) donors, alongside downregulation of transcription factors MYC and USF1. In MDMs from young donors, knockdown of MYC or USF1 decreases phagocytosis and chemotaxis and alters the expression of associated genes, alongside adhesion and extracellular matrix remodeling. A concordant dysregulation of MYC and USF1 target genes is also seen in MDMs from older donors. Furthermore, older age and loss of either MYC or USF1 in MDMs leads to an increased cell size, altered morphology, and reduced actin content. Together, these results define MYC and USF1 as key drivers of MDM age-related functional decline and identify downstream targets to improve macrophage function in aging.
Assuntos
Envelhecimento , Macrófagos , Fagocitose , Proteínas Proto-Oncogênicas c-myc , Fatores Estimuladores Upstream , Humanos , Macrófagos/metabolismo , Proteínas Proto-Oncogênicas c-myc/metabolismo , Proteínas Proto-Oncogênicas c-myc/genética , Adulto , Fatores Estimuladores Upstream/metabolismo , Fatores Estimuladores Upstream/genética , Pessoa de Meia-Idade , Adolescente , Fagocitose/genética , Adulto Jovem , Transcrição Gênica , Idoso , Quimiotaxia/genéticaRESUMO
BACKGROUND: Upstream stimulatory factors (USFs) are members of the basic helix-loop-helix leucine zipper transcription factor family, including USF1, USF2, and USF3. The first two members have been well studied compared to the third member, USF3, which has received scarce attention in cancer research to date. Despite a recently reported association of its alteration with thyroid carcinoma, its expression has not been previously analyzed. METHODS: We comprehensively analyzed differential levels of USFs expression, genomic alteration, DNA methylation, and their prognostic value across different cancer types and the possible correlation with tumor-infiltrating immune cells and drug response by using different bioinformatics tools. RESULTS: Our findings established that USFs play an important role in cancers related to the urinary system and justify the necessity for further investigation. We implemented and offer a useful ShinyApp to facilitate researchers' efforts to inquire about any other gene of interest and to perform the analysis of drug response in a user-friendly fashion at http://zzdlab.com:3838/Drugdiscovery/.
Assuntos
Proteínas de Ligação a DNA , Neoplasias , Humanos , Fatores Estimuladores Upstream/genética , Fatores Estimuladores Upstream/metabolismo , Proteínas de Ligação a DNA/metabolismo , Neoplasias/genéticaRESUMO
Upstream-stimulating factor 1 (USF1) is a ubiquitously expressed transcription factor implicated in multiple cellular processes, including metabolism and proliferation. This study focused on the function of USF1 in glycolysis and the malignant development of prostate adenocarcinoma (PRAD). Bioinformatics predictions suggested that USF1 is poorly expressed in PRAD. The clinical PRAD samples revealed a low level of USF1, which was correlated with an unfavorable prognosis. Artificial upregulation of USF1 significantly repressed glycolytic activity in PRAD cells and reduced cell growth and metastasis in vitro and in vivo. Potential downstream genes of USF1 were probed by integrated bioinformatics analyses. The chromatin immunoprecipitation and luciferase assays indicated that USF1 bound to the α-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5) promoter for transcription activation. Flightless I (FLII) was identified as the gene showing the highest degree of correlation with ALKBH5. As an m6A demethylase, ALKBH5 enhanced FLII mRNA stability by inducing m6A demethylation in an m6A-YTH N6-methyladenosine RNA-binding protein F2 (YTHDF2)-dependent manner. Either silencing of ALKBH5 or FLII blocked the role of USF1 in PARD cells and restored glycolysis, cell proliferation, and invasion. This study demonstrates that USF1 activates ALKBH5 to stabilize FLII mRNA in an m6A-YTHDF2-dependent manner, thereby repressing glycolysis processes and the progression of PRAD.
