Biomedical subjects

Quan Zhao

Publications and source records attributed to Quan Zhao.

14 recordsLinked to original sources

PubMed2026

PEARL: integrative multi-omics classification and omics feature discovery via deep graph learning.

MOTIVATION: Integrating multi-omics data provides valuable insights into biological processes by capturing information across multiple molecular layers, enabling a comprehensive understanding of complex diseases and driving advancements in precision medicine. However, existing computational methods for multi-omics integration face significant challenges, such as low reliability and poor generalizability, due to the high dimensionality and low sample size nature of omics data. RESULTS: To address these challenges, we present PEARL (Pearson-Enhanced spectrAl gRaph convoLutional networks), a novel deep graph learning method for biomedical classification and functional important omics features identification. PEARL leverages a simple yet effective learning architecture to achieve superior and robust performance in high-dimensional, low-sample-size multi-omics settings. Our results demonstrate that PEARL significantly outperforms existing state-of-the-art methods on both synthetic and real biomedical datasets. Furthermore, applied to Alzheimer's disease (AD) brain multi-omics data, features prioritized by PEARL lead to functionally important genes that demonstrate significant enrichment in AD-related pathways. These findings highlight PEARL's practical utility in biomedical research and its potential to enhance biological interpretability in multi-omics studies. AVAILABILITY AND IMPLEMENTATION: The source code of our computational framework is available at https://github.com/zqq121017/PEARL.

Multiomics↗

PubMed2007

IOP1, a novel hydrogenase-like protein that modulates hypoxia-inducible factor-1alpha activity.

A central means by which mammalian cells respond to low oxygen tension is through the activation of the transcription factor HIF-1 (hypoxia-inducible factor-1). Under normoxic conditions, HIF-1alpha (the alpha subunit of HIF-1) is targeted for rapid degradation by the ubiquitin-proteasome pathway. Under hypoxic conditions, this degradation is inhibited, thereby leading to the stabilization and activation of HIF-1alpha. Here, we report the identification of IOP1 (iron-only hydrogenase-like protein 1), a protein homologous with enzymes present in anaerobic organisms that contain a distinctive iron-sulfur cluster. IOP1 is present in a broad range of cell types. Knockdown of IOP1 using siRNA (small interfering RNA) in mammalian cells increases protein levels of HIF-1alpha under both normoxic and hypoxic conditions, and augments hypoxia-induced HRE (hypoxia response element) reporter gene and endogenous HIF-1alpha target gene expressions. We find that IOP1 knockdown up-regulates HIF-1alpha mRNA levels, thereby providing a mechanism by which knockdown induces the observed effects. The results collectively provide evidence that IOP1 is a component of the protein network that regulates HIF-1alpha in mammalian cells.

Amino Acid Sequence↗

PubMed2006

Can the Internet be used effectively to provide sex education to young people in China?

PURPOSE: To assess the feasibility and effectiveness of sex education conducted through the Internet. METHODS: Two high schools and four colleges of a university in Shanghai were selected as the research sites. Half of these were assigned to the intervention group and the other half to the control group. The interventions consisted of offering sexual and reproductive health knowledge, service information, counseling and discussion to all grade one students in the intervention group. The intervention phase lasted for 10 months and was implemented through a special website, with web pages, online videos, Bulletin Board System (BBS) and expert mailbox. In total, 624 students from the intervention, and 713 from the control schools and colleges participated in the baseline survey, and about 97% of them were followed up in postintervention survey to assess changes that can be attributed to the sex education interventions provided through the Internet. RESULTS: The median scores of the overall knowledge and of each specific aspect of reproductive health such as reproduction, contraception, condom, sexually transmitted infections (STIs) and human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) were significantly higher in the intervention group as compared with those in the control group at postintervention (p < .0001), although no significant differences were found between these two groups in the baseline survey (p > .05). Group by time interaction effects in ordinal logistic regression analysis were found on knowledge score (p < .0001) and in attitude of high school students toward sex-related issues (p < .05), suggesting that interventions increased subjects' knowledge significantly and changed high school students' attitudes to being less liberal toward sex. The intervention also had positive influence on students' attitudes toward providing contraceptive service for unmarried people. CONCLUSIONS: Providing sex education to students in Shanghai through the Internet was found feasible and effective. The Internet-based sex education program increased students' reproductive health knowledge effectively and changed their attitudes toward sex-related issues in terms of being less liberal toward sex and more favorable to providing services to unmarried young people. The Internet thus offers an important and hitherto untapped potential for providing sex education to students and young people in China.

