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Biomedical subjects

Yan Liu

Publications and source records attributed to Yan Liu.

At least 37 records · Page 2Linked to original sources
PubMed2025

Targeting RECQL4 in hepatocellular carcinoma: from prognosis to therapeutic potential.

OBJECTIVE: The aim of this study is to assess the clinical utility of RecQ Like Helicase 4 (RECQL4) as a prognostic marker in hepatocellular carcinoma (HCC) and investigate its associations with various biological processes, angiogenesis-related factors, immune cell infiltration, immune checkpoints, and drug sensitivity. METHODS: RECQL4 expression was analyzed across a range of cancer types utilizing data from the TCGA database. Disparities in RECQL4 expression levels between normal and malignant tissues were evaluated, alongside an analysis of progression-free interval (PFI), disease-specific survival (DSS), and overall survival (OS) curves. Exploration of pertinent pathways, immune cell infiltration, single-cell RNA-seq data, and drug sensitivity was conducted employing The Cancer Genome Atlas (TCGA) and Tumor Immune Single-Cell Hub (TISCH) databases. Furthermore, validation of in-silico results was validated through qPCR, Western blotting, CCK-8 assay, EdU assay, clonogenic assay, wound-healing assay, and transwell assay. RESULTS: In HCC, RECQL4 was highly expressed and associated with poorer prognosis (p&#x2009;<&#x2009;0.05). It positively correlated with pathways related to MYC targets, DNA replication, PI3K/AKT/mTOR signaling, DNA repair mechanisms, and the G2/M checkpoint (R&#x2009;>&#x2009;0.24, p&#x2009;<&#x2009;0.001). RECQL4 also showed significant correlations with angiogenesis-related genes, including PTK2 (R&#x2009;>&#x2009;0.4, p&#x2009;<&#x2009;0.05), suggesting a potential role in angiogenesis regulation. Immune analysis indicated that RECQL4 was associated with immune cell types such as T helper 2 cells, NK CD56bright cells, and follicular helper T cells, suggesting a positive relationship with their infiltration. High RECQL4 expression was also linked to increased sensitivity to drugs including Sorafenib, 5-Fluorouracil, Cisplatin, and Doxorubicin. Cellular experiments showed that RECQL4 expression at the mRNA and protein levels were significantly higher in HCC cell lines Hep3B and Huh7 compared to the normal liver cell line MHA. Moreover, RECQL4 knockdown resulted in reduced proliferation and migration in HCC cell lines (p&#x2009;<&#x2009;0.05). CONCLUSIONS: RECQL4 shows promise as a biomarker for predicting recurrence and survival in HCC and may affect angiogenesis regulation. Its expression also appears to impact sensitivity to drugs such as Sorafenib, 5-Fluorouracil, Cisplatin, and Doxorubicin. Furthermore, silencing RECQL4 significantly inhibits HCC cell line proliferation and migration.

Humans↗
PubMed2024

PRC1 and CTCF-Mediated Transition from Poised to Active Chromatin Loops Drives Bivalent Gene Activation.

Polycomb Repressive Complex 1 (PRC1) and CCCTC-binding factor (CTCF) are critical regulators of 3D chromatin architecture that influence cellular transcriptional programs. Spatial chromatin structures comprise conserved compartments, topologically associating domains (TADs), and dynamic, cell-type-specific chromatin loops. Although the role of CTCF in chromatin organization is well-known, the involvement of PRC1 is less understood. In this study, we identified an unexpected, essential role for the canonical Pcgf2-containing PRC1 complex (cPRC1.2), a known transcriptional repressor, in activating bivalent genes during differentiation. Our Hi-C analysis revealed that cPRC1.2 forms chromatin loops at bivalent promoters, rendering them silent yet poised for activation. Using mouse embryonic stem cells (ESCs) with CRISPR/Cas9-mediated gene editing, we found that the loss of Pcgf2, though not affecting the global level of H2AK119ub1, disrupts these cPRC1.2 loops in ESCs and impairs the transcriptional induction of crucial target genes necessary for neuronal differentiation. Furthermore, we identified CTCF enrichment at cPRC1.2 loop anchors and at Polycomb group (PcG) bodies, nuclear foci with concentrated PRC1 and its tethered chromatin domains, suggesting that PRC1 and CTCF cooperatively shape chromatin loop structures. Through virtual 4C and other genomic analyses, we discovered that establishing neuronal progenitor cell (NPC) identity involves a switch from cPRC1.2-mediated chromatin loops to CTCF-mediated active loops, enabling the expression of critical lineage-specific factors. This study uncovers a novel mechanism by which pre-formed PRC1 and CTCF loops at lineage-specific genes maintain a poised state for subsequent gene activation, advancing our understanding of the role of chromatin architecture in controlling cell fate transitions.