Assuntos
Adenocarcinoma , Próstata , Masculino , Humanos , Fatores de Transcrição , Ativação Transcricional , Adenocarcinoma/genética , Anticorpos , Glicólise/genética , Proteínas dos Microfilamentos , Transativadores , Fatores Estimuladores Upstream/genética , Homólogo AlkB 5 da RNA Desmetilase/genética , Proteínas de Ligação a RNARESUMO
HIV-1 provirus expression is controlled by signaling pathways that are responsive to T cell receptor engagement, including those involving Ras and downstream protein kinases. The induction of transcription from the HIV-1 LTR in response to Ras signaling requires binding of the Ras-responsive element binding factor (RBF-2) to conserved cis elements flanking the enhancer region, designated RBE3 and RBE1. RBF-2 is composed minimally of the USF1, USF2, and TFII-I transcription factors. We recently determined that TFII-I regulates transcriptional elongation from the LTR through recruitment of the co-activator TRIM24. However, the function of USF1 and USF2 for this effect are uncharacterized. Here, we find that genetic deletion of USF2 but not USF1 in T cells inhibits HIV-1 expression. The loss of USF2 caused a reduction in expression of the USF1 protein, an effect that was not associated with decreased USF1 mRNA abundance. USF1 and USF2 were previously shown to exist predominately as heterodimers and to cooperatively regulate target genes. To examine cooperativity between these factors, we performed RNA-seq analysis of T cell lines bearing knockouts of the genes encoding these factors. In untreated cells, we found limited evidence of coordinated global gene regulation between USF1 and USF2. In contrast, we observed a high degree of genome-wide cooperative regulation of RNA expression between these factors in cells stimulated with the combination of PMA and ionomycin. In particular, we found that the deletion of USF1 or USF2 restricted T cell activation response. These observations indicate that USF2, but not USF1, is crucial for HIV-1 expression, while the combined function of these factors is required for a robust T cell inflammatory response.
Assuntos
HIV-1 , Fatores Estimuladores Upstream/genética , Fatores Estimuladores Upstream/metabolismo , HIV-1/fisiologia , Regulação da Expressão Gênica , Linfócitos T/metabolismo , Receptores de Antígenos de Linfócitos T/genéticaRESUMO
Cellular senescence is a program of cell cycle arrest, apoptosis resistance, and cytokine release induced by stress exposure in metazoan cells. Landmark studies in laboratory mice have characterized a number of master senescence regulators, including p16INK4a, p21, NF-κB, p53, and C/EBPß. To discover other molecular players in senescence, we developed a screening approach to harness the evolutionary divergence between mouse species. We found that primary cells from the Mediterranean mouse Mus spretus, when treated with DNA damage to induce senescence, produced less cytokine and had less-active lysosomes than cells from laboratory Mus musculus. We used allele-specific expression profiling to catalog senescence-dependent cis-regulatory variation between the species at thousands of genes. We then tested for correlation between these expression changes and interspecies sequence variants in the binding sites of transcription factors. Among the emergent candidate senescence regulators, we chose a little-studied cell cycle factor, upstream stimulatory factor 2 (USF2), for molecular validation. In acute irradiation experiments, cells lacking USF2 had compromised DNA damage repair and response. Longer-term senescent cultures without USF2 mounted an exaggerated senescence regulatory program-shutting down cell cycle and DNA repair pathways, and turning up cytokine expression, more avidly than wild-type. We interpret these findings under a model of pro-repair, anti-senescence regulatory function by USF2. Our study affords new insights into the mechanisms by which cells commit to senescence, and serves as a validated proof of concept for natural variation-based regulator screens.
Assuntos
Senescência Celular , Dano ao DNA , Animais , Camundongos , Ciclo Celular , Senescência Celular/genética , Citocinas/metabolismo , Proteína Supressora de Tumor p53/genética , Fatores Estimuladores Upstream/genéticaRESUMO
BACKGROUND: WD repeat domain 3 (WDR3) is involved in tumor growth and proliferation, but its role in the pathological mechanism of prostate cancer (PCa) is still unclear. METHODS: WDR3 gene expression levels were obtained by analyzing databases and our clinical specimens. The expression levels of genes and proteins were determined by a real-time polymerase chain reaction, western blotting and immunohistochemistry, respectively. Cell-counting kit-8 assays were used to measure the proliferation of PCa cells. Cell transfection was used to investigate the role of WDR3 and USF2 in PCa. Fluorescence reporter and chromatin immunoprecipitation assays were used to detect USF2 binding to the promoter region of RASSF1A. Mouse experiments were used to confirm the mechanism in vivo. RESULTS: By analyzing the database and our clinical specimens, we found that WDR3 expression was significantly increased in PCa tissues. Overexpression of WDR3 enhanced PCa cell proliferation, decreased cell apoptosis rate, increased spherical cell number and increased indicators of stem cell-like properties. However, these effects were reversed by WDR3 knockdown. WDR3 was negatively correlated with USF2, which was degraded by promoting ubiquitination of USF2, and USF2 interacted with promoter region-binding elements of RASSF1A to depress PCa stemness and growth. In vivo studies showed that WDR3 knockdown reduced tumor size and weight, reduced cell proliferation and enhanced cell apoptosis. CONCLUSIONS: WDR3 ubiquitinated USF2 and inhibited its stability, whereas USF2 interacted with promoter region-binding elements of RASSF1A. USF2 transcriptionally activated RASSF1A, which inhibited the carcinogenic effect of WDR3 overexpression.
