Biomedical subjects

Xinmin Li

Publications and source records attributed to Xinmin Li.

At least 19 recordsLinked to original sources

PubMed2007

Genetic network and pathway analysis of differentially expressed proteins during critical cellular events in fracture repair.

Bone repair consists of inflammation, intramembranous ossification, chondrogenesis, endochondral ossification, and remodeling. To better understand the translational regulation of these distinct but interrelated cellular events, we used the second generation of BD Clontechtrade mark Antibody Microarray to dissect and functionally characterize proteins differentially expressed between intact and fractured rat femur at each of these cellular events. Genetic network analysis showed that proteins differentially expressed within a given cellular event tend to be physically or functionally correlated. Seventeen such interacting networks were established over five cellular events that were most frequently associated with cell cycle, cell death, cell-to-cell signaling and interaction, and cell growth and proliferation. Eighteen molecular pathways were significantly enriched during the bone repair process, of which ERK/MAPK, NF-kB, PDGF, and T-cell receptor signaling pathways were significant during three or more cellular events. The analyses revealed dynamic temporal expression patterns and cellular-event-specific functions. The inflammation event on Day 1 was characteristic of the cell cycle-related molecular changes. The relative quiet stage of intramembranous ossification on Day 4 and the molecularly most active stage of chondrogenesis on Day 7 were featured by coordinated cell death and cell-proliferation signals. Endochondral ossification on Day 14 experienced a clear transition from the molecular/cellular function to the physiological system development/function. The osteoclast-mediated remodeling on Day 28 was highlighted by the integrin signaling pathway. The distinct changes in protein expression during these cellular events provide a molecular basis for developing cellular event-targeted therapeutic strategy to accelerate bone healing.

Animals↗

PubMed2006

Effects of carbonic anhydrase VIII deficiency on cerebellar gene expression profiles in the wdl mouse.

Recently, the waddles (wdl) mouse was identified as a carbonic anhydrase VIII (Car8) mutant. The mutation is associated with marked deficiency of Car8, an inositol triphosphate receptor 1-binding protein expressed at high levels in cerebellar Purkinje cells. To help unravel the molecular aberrations contributing to motor dysfunction in wdl mice, cerebellar gene expression profiles were examined in the mutants and their wild-type littermates. Genes involved in signaling, cell division, zinc ion-binding, synapse integrity and plasticity were downregulated in wdl mice. Several of the upregulated genes encode proteins that function in the Golgi apparatus which suggests that Car8 deficiency has important effects on synaptic vesicle formation and transport.

Animals↗

PubMed2006

Phase I study of decitabine-mediated gene expression in patients with cancers involving the lungs, esophagus, or pleura.

PURPOSE: The DNA methylation paradox, manifested as derepression of cancer-testis antigens, and silencing of tumor suppressors during malignant transformation, provides the rationale for the utilization of chromatin remodeling agents for cancer therapy. A phase I trial was done to examine pharmacokinetics, toxicities, and gene expression mediated by 5-aza-2'-deoxycytidine (DAC) in patients with thoracic malignancies. EXPERIMENTAL DESIGN: Thirty-five patients with cancers refractory to standard therapy received continuous 72-hour DAC infusions using a phase I dose-escalation schema. Each full course of therapy consisted of two identical 35-day cycles. Plasma DAC levels were evaluated by liquid chromatography-mass spectrometry techniques. Quantitative reverse transcription-PCR, methylation-specific PCR, and immunohistochemical techniques were used to evaluate NY-ESO-1, MAGE-3, and p16 expression in tumor biopsies. Long oligonucleotide arrays were used to evaluate gene expression profiles in laser-captured tumor cells before and after DAC exposure. RESULTS: Thirty-five patients were evaluable for toxicities; 25 were evaluable for treatment response. Myelosuppression constituted dose-limiting toxicity. The maximum tolerated dose of DAC was 60 to 75 mg/m(2) depending on the number of prior cytotoxic chemotherapy regimens. No objective responses were observed. Plasma DAC concentrations approximated thresholds for gene induction in cultured cancer cells. Target gene induction was observed in 36% of patients. Posttreatment antibodies to NY-ESO-1 were detected in three patients exhibiting NY-ESO-1 induction in their tumor tissues. Complex, heterogeneous gene expression profiles were observed in pretreatment and posttreatment tissues. CONCLUSION: Prolonged DAC infusions can modulate gene expression in primary thoracic malignancies. These findings support further evaluation of DNA-demethylating agents alone or in combination with other regimens targeting induced gene products for the treatment of these neoplasms.