Journal Article↗
PubMed2024

Identifying inversions with breakpoints in the Dystrophin gene through long-read sequencing: report of two cases.

BACKGROUND: Duchenne Muscular Dystrophy (DMD) is an X-linked disorder caused by mutations in the DMD gene, with large deletions being the most common type of mutation. Inversions involving the DMD gene are a less frequent cause of the disorder, largely because they often evade detection by standard diagnostic methods such as multiplex ligation probe amplification (MLPA) and whole exome sequencing (WES). CASE PRESENTATION: Our research identified two intrachromosomal inversions involving the dystrophin gene in two unrelated families through Long-read sequencing (LRS). These variants were subsequently confirmed via Sanger sequencing. The first case involved a pericentric inversion extending from DMD intron 47 to Xq27.3. The second case featured a paracentric inversion between DMD intron 42 and Xp21.1, inherited from the mother. In both cases, simple repeat sequences (SRS) were present at the breakpoints of these inversions. CONCLUSIONS: Our findings demonstrate that LRS is an effective tool for detecting atypical mutations. The identification of SRS at the breakpoints in DMD patients enhances our understanding of the mechanisms underlying structural variations, thereby facilitating the exploration of potential treatments.

Humans↗
PubMed2024

Proteomics analysis of deep fascia in acute compartment syndrome.

Acute compartment syndrome (ACS) is a syndrome in which local circulation is affected due to increased pressure within the compartment. We previously found in patients with calf fractures, the pressure of fascial compartment could be sharply reduced upon the appearance of tension blisters. Deep fascia, as the important structure for compartment, might play key role in this process. Therefore, the aim of the present study was to examine the differences in gene profile in deep fascia tissue in fracture patients of the calf with or without tension blisters, and to explore the role of fascia in pressure improvement in ACS. Patients with lower leg fracture were enrolled and divided into control group (CON group, n = 10) without tension blister, and tension blister group (TB group, n = 10). Deep fascia tissues were collected and LC-MS/MS label-free quantitative proteomics were performed. Genes involved in fascia structure and fibroblast function were further validated by Western blot. The differentially expressed proteins were found to be mainly enriched in pathways related to protein synthesis and processing, stress fiber assembly, cell-substrate adhesion, leukocyte mediated cytotoxicity, and cellular response to stress. Compared with the CON group, the expression of Peroxidasin homolog (PXDN), which promotes the function of fibroblasts, and Leukocyte differentiation antigen 74 (CD74), which enhances the proliferation of fibroblasts, were significantly upregulated (p all <0.05), while the expression of Matrix metalloproteinase-9 (MMP9), which is involved in collagen hydrolysis, and Neutrophil elastase (ELANE), which is involved in elastin hydrolysis, were significantly reduced in the TB group (p all <0.05), indicating fascia tissue underwent microenvironment reconstruction during ACS. In summary, the ACS accompanied by blisters is associated with the enhanced function and proliferation of fibroblasts and reduced hydrolysis of collagen and elastin. The adaptive alterations in the stiffness and elasticity of the deep fascia might be crucial for pressure release of ACS.

Humans↗
PubMed2007

Vesicular glutamate transport at a central synapse limits the acuity of visual perception in zebrafish.