Assuntos
Neoplasias da Próstata , Animais , Humanos , Masculino , Camundongos , Apoptose/genética , Linhagem Celular Tumoral , Proliferação de Células/genética , Regulação Neoplásica da Expressão Gênica , Neoplasias da Próstata/genética , Células-Tronco , Transfecção , Fatores Estimuladores Upstream/genéticaRESUMO
Thioredoxin reductase 1 (TXNRD1) is one of the major redox regulators in mammalian cells, which has been reported to be involved in tumorigenesis. However, its roles and regulatory mechanism underlying the progression of HCC remains poorly understood. In this study, we demonstrated that TXNRD1 was significantly upregulated in HCC tumor tissues and correlated with poor survival in HCC patients. Functional studies indicated TXNRD1 knockdown substantially suppressed HCC cell proliferation and metastasis both in vitro and in vivo, and its overexpression showed opposite effects. Mechanistically, TXNRD1 attenuated the interaction between Trx1 and PTEN which resulting in acceleration of PTEN degradation, thereby activated Akt/mTOR signaling and its target genes which conferred to elevated HCC cell mobility and metastasis. Moreover, USF2 was identified as a transcriptional suppressor of TXNRD1, which directly interacted with two E-box sites in TXNRD1 promoter. USF2 functioned as tumor suppressor through the downstream repression of TXNRD1. Further clinical data revealed negative co-expression correlations between USF2 and TXNRD1. In conclusion, our findings reveal that USF2-mediated upregulation of TXNRD1 contributes to hepatocellular carcinoma progression by activating Akt/mTOR signaling.
Assuntos
Carcinoma Hepatocelular , Neoplasias Hepáticas , Animais , Humanos , Carcinoma Hepatocelular/patologia , Tiorredoxina Redutase 1/genética , Proteínas Proto-Oncogênicas c-akt/metabolismo , Neoplasias Hepáticas/patologia , Regulação para Cima , Proliferação de Células , Serina-Treonina Quinases TOR/metabolismo , Linhagem Celular Tumoral , Regulação Neoplásica da Expressão Gênica , Mamíferos , Fatores Estimuladores Upstream/genéticaRESUMO
Angiotensin II type 1 receptor-associated protein (ATRAP) is widely expressed in different tissues and organs, although its mechanistic role in breast cancer remains unclear. Here, we show that ATRAP is highly expressed in breast cancer tissues. Its aberrant upregulation promotes breast cancer aggressiveness and is positively correlated with poor prognosis. Functional assays revealed that ATRAP participates in promoting cell growth, metastasis, and aerobic glycolysis, while microarray analysis showed that ATRAP can activate the AKT/mTOR signaling pathway in cancer progression. In addition, ATRAP was revealed to direct Ubiquitin-specific protease 14 (USP14)-mediated deubiquitination and stabilization of Pre-B cell leukemia homeobox 3 (PBX3). Importantly, ATRAP is a direct target of Upstream stimulatory factor 1 (USF1), and that ATRAP overexpression reverses the inhibitory effects of USF1 knockdown. Our study demonstrates the broad contribution of the USF1/ATRAP/PBX3 axis to breast cancer progression and provides a strong potential therapeutic target.