Adult↗

PubMed2006

Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction.

Time-of-flight neutron diffraction has been used to locate hydrogen atoms that define the ionization states of amino acids in crystals of D-xylose isomerase. This enzyme, from Streptomyces rubiginosus, is one of the largest enzymes studied to date at high resolution (1.8 A) by this method. We have determined the position and orientation of a metal ion-bound water molecule that is located in the active site of the enzyme; this water has been thought to be involved in the isomerization step in which D-xylose is converted to D-xylulose or D-glucose to D-fructose. It is shown to be water (rather than a hydroxyl group) under the conditions of measurement (pH 8.0). Our analyses also reveal that one lysine probably has an -NH(2)-terminal group (rather than NH(3)(+)). The ionization state of each histidine residue also was determined. High-resolution x-ray studies (at 0.94 A) indicate disorder in some side chains when a truncated substrate is bound and suggest how some side chains might move during catalysis. This combination of time-of-flight neutron diffraction and x-ray diffraction can contribute greatly to the elucidation of enzyme mechanisms.

Aldose-Ketose Isomerases↗

PubMed2006

Synthesis, capillary crystallization and preliminary joint X-ray and neutron crystallographic study of Z-DNA without polyamine at low pH.

In order to crystallographically study the hydration of the major groove (convex surface) of Z-DNA, the oligonucleotide d(CGCGCG) has been synthesized. Single crystals were grown by vapor diffusion using the hanging-drop and sitting-drop methods for X-ray studies and by batch crystallization and evaporation within silicon tubes for neutron studies. Hexagonal crystals were obtained without the use of duplex-stabilizing polyamines and at an acid pH. X-ray data collected at room temperature (1.5 angstroms resolution; unit-cell parameters a = 17.90, b = 30.59, c = 44.61 angstroms) and at 100 K (1 angstroms resolution; a = 17.99, b = 30.98, c = 44.07 angstroms) and neutron data collected at room temperature (1.6 angstroms resolution; a = 18.00, b = 31.16, c = 44.88 angstroms) indicate that the DNA is in the Z-form packing in space group P2(1)2(1)2(1).

Crystallization↗

PubMed2006

Genetic regulation by non-coding RNAs.

Large scale cDNA sequencing and genome tiling array studies have shown that around 50% of genomic DNA in humans is transcribed, of which 2% is translated into proteins and the remaining 98% is non-coding RNAs (ncRNAs). There is mounting evidence that these ncRNAs play critical roles in regulating DNA structure, RNA expression, protein translation and protein functions through multiple genetic mechanisms, and thus affect normal development of organisms at all levels. Today, we know very little about the regulatory mechanisms and functions of these ncRNAs, which is clearly essential knowledge for understanding the secret of life. To promote this emerging research subject of critical importance, in this paper we review (1) ncRNAs' past and present, (2) regulatory mechanisms and their functions, (3) experimental strategies for identifying novel ncRNAs, (4) experimental strategies for investigating their functions, and (5) methodologies and examples of the application of ncRNAs.

Databases, Nucleic Acid↗

PubMed2006

CCN1/Cyr61 is regulated by the canonical Wnt signal and plays an important role in Wnt3A-induced osteoblast differentiation of mesenchymal stem cells.

Marrow mesenchymal stem cells are pluripotent progenitors that can differentiate into bone, cartilage, muscle, and fat cells. Wnt signaling has been implicated in regulating osteogenic differentiation of mesenchymal stem cells. Here, we analyzed the gene expression profile of mesenchymal stem cells that were stimulated with Wnt3A. Among the 220 genes whose expression was significantly changed by 2.5-fold, we found that three members of the CCN family, CCN1/Cyr61, CCN2/connective tissue growth factor (CTGF), and CCN5/WISP2, were among the most significantly up-regulated genes. We further investigated the role of CCN1/Cyr61 in Wnt3A-regulated osteogenic differentiation. We confirmed that CCN1/Cyr61 was up-regulated at the early stage of Wnt3A stimulation. Chromatin immunoprecipitation analysis indicates that CCN1/Cyr61 is a direct target of canonical Wnt/beta-catenin signaling. RNA interference-mediated knockdown of CCN1/Cyr61 expression diminished Wnt3A-induced osteogenic differentiation. Furthermore, exogenously expressed CCN1/Cyr61 was shown to effectively promote mesenchymal stem cell migration. These findings suggest that tightly regulated CCN1/Cyr61 expression may play an important role in Wnt3A-induced osteoblast differentiation of mesenchymal stem cells.