The neural circuitry that constrains visual acuity in the CNS has not been experimentally identified. We show here that zebrafish blumenkohl (blu) mutants are impaired in resolving rapid movements and fine spatial detail. The blu gene encodes a vesicular glutamate transporter expressed by retinal ganglion cells. Mutant retinotectal synapses release less glutamate, per vesicle and per terminal, and fatigue more quickly than wild-type in response to high-frequency stimulation. In addition, mutant axons arborize more extensively, thus increasing the number of synaptic terminals and effectively normalizing the combined input to postsynaptic cells in the tectum. This presumably homeostatic response results in larger receptive fields of tectal cells and a degradation of the retinotopic map. As predicted, mutants have a selective deficit in the capture of small prey objects, a behavior dependent on the tectum. Our studies successfully link the disruption of a synaptic protein to complex changes in neural circuitry and behavior.

Animals↗
PubMed2007

Identification of a novel tumor suppressor gene p34 on human chromosome 6q25.1.

In this study, we observed loss of heterozygosity (LOH) in human chromosomal fragment 6q25.1 in sporadic lung cancer patients. LOH was observed in 65% of the 26 lung tumors examined and was narrowed down to a 2.2-Mb region. Single-nucleotide polymorphism (SNP) analysis of genes located within this region identified a candidate gene, termed p34. This gene, also designated as ZC3H12D, C6orf95, FLJ46041, or dJ281H8.1, carries an A/G nonsynonymous SNP at codon 106, which alters the amino acid from lysine to arginine. Nearly 73% of heterozygous lung cancer tissues with LOH and the A/G SNP also exhibited loss of the A allele. In vitro clonogenic and in vivo nude mouse studies showed that overexpression of the A allele exerts tumor suppressor function compared with the G allele. p34 is located within a recently mapped human lung cancer susceptibility locus, and association of the p34 A/G SNP was tested among these families. No significant association between the less frequent G allele and lung cancer susceptibility was found. Our results suggest that p34 may be a novel tumor suppressor gene involved in sporadic lung cancer but it seems not to be the candidate familial lung cancer susceptibility gene linked to chromosomal region 6q23-25.

Alleles↗
PubMed2007

Physical impairment and social adaptation in adult survivors of childhood and adolescent rhabdomyosarcoma: A report from the Childhood Cancer Survivors Study.

BACKGROUND: Despite interest in the well-being of adult survivors of childhood rhabdomyosarcoma (RMS), few studies have examined their health-related quality of life (HRQOL). This study evaluated physical and social aspects of HRQOL among long-term childhood RMS survivors relative to a sibling comparison group, and assessed whether physical impairment among RMS survivors adversely affected their ability to achieve adult life goals. METHODS: Using baseline data from the Childhood Cancer Survivor Study, we evaluated self-reported physical impairment and social adaptation among 417 survivors of childhood RMS and 2685 siblings > or =18 years of age at survey completion. RESULTS: Survivors were more likely than siblings to report physical impairment, characterized by: at least one medically diagnosed condition, limitations in the performance of routine activities, a health-related inability to work or attend school, cancer-related pain. Survivors were less likely than siblings to have completed high school, ever worked a job, or ever been married. The odds of completing high school were lower among survivors with performance limitations, a health-related inability to work or attend school, or moderate to high levels of cancer-related pain. Survivors who reported cancer-related pain had an increased likelihood of ever being married. CONCLUSIONS: The majority of adult survivors of pediatric RMS are successful in attaining adult life goals despite higher reported occurrence of physical impairment than their sibling counterparts. Additional studies are needed to advance our understanding of other aspects of HRQOL in this population of pediatric cancer survivors.

Activities of Daily Living↗
PubMed2006

An essential role for RasGRP1 in mast cell function and IgE-mediated allergic response.

Cross-linking of the FcepsilonRI activates the phosphatidyl inositol 3 kinase (PI3K) and mitogen-activated protein kinase pathways. Previous studies demonstrate that Ras guanyl nucleotide-releasing protein (RasGRP)1 is essential in T cell receptor-mediated Ras-Erk activation. Here, we report that RasGRP1 plays an important role in FcepsilonRI-mediated PI3K activation and mast cell function. RasGRP1-deficient mice failed to mount anaphylactic allergic reactions. RasGRP1-/- mast cells had markedly reduced degranulation and cytokine production. Although FcepsilonRI-mediated Erk activation was normal, PI3K activation was diminished. Consequently, activation of Akt, PIP3-dependent kinase, and protein kinase C delta was defective. Expression of a constitutively active form of N-Ras could rescue the degranulation defect and Akt activation. We further demonstrated that RasGRP1-/- mast cells were defective in granule translocation, microtubule formation, and RhoA activation. Our results identified RasGRP1 as an essential regulator of mast cell function.