Assuntos
Neoplasias da Mama , Proteínas Proto-Oncogênicas c-akt , Proteínas Adaptadoras de Transdução de Sinal , Neoplasias da Mama/metabolismo , Feminino , Glicólise/genética , Proteínas de Homeodomínio , Humanos , Fenótipo , Proteínas Proto-Oncogênicas , Proteínas Proto-Oncogênicas c-akt/metabolismo , Receptor Tipo 1 de Angiotensina/genética , Receptor Tipo 1 de Angiotensina/metabolismo , Transdução de Sinais/genética , Serina-Treonina Quinases TOR/genética , Serina-Treonina Quinases TOR/metabolismo , Ubiquitina Tiolesterase/genética , Fatores Estimuladores Upstream/genética , Fatores Estimuladores Upstream/metabolismo , Fatores Estimuladores Upstream/farmacologiaRESUMO
BACKGROUND: Gastric cancer (GC) is one of the most common malignancies, and an increasing number of studies have shown that its pathogenesis is regulated by various miRNAs. In this study, we investigated the role of miR-875-5p in GC. METHODS: The expression of miR-875-5p was detected in human GC specimens and cell lines by miRNA qRT-PCR. The effect of miR-875-5p on GC proliferation was determined by Cell Counting Kit-8 (CCK-8) proliferation and 5-ethynyl-2'-deoxyuridine (EdU) assays. Migration and invasion were examined by transwell migration and invasion assays as well as wound healing assays. The interaction between miR-875-5p and its target gene upstream stimulatory factor 2(USF2) was verified by dual luciferase reporter assays. The effects of miR-875-5p in vivo were studied in xenograft nude mouse models. Related proteins were detected by western blot. RESULTS: The results showed that miR-875-5p inhibited the proliferation, migration and invasion of GC cells in vitro and inhibited tumorigenesis in vivo. USF2 was proved to be a direct target of miR-875-5p. Knockdown of USF2 partially counteracted the effects of miR-875-5p inhibitor. Overexpression of miR-875-5p could inhibit proliferation, migration and invasion and suppress the TGF-ß signalling pathway by downregulating USF2. CONCLUSIONS: MiR-875-5p can inhibit the progression of GC by directly targeting USF2. And in the future, miR-875-5p is expected to be a potential target for GC diagnosis and treatment.
Assuntos
MicroRNAs , Neoplasias Gástricas , Animais , Carcinogênese/genética , Linhagem Celular Tumoral , Movimento Celular/genética , Proliferação de Células/genética , Regulação Neoplásica da Expressão Gênica , Humanos , Camundongos , MicroRNAs/genética , MicroRNAs/metabolismo , Neoplasias Gástricas/patologia , Fator de Crescimento Transformador beta/metabolismo , Fatores Estimuladores Upstream/genética , Fatores Estimuladores Upstream/metabolismoRESUMO
OBJECTIVE: Acute kidney injury (AKI) is a serious complication of sepsis. This study was performed to explore the mechanism that THBS1 mediated pyroptosis by regulating the TGF-ß signaling pathway in sepsis-induced AKI. METHODS: Gene expression microarray related to sepsis-induced AKI was obtained from the GEO database, and the mechanism in sepsis-induced AKI was predicted by bioinformatics analysis. qRT-PCR and ELISA were performed to detect expressions of THBS1, USF2, TNF-α, IL-1ß, and IL-18 in sepsis-induced AKI patients and healthy volunteers. The mouse model of sepsis-induced AKI was established, with serum creatinine, urea nitrogen, 24-h urine output measured, and renal tissue lesions observed by HE staining. The cell model of sepsis-induced AKI was cultured in vitro, with expressions of TNF-α, IL-1ß, and IL-18, pyroptosis, Caspase-1 and GSDMD-N, and activation of TGF-ß/Smad3 pathway detected. The upstream transcription factor USF2 was knocked down in cells to explore its effect on sepsis-induced AKI. RESULTS: THBS1 and USF2 were highly expressed in patients with sepsis-induced AKI. Silencing THBS1 protected mice against sepsis-induced AKI, and significantly decreased the expressions of NLRP3, Caspase-1, GSDMD-N, IL-1ß, and IL-18, increased cell viability, and decreased LDH activity, thus partially reversing the changes in cell morphology. Mechanistically, USF2 promoted oxidative stress responses by transcriptionally activating THBS1 to activate the TGF-ß/Smad3/NLRP3/Caspase-1 signaling pathway and stimulate pyroptosis, and finally exacerbated sepsis-induced AKI. CONCLUSION: USF2 knockdown downregulates THBS1 to inhibit the TGF-ß/Smad3 signaling pathway and reduce pyroptosis and further ameliorate sepsis-induced AKI.