Adolescent↗

PubMed2006

A critical role for the transcription factor Scl in platelet production during stress thrombopoiesis.

The generation of platelets from megakaryocytes in the steady state is regulated by a variety of cytokines and transcription factors, including thrombopoietin (TPO), GATA-1, and NF-E2. Less is known about platelet production in the setting of stress thrombopoiesis, a pivotal event in the context of cytotoxic chemotherapy. Here we show in mice that the transcription factor Scl is critical for platelet production after chemotherapy and in thrombopoiesis induced by administration of TPO. Megakaryocytes from these mice showed appropriate increases in number and ploidy but failed to shed platelets. Ultrastructural examination of Scl-null megakaryocytes revealed a disorganized demarcation membrane and reduction in platelet granules. Quantitative real-time polymerase chain reaction showed that Scl-null platelets lacked NF-E2, and chromatin immunoprecipitation analysis demonstrated Scl binding to the NF-E2 promoter in the human megakaryoblastic-cell line Meg-01, along with its binding partners E47, Lmo2, and the cofactors Ldb1 and GATA-2. These findings suggest that Scl acts up-stream of NF-E2 expression to control megakaryocyte development and platelet release in settings of thrombopoietic stress.

Animals↗

PubMed2006

A family with erythrocytosis establishes a role for prolyl hydroxylase domain protein 2 in oxygen homeostasis.

The number of red blood cells is normally tightly regulated by a classic homeostatic mechanism based on oxygen sensing in the kidney. Decreased oxygen delivery resulting from anemia induces the production of erythropoietin, which increases red cell production and hence oxygen delivery. Investigations of erythropoietin regulation identified the transcription factor hypoxia-inducible factor (HIF). HIF is now recognized as being a key regulator of genes that function in a comprehensive range of processes besides erythropoiesis, including energy metabolism and angiogenesis. HIF itself is regulated through the alpha-subunit, which is hydroxylated in the presence of oxygen by a family of three prolyl hydroxylase domain proteins (PHDs)/HIF prolyl hydroxylases/egg-laying-defective nine enzymes. Hydroxylation allows capture by the von Hippel-Lindau tumor suppressor gene product, ubiquitination, and destruction by the proteasome. Here we describe an inherited mutation in a mammalian PHD enzyme. We show that this mutation in PHD2 results in a marked decrease in enzyme activity and is associated with familial erythrocytosis, identifying a previously unrecognized cause of this condition. Our findings indicate that PHD2 is critical for normal regulation of HIF in humans.

Adult↗

PubMed2006

Functional interaction of CP2 with GATA-1 in the regulation of erythroid promoters.

We observed that binding sites for the ubiquitously expressed transcription factor CP2 were present in regulatory regions of multiple erythroid genes. In these regions, the CP2 binding site was adjacent to a site for the erythroid factor GATA-1. Using three such regulatory regions (from genes encoding the transcription factors GATA-1, EKLF, and p45 NF-E2), we demonstrated the functional importance of the adjacent CP2/GATA-1 sites. In particular, CP2 binds to the GATA-1 HS2 enhancer, generating a ternary complex with GATA-1 and DNA. Mutations in the CP2 consensus greatly impaired HS2 activity in transient transfection assays with K562 cells. Similar results were obtained by transfection of EKLF and p45 NF-E2 mutant constructs. Chromatin immunoprecipitation with K562 cells showed that CP2 binds in vivo to all three regulatory elements and that both GATA-1 and CP2 were present on the same GATA-1 and EKLF regulatory elements. Adjacent CP2/GATA-1 sites may represent a novel module for erythroid expression of a number of genes. Additionally, coimmunoprecipitation and glutathione S-transferase pull-down experiments demonstrated a physical interaction between GATA-1 and CP2. This may contribute to the functional cooperation between these factors and provide an explanation for the important role of ubiquitous CP2 in the regulation of erythroid genes.

Amino Acid Motifs↗

PubMed2005

Repression of human gamma-globin gene expression by a short isoform of the NF-E4 protein is associated with loss of NF-E2 and RNA polymerase II recruitment to the promoter.