Anaphylaxis↗
PubMed2006

A new approach of pellet formation of a filamentous fungus -Rhizopus oryzae.

The effects of inoculum and medium composition (i.e. potato dextrose broth as carbon source, soybean peptone, calcium carbonate, and metal ions) on pellet formation of Rhizopus oryzae ATCC 20344 have been studied. Metal ions were found to have a significant negative effect on pellet formation while soybean peptone had a positive effect. In addition, potato dextrose broth and calcium carbonate were beneficial to R. oryzae for growing small, smooth pellets during the culture. The study also demonstrated that an inoculum size of less than 1.5x10(9)spores/L had no significant influence on pellet formation although it had large impacts on pellet growth. Thus, a new approach to form pellets has been developed using only potato dextrose broth, soybean peptone, and calcium carbonate allowing for pellet size to be controlled by adjusting inoculum size and the concentrations of potato dextrose broth, soybean peptone, and calcium carbonate in the medium.

Biomass↗
PubMed2006

Production of recombinant ScFv antibodies against methamidophos from a phage-display library of a hyperimmunized mouse.

A recombinant phage display library was generated using splenocyte mRNA isolated from a Balb/c mouse hyperimmunized with a hapten conjugate that mimicked the structure of methamidophos, one of the most acutely toxic organophosphate pesticides. Three recombinant single-chain variable fragment (scFv) antibodies with the highest specificity for methamidophos, termed 28D4, 29D0, and 36B2, were produced via a stringent selection protocol. In a competitive enzyme-linked immunosorbent assay, the IC50 values for 28D4, 29D0, and 36B2 were 46.25, 35.39, and 17.99 ng/mL, respectively. The cross-reactivity of the three scFv antibodies with other organophosphate pesticides was below 0.1% except for acephate (O,S-dimethyl acetylphosphoramidothioate). Nucleotide and deduced amino acid sequences indicated that the respective heavy chains and light chains of the three scFvs were involved in the distinctive VDJ segment rearrangements associated with somatic hypermutations during the process of several immunizations with higher dosages of immunogen. Taken together, these data constitute the first detailed description of an immunoassay that utilizes scFvs against the methamidophos, an analyte with a simple structure and low molecular mass (141 Da).

Animals↗
PubMed2006

Cancer incidence and mortality and vitamin D in black and white male health professionals.

Blacks have been documented to have low vitamin D levels. We thus examined whether total cancer incidence and mortality rates differ between Blacks and Whites in a population of male health professionals, and particularly for digestive system cancers (oral, esophagus, stomach, pancreas, and colorectum), which have been most consistently linked to poor vitamin D status. Second, we examined whether Blacks might be more susceptible to these cancers if they concurrently had other risk factors for hypovitaminosis D. In the Health Professionals Follow-up Study, from 1986 to 2002, 99 of 481 Black men and 7,019 of 43,468 White men were diagnosed with cancer. Adjusting for multiple dietary, lifestyle, and medical risk factors, using Cox modeling, Black men were at higher risk of total cancer incidence [relative risk (RR), 1.32; 95% confidence interval (95% CI), 1.08-1.61; P = 0.007] and total cancer mortality (RR, 1.89; 95% CI, 1.40-2.56; P < 0.0001) and especially digestive system cancer mortality (RR, 2.24; 95% CI, 1.35-3.70). Compared with Whites with relatively few risk factors for hypovitaminosis D, Blacks also with few risk factors for hypovitaminosis D were not at appreciably higher risk of total cancer incidence (RR, 0.95; 95% CI, 0.60-1.51) or mortality (RR, 1.55; 95% CI, 0.91-2.62), but Black men with additional risk factors for poorer vitamin D status had a much higher cancer incidence (RR, 1.57; 95% CI, 1.16-2.11) and mortality risk (RR, 2.27; 95% CI, 1.57-3.28). This pattern was even more pronounced for digestive system cancer. Our results suggest that the high frequency of hypovitaminosis D in Blacks may be an important, and easily modifiable, contributor to their higher risk of cancer incidence and mortality.