Assuntos
Injúria Renal Aguda/etiologia , Citocinas/genética , Sepse/complicações , Trombospondina 1/genética , Fatores Estimuladores Upstream/genética , Injúria Renal Aguda/genética , Injúria Renal Aguda/metabolismo , Animais , Caspase 1/metabolismo , Linhagem Celular , Sobrevivência Celular , Citocinas/metabolismo , Regulação para Baixo , Feminino , Humanos , Rim/metabolismo , Masculino , Camundongos Endogâmicos C57BL , Pessoa de Meia-Idade , Proteína 3 que Contém Domínio de Pirina da Família NLR/metabolismo , Piroptose , Sepse/genética , Sepse/metabolismo , Transdução de Sinais , Proteína Smad3/metabolismoRESUMO
BACKGROUND: Ionizing radiation (IR) is a standard modality for the management of solid tumors. Apart from its killing effects, IR can induce pro-survival factors leading to radioresistance of cancer. Mechanistic understanding of radiation resistance is warranted to overcome the pro-survival effects of IR. AIM: The aim of this study was to investigate the role of upstream stimulatory factor-1 (USF-1) in the induction of radioresistance in prostate cancer and its targeting by histone deacetylase (HDAC) inhibitors to reverse resistance. METHODS AND RESULTS: This study reports here that USF-1 is a marker for radioresistance in PC-3 cells. Using protein-DNA array analysis, it was documented that DNA binding activity of USF-1 was elevated following IR in PC-3 cells. Novel HDAC inhibitors downregulated USF-1 binding either alone or in combination with IR. A 5 Gy dose of IR induced the expression of target genes of USF-1 (human telomerase reverse transcriptase [hTERT], IGF2R, CyclinB1, and Cdk1), however, HDAC inhibitors alone or in combination with IR reduced their expression as measured by real time RT PCR analysis. Furthermore, immunofluorescence analysis revealed that while USF-1 localized primarily in the nucleus following IR, it localized in the cytoplasm when treated with HDAC inhibitors/combination. Maximum effects of modulation of USF-1 expression (overexpression or suppression) were observed on hTERT activity as determined by dual-luciferase reporter assay. To further confirm the role of USF-1 in radioresistance, cell growth was analyzed using the real-time cell electronic sensing (RT-CES) system. This study found that USF-1-transfected cells proliferated faster than the vector-transfected cells with or without treatments with HDAC inhibitors/IR/combination. Colony forming assay also confirmed that USF-1 overexpression led to increased survival following IR. Importantly, colony-forming assay demonstrated that HDAC inhibitors reversed the radioresistance in both PC-3 and DU-145 cells. CONCLUSION: These studies demonstrate that HDAC inhibitors reverse the radioresistance in prostate cancer through down-modulation of USF-1-mediated transactivation of target genes involved in cell proliferation and cell cycle.