Adenoviridae↗

PubMed2006

Experimental study of effect of Fontan circuit on pulmonary microcirculation.

Pulsatile pulmonary blood flow plays an important role in regulating shear-stress-mediated release of endothelium-derived nitric oxide and endothelin-1, and it reduces pulmonary vascular resistance by passive capillary recruitment. The aim of this study was to demonstrate changes in pulmonary capillary structure and endothelial function induced by the chronic nonpulsatile flow of the Fontan circulation. A canine model with nonpulsatile flow in the right lung was established, and sacrificed 3 months later. Compared to the left lung, wall thickness of the pulmonary arterioles was thinner, endothelin-1 expression was weaker, endothelial nitric oxide synthase activity was stronger, and there was a good correlation between the histomorphometric and immunohistochemical findings. These data indicate that long-term nonpulsatile flow can lead to endothelial dysfunction, which may be involved in distention and vascular structure remodeling due to the increase in pulmonary vascular resistance; but it also can lead to increased patency of the arteriovenous shunt, which might be at least partly involved in pulmonary arteriovenous fistula development and exercise limitation after the Fontan operation.

Animals↗

PubMed2005

Role of GADD34 in modulation of cisplatin cytotoxicity.

Cisplatin and carboplatin are widely used clinical chemotherapeutic agents, especially against testicular, ovarian, and head and neck cancers. O(6)-Benzylguanine (BG) has been shown to result in enhanced cytotoxicity, apoptosis, and DNA platination when used in conjunction with cisplatin and carboplatin in head and neck cancer cell lines. Microarray expression data indicated overexpression of 19 genes and underexpression of 22 genes specific to treatment with the combination of BG+/-cisplatin compared to cisplatin alone treatment in SQ20b head and neck cancer cells (p<0.05) using the Affymetrix HG-U133A GeneChip((R)). Among the overexpressed probe sets were genes involved in DNA damage and apoptosis, including GADD34, DDIT4, ATF4, and PTHLH. A similarly structured analog, 9-CH(3)-BG, does not enhance cisplatin-induced cytotoxicity or apoptosis nor is there enhanced expression of GADD34 in cisplatin or 9-CH(3)-BG+/-cisplatin-treated cells compared to control cells. Analysis of cells exposed to 9-CH(3)-BG+/-cisplatin allowed us to focus our array list on 32 probe sets specific to BG+cisplatin versus cisplatin, ruling out differentially expressed probe sets common to 9-CH(3)-BG+cisplatin versus cisplatin. Similarly, 14 probe sets were specific to BG+/-cisplatin versus BG, ruling out differentially expressed probe sets common to 9-CH(3)-BG+/-cisplatin versus 9-CH(3)-BG. Quantitative real-time PCR demonstrated a dose dependent increase in GADD34 expression in cells exposed to BG+/-cisplatin with levels approximately >2-fold for cells exposed to BG+cisplatin compared to cisplatin alone. Levels of GADD34 transcripts were determined with both cisplatin and BG+cisplatin at several different time points concomitant with and following drug treatment. At all timepoints, GADD34 transcript levels are approximately two-fold elevated in cells treated with BG+cisplatin compared to cisplatin alone. Furthermore, significant changes in GADD34 expression levels in SQ20b, SCC35, and SCC61 cells, with approximately three-fold, two-fold, and 3.5-fold increases in expression, respectively, upon treatment with BG+/-cisplatin compared with control. Elucidation of these molecular pathways will aid in our goal of synthesizing more powerful modulators to increase efficacy of platinum agents.

Antigens, Differentiation↗

PubMed2005

Phosphatidylinositol transfer protein function in the yeast Saccharomyces cerevisiae.