Binding of the stage selector protein (SSP) to the stage selector element (SSE) in the human gamma-globin promoter contributes to the preferential expression of the gamma-gene in fetal erythroid cells. The SSP contains the transcription factor CP2 and an erythroid-specific partner, NF-E4. The NF-E4 gene encodes a 22-kDa polypeptide employing a non-AUG initiation codon. Antisera specific to NF-E4 detects this species and an additional 14 kDa protein, which initiates from an internal methionine. Enforced expression of p14 NF-E4 in the K562 fetal/erythroid cell line, and in primary erythroid cord blood progenitors, results in repression of gamma-gene expression. Biochemical studies reveal that p14 NF-E4 interacts with CP2, resulting in diminished association of CP2 with the SSE in chromatin immunoprecipitation assays. p45 NF-E2 recruitment to the gamma-promoter is also lost, resulting in a reduction in RNA polymerase II and TBP binding and a fall in promoter transcriptional activity. This effect is specific, as enforced expression of a mutant form of p14 NF-E4, which fails to interact with CP2, also fails to repress gamma-gene expression in K562 cells. These findings provide one potential mechanism that could contribute to the autonomous silencing of the human gamma-genes in adult erythroid cells.

Erythroid Precursor Cells↗

PubMed2004

Site-specific acetylation of the fetal globin activator NF-E4 prevents its ubiquitination and regulates its interaction with the histone deacetylase, HDAC1.

Acetylation provides one mechanism by which the functional diversity of individual transcription factors can be expanded. This is valuable in the setting of complex multigene loci that are regulated by a limited number of proteins, such as the human beta-globin locus. We have studied the role of acetylation in the regulation of the transcription factor NF-E4, a component of a protein complex that facilitates the preferential expression of the human gamma-globin genes in fetal erythroid cells. We have shown that NF-E4 interacts directly with, and serves as a substrate for, the acetyltransferase co-activator PCAF. Acetylation of NF-E4 is restricted to a single residue (Lys(43)) in the amino-terminal domain of the protein and results in two important functional consequences. Acetylation of NF-E4 prolongs the protein half-life by preventing ubiquitin-mediated degradation. This stabilization is PCAF-dependent, since enforced expression in fetal/erythroid cells of a mutant form of PCAF lacking the histone acetyltransferase domain (PCAFDeltaHAT) decreases NF-E4 stability. Acetylation of Lys(43) also reduces the interaction between NF-E4 and HDAC1, potentially maximizing the activating ability of the factor at the gamma-promoter. These results provide further demonstration that co-activators, such as PCAF, can influence individual transcription factor properties at multiple levels to alter their effects on gene expression.

Acetylation↗

PubMed2004

The role of p22 NF-E4 in human globin gene switching.

The human stage selector protein, a complex containing the ubiquitous transcription factor CP2 and the erythroid-specific factor p22 NF-E4, facilitates the interaction of the gamma-globin genes with the locus control region in fetal erythroid cells. Enforced expression of p22 NF-E4 in K562 cells and human cord blood progenitors increases fetal globin gene expression, and in progenitors, reduces beta-globin expression. To examine the role of NF-E4 in an in vivo model of hemoglobin switching, we enforced the expression of p22 NF-E4 in transgenic mice carrying the human beta-globin locus yeast artificial chromosome. Although murine erythropoiesis and globin gene expression is unaffected in these mice, the expression profile of the human globin genes is altered. All three transgenic lines displayed an increased gamma:beta-globin ratio in E12.5-14.5 fetal liver, resulting in a delay in the fetal/adult switch. At E12.5, this is primarily due to a reduction of beta-gene expression, whereas at E14.5, the increased gamma:beta ratio is due to enhanced gamma-gene expression. Despite this, the switch in globin subtype is fully completed in the adult bone marrow. These findings indicate that p22 NF-E4 is capable of influencing human globin gene expression in vivo but is incapable of overriding the intrinsic mechanisms governing gamma-gene silencing in this context.

Animals↗

PubMed2004

[Development of hybrid strains from geographic isolates of Eimeria tenella and their immunoprotection].

OBJECTIVE: To cultivate hybrid strains from three geographic isolates of Eimeria tenella and to explore the possibility of developing vaccine candidates. METHODS: Three parental strains were selected from five geographic isolates of E. tenella through immune experiment, and hybrid strains were cultivated. The genomic DNA of the three parental strains and their filial generation were analyzed by random amplified polymorphic DNA (RAPD) technique with 30 optimization primers screened from 200 primers, the hybrid strains were isolated from the filial generation by RAPD. Chicken were inoculated with hybrid strains, and challenged with different strains to compare the immunogenicity and immunoprotection. RESULTS: Immunogenicity and immunoprotection of the three strains isolated from Guangzhou, Baoding and Changchun were stronger than those of other strains. Hybridization was performed to cultivate hybrid strain. Two hybrid strains were isolated from Changchun x Baoding and Guangzhou x F1 by RAPD. The result of immune experiment proved that immunoprotecion of F1 and F2 were higher than their parental strains. CONCLUSION: Two hybrid strains have been cultivated from the three geographic isolates of E. tenella, with the immunogenicity of their parental strains. Chicken immunized by F2 strain have shown strong resistance against the infection of the geographic strains, with an average protection rate of 84%.