Assuntos
Proteínas de Ligação a DNA , Inibidores de Histona Desacetilases , Neoplasias da Próstata , Tolerância a Radiação , Fatores Estimuladores Upstream , Humanos , Masculino , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Inibidores de Histona Desacetilases/farmacologia , Neoplasias da Próstata/metabolismo , Neoplasias da Próstata/radioterapia , Fatores Estimuladores Upstream/genética , Fatores Estimuladores Upstream/metabolismo , Tolerância a Radiação/efeitos dos fármacos , Células PC-3 , Regulação para BaixoRESUMO
BACKGROUND: To further understand the development of the spinal cord, an exploration of the patterns and transcriptional features of spinal cord development in newborn mice at the cellular transcriptome level was carried out. METHODS: The mouse single-cell sequencing (scRNA-seq) dataset was downloaded from the GSE108788 dataset. Single-cell RNA-Seq (scRNA-Seq) was conducted on cervical and lumbar spinal V2a interneurons from 2 P0 neonates. Single-cell analysis using the Seurat package was completed, and marker mRNAs were identified for each cluster. Then, pseudotemporal analysis was used to analyze the transcription changes of marker mRNAs in different clusters over time. Finally, the functions of these marker mRNAs were assessed by enrichment analysis and protein-protein interaction (PPI) networks. A transcriptional regulatory network was then constructed using the TRRUST dataset. RESULTS: A total of 949 cells were screened. Single-cell analysis was conducted based on marker mRNAs of each cluster, which revealed the heterogeneity of neonatal mouse spinal cord neuronal cells. Functional analysis of pseudotemporal trajectory-related marker mRNAs suggested that pregnancy-specific glycoproteins (PSGs) and carcinoembryonic antigen cell adhesion molecules (CEACAMs) were the core mRNAs in cluster 3. GSVA analysis then demonstrated that the different clusters had differences in pathway activity. By constructing a transcriptional regulatory network, USF2 was identified to be a transcriptional regulator of CEACAM1 and CEACAM5, while KLF6 was identified to be a transcriptional regulator of PSG3 and PSG5. This conclusion was then validated using the Genotype-Tissue Expression (GTEx) spinal cord transcriptome dataset. CONCLUSIONS: This study completed an integrated analysis of a single-cell dataset with the utilization of marker mRNAs. USF2/CEACAM1&5 and KLF6/PSG3&5 transcriptional regulatory networks were identified by spinal cord single-cell analysis.
Assuntos
Moléculas de Adesão Celular/genética , Redes Reguladoras de Genes , Glicoproteínas/genética , Fator 6 Semelhante a Kruppel/genética , Neuropeptídeo Y/metabolismo , Proteínas da Gravidez/genética , Análise de Sequência de RNA/métodos , Análise de Célula Única/métodos , Medula Espinal/metabolismo , Transcrição Gênica , Fatores Estimuladores Upstream/genética , Animais , Biomarcadores/metabolismo , Camundongos , Mapas de Interação de Proteínas , RNA Mensageiro/genéticaRESUMO
Total body upstream stimulatory factor 1 (USF1) deficiency in mice is associated with brown adipose tissue activation and a marked protection against the development of obesity and atherosclerotic lesions. Functional expression of USF1 has also been detected in monocytes and monocyte-derived macrophages. In the current study we therefore tested whether selective hematopoietic USF1 deficiency can also beneficially impact the development of atherosclerosis. For this purpose, LDL receptor knockout mice were transplanted with bone marrow from USF1 knockout mice or their wild-type littermate controls and subsequently fed a Western-type diet for 20 weeks to stimulate atherosclerotic lesion development. Strikingly, absence of USF1 function in bone marrow-derived cells was associated with exacerbated blood leukocyte (+ 100%; P < 0.01) and peritoneal leukocyte (+ 50%; P < 0.05) lipid loading and an increased atherosclerosis susceptibility (+ 31%; P < 0.05). These effects could be attributed to aggravated hyperlipidemia, i.e. higher plasma free cholesterol (+ 33%; P < 0.001) and cholesteryl esters (+ 39%; P < 0.001), and the development of hepatosteatosis. In conclusion, we have shown that hematopoietic USF1 deficiency is associated with an increased atherosclerosis susceptibility in LDL receptor knockout mice. These findings argue against a contribution of macrophage-specific USF1 deficiency to the previously described beneficial effect of total body USF1 deficiency on atherosclerosis susceptibility in mice.
Assuntos
Aterosclerose/genética , Predisposição Genética para Doença , Receptores de LDL/genética , Fatores Estimuladores Upstream/genética , Animais , Camundongos , Camundongos Endogâmicos C57BL , Camundongos KnockoutRESUMO
ZNFO is a Krüppel-associated box (KRAB) containing zinc finger transcription factor, which is exclusively expressed in bovine oocytes. Previous studies have demonstrated that ZNFO possesses an intrinsic transcriptional repressive activity and is essential for early embryonic development in cattle. However, the mechanisms regulating ZNFO transcription remain elusive. In the present study, the core promoter that controls the ZNFO basal transcription was identified. A 1.7 kb 5' regulatory region of the ZNFO gene was cloned and its promoter activity was confirmed by a luciferase reporter assay. A series of 5' deletion in the ZNFO promoter followed by luciferase reporter assays indicated that the core promoter region has to include the sequence located within 57 bp to 31 bp upstream of the transcription start site. Sequence analysis revealed that a putative USF1/USF2 binding site (GGTCACGTGACC) containing an E-box motif (CACGTG) is located within the essential region. Depletion of USF1/USF2 by RNAi and E-box mutation analysis demonstrated that the USF1/USF2 binding site is required for the ZNFO basal transcription. Furthermore, EMSA and super-shift assays indicated that the observed effects are dependent on the specific interactions between USF proteins and the ZNFO core promoter. From these results, it is concluded that USF1 and USF2 are essential for the basal transcription of the ZNFO gene.