PITPs regulate the interface between lipid metabolism and cellular functions, but the fundamental nature of this regulation is not understood. Yeast and mouse studies demonstrate strict coupling of individual PITPs to specific cellular activities, but the invisibility of these specificities in in vitro models for PITP activity is remarkable. In our opinion, delineation of PITP functions requires the continued application of genetic approaches such as those summarized here. Future studies dedicated to enhancing our understanding of the mechanisms of action of Sec14p-like and metazoan PITPs are worthy goals for three reasons. First, it is becoming abundantly clear that PITPs act at important biological interfaces that involve lipid and protein trafficking, phospholipid biosynthesis and polarized membrane growth. Because these interfaces are critical not only to cellular functions, but also to developmental processes, the function of PITPs in development of multicellular organisms is a particularly attractive area of research that remains essentially untapped. Second, the yeast studies indicate functional linkages between Sec14p-like PITPs and members of ubiquitous but entirely uncharacterized eukaryotic proteins such as OSBP family members. Finally, the link of PITPs to disease is already clear since PITP deficiencies lie at the foundation of novel mechanisms of neurodegenerative, glucose homeostatic and gastrointestinal disorders in mammals. Given that the contribution of Sec14p-like proteins to the PITP complement of mammalian cells is completely uninvestigated, and that the mammalian genome encodes many proteins of this class, we anticipate such advances will directly and positively impact our understanding of the molecular basis of such diseases.

Amino Acid Sequence↗

PubMed2005

Carbonic anhydrase-related protein VIII deficiency is associated with a distinctive lifelong gait disorder in waddles mice.

The waddles (wdl) mouse is a unique animal model that exhibits ataxia and appendicular dystonia without pathological abnormalities of either the central or the peripheral nervous systems. A 19-bp deletion in exon 8 of the carbonic anhydrase-related protein VIII gene (Car8) was detected by high-throughput temperature-gradient capillary electrophoresis heteroduplex analysis of PCR amplicons of genes and ESTs within the wdl locus on mouse chromosome 4. Although regarded as a member of the carbonic anhydrase gene family, the encoded protein (CAR8) has no reported enzymatic activity. In normal mice, CAR8 is abundantly expressed in cerebellar Purkinje cells as well as in several other cell groups. Compatible with nonsense-mediated decay of mutant transcripts, CAR8 is virtually absent in mice homozygous for the wdl mutation. These data indicate that the wdl mouse is a Car8 null mutant and that CAR8 plays a central role in motor control.

Amino Acid Sequence↗

PubMed2005

Early signals for fracture healing.

Fracture healing requires the cooperation of multiple molecular signaling pathways. To better understand this cascade of transcriptional events, we compared the gene expression profiles between intact bone and fractured bone at days 1, 2, and 4 using a rat femur model of bone healing. Cluster analysis identified several groups of genes with dynamic temporal expression patterns and stage-specific functions. The immediate-response genes are highlighted by binding activity, transporter activity, and energy derivation. We consider these activities as critical signals for initiation of fracture healing. The continuously increased genes are characterized by those directly involved in bone repair, thus, representing bone specific forefront workers. The constantly upregulated genes tend to regulate general cell growth and are enriched with genes that are involved in tumorigenesis, suggesting common pathways between two processes. The constantly downregulated genes predominantly involve immune response, the significance of which remains for further investigation. Knowledge acquired through this analysis of transcriptional activities at the early stage of bone healing will contribute to our understanding of fracture repair and bone-related pathological conditions.

Animals↗

PubMed2005

Isolation of wound healing/regeneration genes using restrictive fragment differential display-PCR in MRL/MPJ and C57BL/6 mice.

Wound healing in mammals can take several weeks to months and the process is always accompanied by scar formation. Wound healing mechanisms that mimic regeneration are not found in most mature mammalian tissues. However, the MRL/MPJ (MRL) mouse has the unique capacity to regenerate ear hole wound completely in less than a month. To identify genes involved in wound healing without a scar, we chose to use restriction fragment differential display-PCR to isolate genes differentially expressed in the MRL (good healer) mouse and the C57BL/6 (poor healer) mouse at different stages of wound healing. We identified 36 genes that were differentially expressed in the regenerating tissue of good and poor healer strains of which several genes are also genetically linked to wound healing and thus are potential candidate genes for scarless wound healing.

Animals↗

PubMed2005

Bayesian shrinkage estimation of quantitative trait loci parameters.