Adult↗
PubMed2006

Isobolographic analysis of the antinociceptive interactions between ketoprofen and paracetamol.

The present study was undertaken to evaluate the antinociceptive interaction between paracetamol and ketoprofen. The antinociceptive effect of oral administration of the drugs alone or in combination was evaluated using the mouse abdominal constriction test. The data were interpreted by isobolographic analysis to establish the nature of the interaction. The effective dose that produced 50% antinociception (ED(50,mix)) was calculated from the log dose-response curve of fixed-ratio combinations of paracetamol with ketoprofen. This ED(50,mix) was compared to the theoretical additive ED(50,add) by isobolographic analysis. The experimental ED(50,mix) was found to be significantly smaller than the theoretically calculated ED(50,add), indicating a synergistic antinociceptive interaction between ketoprofen and paracetamol. Pharmacokinetic studies were carried out with mice treated with combined ketoprofen (12 mg/kg) and paracetamol (36 mg/kg). Plasma levels of ketoprofen were not changed by concurrent paracetamol treatment, and similarly no statistically significant difference was observed between paracetamol alone and the combination with ketoprofen. The pharmacokinetic analysis revealed that the combination of ketoprofen with paracetamol exerted a synergistic (supra-additive) interaction that was not associated with a pharmacokinetic interaction. The results of this study demonstrate significant synergism between ketoprofen and paracetamol.

Acetaminophen↗
PubMed2006

The orphan receptor tyrosine kinase Ror2 promotes osteoblast differentiation and enhances ex vivo bone formation.

Ror2 is a receptor tyrosine kinase, the expression of which increases during differentiation of pluripotent stem cells to osteoblasts and then declines as cells progress to osteocytes. To test whether Ror2 plays a role in osteoblastogenesis, we investigated the effects of Ror2 overexpression and down-regulation on osteoblastic lineage commitment and differentiation. Expression of Ror2 in pluripotent human mesenchymal stem cells (hMSCs) by adenoviral infection caused formation of mineralized extracellular matrix, which is the ultimate phenotype of an osteogenic tissue. Concomitantly, Ror2 over-expression inhibited adipogenic differentiation of hMSCs as monitored by lipid formation. Ror2 shifted hMSC fate toward osteoblastogenesis by inducing osteogenic transcription factor osterix and suppressing adipogenic transcription factors CCAAT/enhancer-binding protein alpha and peroxisome proliferator activated receptor gamma. Infection with Ror2 virus also strongly promoted matrix mineralization in committed osteoblast-like MC3T3-E1 cells. Expression of Ror2 in a human preosteocytic cell line by stable transfection also promoted further differentiation, as judged by inhibited alkaline phosphatase activity, potentiated osteocalcin secretion, and increased cellular apoptosis. In contrast, down-regulation of Ror2 expression by short hairpin RNA essentially abrogated dexamethasone-induced mineralization of hMSCs. Furthermore, down-regulation of Ror2 expression in fully differentiated SaOS-2 osteosarcoma cells inhibited alkaline phosphatase activity. We conclude that Ror2 initiates commitment of MSCs to osteoblastic lineage and promotes differentiation at early and late stages of osteoblastogenesis. Finally, using a mouse calvariae ex vivo organ culture model, we demonstrate that these effects of Ror2 result in increased bone formation, suggesting that it may also activate mature osteoblasts.

Animals↗
PubMed2006

Hydrogen bonding makes a difference in the rhodium-catalyzed enantioselective hydrogenation using monodentate phosphoramidites.

A new generation of monodentate phosphoramidite ligands bearing a primary amine moiety was found to display comparable or better efficiency than bisphosphines in the Rh-catalyzed asymmetric hydrogenation of challenging substrates, such as (Z)-methyl alpha-acetoxyacrylate or (E)-beta-aryl itaconate derivatives, affording the corresponding hydrogenation products with excellent enantioselectivities (up to >99% ee). The presence of intermolecular hydrogen bonding (HB) between two monodentate ligands in the catalyst was found to be critical for excellent catalyst performance. This finding provides a basis for design and development of further catalyst systems using this type of monodentate phosphoramidite ligands.