Assuntos
Oócitos/metabolismo , Fatores de Transcrição/genética , Fatores Estimuladores Upstream/genética , Animais , Sequência de Bases/genética , Sítios de Ligação , Bovinos/genética , Núcleo Celular/genética , Núcleo Celular/metabolismo , Proteínas de Ligação a DNA/genética , Elementos E-Box/genética , Regulação da Expressão Gênica/genética , Regulação da Expressão Gênica no Desenvolvimento/genética , Herança Materna/genética , Oócitos/fisiologia , Oogênese/genética , Regiões Promotoras Genéticas/genética , Ligação Proteica , RNA Mensageiro/metabolismo , Fatores de Transcrição/metabolismo , Sítio de Iniciação de Transcrição , Transcrição Gênica/genética , Fatores Estimuladores Upstream/metabolismo , Dedos de Zinco/genéticaRESUMO
Epigenetic modifications of DNA play important roles in many biological processes. Identifying readers of these epigenetic marks is a critical step towards understanding the underlying mechanisms. Here, we present an all-to-all approach, dubbed digital affinity profiling via proximity ligation (DAPPL), to simultaneously profile human TF-DNA interactions using mixtures of random DNA libraries carrying different epigenetic modifications (i.e., 5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine) on CpG dinucleotides. Many proteins that recognize consensus sequences carrying these modifications in symmetric and/or hemi-modified forms are identified. We further demonstrate that the modifications in different sequence contexts could either enhance or suppress TF binding activity. Moreover, many modifications can affect TF binding specificity. Furthermore, symmetric modifications show a stronger effect in either enhancing or suppressing TF-DNA interactions than hemi-modifications. Finally, in vivo evidence suggests that USF1 and USF2 might regulate transcription via hydroxymethylcytosine-binding activity in weak enhancers in human embryonic stem cells.
Assuntos
5-Metilcitosina/análogos & derivados , DNA/metabolismo , Epigenômica/métodos , 5-Metilcitosina/metabolismo , Linhagem Celular , Ilhas de CpG/genética , DNA/genética , Elementos Facilitadores Genéticos , Epigênese Genética , Biblioteca Gênica , Células-Tronco Embrionárias Humanas , Humanos , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Fatores Estimuladores Upstream/genética , Fatores Estimuladores Upstream/isolamento & purificação , Fatores Estimuladores Upstream/metabolismoRESUMO
mir-33a and mir-33b are co-transcribed with the SREBF2 and SREBF1 transcription factors, respectively. The main role of SREBF1 is the regulation of genes involved in fatty acid metabolism, while SREBF2 regulates genes participating in cholesterol biosynthesis and uptake. Our objective was to study the expression of both miR-33a and miR-33b, together with their host SREBF genes, in liver, adipose tissue and muscle to better understand the role of miR-33a/b in the lipid metabolism of pigs. In our study, the expression of miR-33a, miR-33b and SREBF2 in liver, adipose tissue, and muscle was studied in 42 BC1_LD (25% Iberian x 75% Landrace backcross) pigs by RT-qPCR. In addition, the expression of in-silico predicted target genes and fatty acid composition traits were correlated with the miR-33a/b expression. We observed different tissue expression patterns for both miRNAs. In adipose tissue and muscle a high correlation between miR-33a and miR-33b expression was found, whereas a lower correlation was observed in liver. The expression analysis of in-silico predicted target-lipid related genes showed negative correlations between miR-33b and CPT1A expression in liver. Conversely, positive correlations between miR-33a and PPARGC1A and USF1 gene expression in liver were observed. Lastly, positive and negative correlations between miR-33a/b expression and saturated fatty acid (SFA) and polyunsaturated fatty acid (PUFA) content, respectively, were identified. Overall, our results suggested that both miRNAs are differentially regulated and have distinct functions in liver, in contrast to muscle and adipose tissue. Furthermore, the correlations between miR-33a/b expression both with the expression of in-silico predicted target-lipid related genes and with fatty acid composition, opens new avenues to explore the role of miR33a/b in the regulation of lipid metabolism.