Animals↗

PubMed2003

The transcriptional activity of the APP intracellular domain-Fe65 complex is inhibited by activation of the NF-kappaB pathway.

The beta-amyloid precursor protein (APP) is an integral membrane protein that is the subject of proteolytic processing. Sequential cleavage of APP by beta-secretase and subsequently gamma-secretase generates the beta-amyloid peptide as well as a cytoplasmic intracellular domain (AICD). AICD binds to the transcriptional coactivator Fe65, and this complex has been shown to display transcriptional activity. The regulation of this complex is poorly understood. We show here that activation of the NF-kappaB pathway, either by overexpression of NF-kappaB-inducing kinase (NIK) or by treatment with the proinflammatory cytokine IL-1beta, downregulates the transcriptional activity of the AICD-Fe65 complex. This therefore provides a mechanism by which the activity of AICD might be modulated by extracellular stimuli. These results also identify an intracellular signal transduction pathway influenced by the NF-kappaB signaling pathway.

Amyloid beta-Protein Precursor↗

PubMed2003

[Iodine-125 interstitial brachytherapy for malignant tumor].

OBJECTIVE: To assess the clinical effects of (125)I interstitial brachytherapy for malignant tumors. METHODS: One hundred and twelve patients with malignant tumors of stage II stage and III under went radical resection combined with (125)I intraoperative implantation. Seven days and three month after operation WBC count and immune markers were observed. Blood biochemistry ultrasonography and X-ray were performed to observe recurrence and metastasis of tumors per three months. RESULTS: In the 112 patients, 3 died of tumor recurrence in six months, and others survived with the longest time of 35 months. CONCLUSION: (125)I interstitial brachytherapy for malignant tumor is simple, safe and effective.

Adult↗

PubMed2002

A mitochondrial specific stress response in mammalian cells.

Cells respond to a wide variety of stresses through the transcriptional activation of genes that harbour stress elements within their promoters. While many of these elements are shared by genes encoding proteins representative of all subcellular compartments, cells can also respond to stresses that are specific to individual organelles, such as the endoplasmic reticulum un folded protein response. Here we report on the discovery and characterization of a mitochondrial stress response in mammalian cells. We find that the accumulation of unfolded protein within the mitochondrial matrix results in the transcriptional upregulation of nuclear genes encoding mitochondrial stress proteins such as chaperonin 60, chaperonin 10, mtDnaJ and ClpP, but not those encoding stress proteins of the endoplasmic reticulum. Analysis of the chaperonin 60/10 bidirectional promoter identified a CHOP element as the mitochondrial stress response element. Dominant-negative mutant forms of CHOP and overexpression of CHOP revealed that this transcription factor, in association with C/EBPbeta, regulates expression of mitochondrial stress genes in response to the accumulation of unfolded proteins.

Adenosine Triphosphatases↗

PubMed2002

Sequence determinants in hypoxia-inducible factor-1alpha for hydroxylation by the prolyl hydroxylases PHD1, PHD2, and PHD3.

Hypoxia-inducible factor (HIF) is a heterodimeric transcription factor induced by hypoxia. Under normoxic conditions, site-specific proline hydroxylation of the alpha subunits of HIF allows recognition by the von Hippel-Lindau tumor suppressor protein (VHL), a component of an E3 ubiquitin ligase complex that targets these subunits for degradation by the ubiquitin-proteasome pathway. Under hypoxic conditions, this hydroxylation is inhibited, allowing the alpha subunits of HIF to escape VHL-mediated degradation. Three enzymes, prolyl hydroxylase domain-containing proteins 1, 2, and 3 (PHD1, -2, and -3; also known as HIF prolyl hydroxylase 3, 2, and 1, respectively), have recently been identified that catalyze proline hydroxylation of HIF alpha subunits. These enzymes hydroxylate specific prolines in HIF alpha subunits in the context of a strongly conserved LXXLAP sequence motif (where X indicates any amino acid and P indicates the hydroxylacceptor proline). We report here that PHD2 has the highest specific activity toward the primary hydroxylation site of HIF-1alpha. Furthermore, and unexpectedly, mutations can be tolerated at the -5, -2, and -1 positions (relative to proline) of the LXXLAP motif. Thus, these results provide evidence that the only obligatory residue for proline hydroxylation in HIF-1alpha is the hydroxylacceptor proline itself.

Amino Acid Motifs↗