Catalysis↗
PubMed2006

Dynamic expression of the osmosensory channel trpv4 in multiple developing organs in zebrafish.

Transient receptor potential channels function in a wide spectrum of tissues and transduce sensory stimuli. The vanilloid (capsaicin) channel TRPV4 is sensitive to osmotic changes and plays a central role in osmoregulatory responses in a variety of organisms. We cloned a zebrafish trpv4 cDNA and assayed its expression during embryogenesis. trpv4 is expressed as maternal mRNA in 4-cell embryos and later zygotic expression is first observed in the forming notochord at the one somite stage. Notochord expression persists to 24 hpf when broad expression in the brain is observed. At 32 hpf trpv4 expression is observed in the endocardium, restricted primarily to the ventricular endothelium. Low level expression of trpv4 is also seen from 32-48 hpf in the pronephric kidney with strongest expression in the most distal nephron segment and in the cloaca. Expression is also observed in lateral line organs starting at 32 hpf, primarily in the hair cells. At 72 hpf, expression of trpv4 in heart, kidney, brain, and lateral line organs persists while expression in the notochord is down-regulated.

Amino Acid Sequence↗
PubMed2006

Late-occurring stroke among long-term survivors of childhood leukemia and brain tumors: a report from the Childhood Cancer Survivor Study.

PURPOSE: This report examines the incidence of and risk factors for strokes that occur in > or = 5-year survivors of childhood leukemia and brain tumors. PATIENTS AND METHODS: The rate of first occurrence of self-reported late-occurring strokes was determined for leukemia survivors (n = 4,828), brain tumor survivors (n = 1,871), and a comparison group of a random sample of cancer survivor siblings (n = 3,846). Relative risks (RRs) and 95% confidence intervals (CIs) of stroke by treatment exposures were examined by multivariate analyses. RESULTS: Thirty-seven leukemia survivors and 63 brain tumor survivors reported a late-occurring stroke. The rate of late-occurring stroke for leukemia survivors was 57.9 per 100,000 person-years (95% CI, 41.2 to 78.7). The RR of stroke for leukemia survivors compared with the sibling comparison group was 6.4 (95% CI, 3.0 to 13.8; P < .0001). The rate of late-occurring stroke for brain tumor survivors was 267.6 per 100,000 person-years (95% CI, 206.8 to 339.2). The RR of stroke for brain tumor survivors compared with the sibling comparison group was 29.0 (95% CI, 13.8 to 60.6; P < .0001). Mean cranial radiation therapy (CRT) dose of > or = 30 Gy was associated with an increased risk in both leukemia and brain tumor survivors in a dose-dependent fashion, with the highest risk after doses of > or = 50 Gy CRT. CONCLUSION: Survivors of childhood leukemia and brain tumors, particularly those with brain tumors treated with CRT at doses of greater than 30 Gy, are at an increased risk of stroke.

Actuarial Analysis↗
PubMed2006

Negative regulation of T cell activation and autoimmunity by the transmembrane adaptor protein LAB.

LAB (linker for activation of B cells), also known as NTAL (non-T cell activation linker), is a LAT (linker for activation of T cells)-like adaptor protein that is expressed in B, NK, and mast cells. Its role in lymphocytes has not been clearly demonstrated. Here, we showed that aged LAB-deficient (Lat2(-/-)) mice developed an autoimmune syndrome. Lat2(-/-) T cells were hyperactivated and produced more cytokines than Lat2(+/+) T cells. Even though LAB was absent in naive T cells, LAB could be detected in activated Lat2(+/+) T cells. LAT-mediated signaling events were enhanced in Lat2(-/-) T cells; however, they were suppressed in T cells that overexpressed LAB. Mice with the Lat2 gene conditionally deleted from T cells also developed the autoimmune syndrome like Lat2(-/-) mice. Together, these data demonstrated an important role of LAB in limiting autoimmune response and exposed a mechanism regulating T cell activation.

Adaptor Proteins, Signal Transducing↗