Assuntos
Tecido Adiposo/metabolismo , Ácidos Graxos/metabolismo , Fígado/metabolismo , MicroRNAs/genética , Músculo Esquelético/metabolismo , Animais , Carnitina O-Palmitoiltransferase/genética , Carnitina O-Palmitoiltransferase/metabolismo , MicroRNAs/metabolismo , Coativador 1-alfa do Receptor gama Ativado por Proliferador de Peroxissomo/genética , Coativador 1-alfa do Receptor gama Ativado por Proliferador de Peroxissomo/metabolismo , Suínos , Fatores Estimuladores Upstream/genética , Fatores Estimuladores Upstream/metabolismoRESUMO
Serum lipid profile which is determined by genotype-phenotype relationship plays a significant role in the development of cardiovascular disease. Upstream stimulatory factor 1 (USF1), has been reported to be associated with serum lipid levels in different population, hence, this study investigated the association of variants in USF1 with serum lipid profile in adults in Lagos state, Nigeria. We genotyped rs3737787 (11235C > T) and rs550376620 (10488G > A) with PCR-RFLP in 384 participants and we used logistic regression to assess the association of these variants with serum lipid levels. The minor allele frequency observed in 10488G > A in both case and control groups was 5% while the minor allele of 11235C > T was observed to be more frequent in the control when compared to the dyslipidemic subjects (24% vs 12%; p = 1.84e-05). Levels of total cholesterol, triglycerides, and LDL-c in dyslipidemic subjects with CC genotype of 11235C > T were significantly higher compared to CT and TT genotypes (p < 0.001; p < 0.0001 and p < 0.0001 respectively). Logistic regression with adjustment for age, gender and BMI, showed that the minor allele carriers of 11235C > T have a reduced risk of dyslipidemia (Odds ratio: 0. 0.043, 95% confidence interval (CI): (0.006-0.331, p = 0.002). Our findings revealed that rs3737787 is associated with lipid phenotype in Nigerian population.
Assuntos
Estudos de Associação Genética , Lipídeos/sangue , Polimorfismo de Nucleotídeo Único/genética , Fatores Estimuladores Upstream/genética , Adulto , Alelos , Dislipidemias/sangue , Dislipidemias/genética , Feminino , Frequência do Gene/genética , Predisposição Genética para Doença , Humanos , Modelos Logísticos , Masculino , Análise Multivariada , Nigéria , Fenótipo , Fatores de RiscoRESUMO
IL-17-producing Th17 cells are implicated in the pathogenesis of rheumatoid arthritis (RA) and TNF-α, a proinflammatory cytokine in the rheumatoid joint, facilitates Th17 differentiation. Anti-TNF therapy ameliorates disease in many patients with rheumatoid arthritis (RA). However, a significant proportion of patients do not respond to this therapy. The impact of anti-TNF therapy on Th17 responses in RA is not well understood. We conducted high-throughput gene expression analysis of Th17-enriched CCR6+CXCR3-CD45RA- CD4+ T (CCR6+ T) cells isolated from anti-TNF-treated RA patients classified as responders or nonresponders to therapy. CCR6+ T cells from responders and nonresponders had distinct gene expression profiles. Proinflammatory signaling was elevated in the CCR6+ T cells of nonresponders, and pathogenic Th17 signature genes were up-regulated in these cells. Gene set enrichment analysis on these signature genes identified transcription factor USF2 as their upstream regulator, which was also increased in nonresponders. Importantly, short hairpin RNA targeting USF2 in pathogenic Th17 cells led to reduced expression of proinflammatory cytokines IL-17A, IFN-γ, IL-22, and granulocyte-macrophage colony-stimulating factor (GM-CSF) as well as transcription factor T-bet. Together, our results revealed inadequate suppression of Th17 responses by anti-TNF in nonresponders, and direct targeting of the USF2-signaling pathway may be a potential therapeutic approach in the anti-TNF refractory RA.