Mapping multiple QTL is a typical problem of variable selection in an oversaturated model because the potential number of QTL can be substantially larger than the sample size. Currently, model selection is still the most effective approach to mapping multiple QTL, although further research is needed. An alternative approach to analyzing an oversaturated model is the shrinkage estimation in which all candidate variables are included in the model but their estimated effects are forced to shrink toward zero. In contrast to the usual shrinkage estimation where all model effects are shrunk by the same factor, we develop a Bayesian method that allows the shrinkage factor to vary across different effects. The new shrinkage method forces marker intervals that contain no QTL to have estimated effects close to zero whereas intervals containing notable QTL have estimated effects subject to virtually no shrinkage. We demonstrate the method using both simulated and real data for QTL mapping. A simulation experiment with 500 backcross (BC) individuals showed that the method can localize closely linked QTL and QTL with effects as small as 1% of the phenotypic variance of the trait. The method was also used to map QTL responsible for wound healing in a family of a (MRL/MPJ x SJL/J) cross with 633 F(2) mice derived from two inbred lines.

Animals↗

PubMed2005

A deletion causing spontaneous fracture identified from a candidate region of mouse Chromosome 14.

Map-based cloning is an iterative approach that identifies the underlying genetic cause of a mutant phenotype. However, the classic protocol of positional cloning is time-consuming and labor-intensive. We now describe a genome sequence-based cloning approach that has led to localizing the underlying genetic cause of spontaneous fractures (sfx) in a mouse model. The sfx/sfx mouse is characterized by a spontaneous femoral fracture seen around 6 weeks of age, which represents a new mouse model for bone fragility. Genetic studies indicate that the phenotype of sfx/sfx mice is caused by an alteration at a single locus that is roughly mapped onto the central region of mouse Chromosome 14. Using our strategy of combining mouse genome resources and high-throughput technology, we discovered a deletion of all 12 exons in the gene for L-gulonolactone oxidase (LGO), a key enzyme in the synthesis of ascorbic acid. We have also examined the expression of LGO and found no expression of LGO in sfx mice while the LGO expresses in several tissues of normal mice. Our data demonstrated the feasibility to positionally clone the mutated gene from a non-fine-mapped locus, which has applicability to the positional cloning of genes from many other animal models, as their genome sequences are sequenced or will be sequenced soon.

Animals↗

PubMed2005

An integrated strategy for the optimization of microarray data interpretation.

The completion of a microarray experiment represents just a starting point toward understanding the biology of interest. A follow-up strategy is needed to fully elucidate the functional significance of microarray-derived measurements of differential expression. Given the fact that no single approach can fully unravel the fundamental biology that is typically quite complex, the follow-up strategy must be integrated at multiple levels encompassing bioinformatics, genomics, and proteomics. In this review, we discuss an integrative approach, which can be used to prioritize microarray-derived candidate genes, define their functions, and place them in the context of the biological system being studied.

Animals↗

PubMed2004

Thrombin peptide (TP508) promotes fracture repair by up-regulating inflammatory mediators, early growth factors, and increasing angiogenesis.

Previous studies have shown that a single injection of thrombin peptide (TP508) accelerates fracture repair in a closed rat femoral fracture model. The present study was conducted to elucidate the molecular mechanisms of TP508 action using Affymetrix genome-scale profiling and to link early gene expression changes to fracture histology and bone strength changes. Treatment of femoral fractures with TP508 accelerated fracture repair as determined by destructive torsion testing. Blinded histological analysis demonstrated that TP508-treated fracture callus had a significant increase in blood vessels relative to the controls. Gene array analysis showed that TP508 significantly induced expression of early growth factors, inflammatory response modifiers, and angiogenesis-related genes. This study therefore suggests that TP508 promotes fracture repair through a mechanism that involves an increased induction of a number of growth factors, enhanced expression of inflammatory mediators, and angiogenesis-related genes.

Animals↗

PubMed2004

Anti-diabetic effect of ginsenoside Re in ob/ob mice.

We evaluated the anti-diabetic effects of ginsenoside Re in adult male C57BL/6J ob/ob mice. Diabetic ob/ob mice with fasting blood glucose levels of approximately 230 mg/dl received daily intraperitoneal injections of 7, 20 and 60 mg/kg ginsenoside Re for 12 consecutive days. Dose-related effects of ginsenoside Re on fasting blood glucose levels were observed. After the 20 mg/kg treatment, fasting blood glucose levels were reduced to 188+/-9.2 and 180+/-10.8 mg/dl on Day 5 and Day 12, respectively (both P<0.01 compared to vehicle group, 229+/-9.5 and 235+/-13.4 mg/dl, respectively). The EC(70) of ginsenoside Re was calculated to be 10.3 mg/kg and was used for subsequent studies. Consistent with the reduction in blood glucose, there were significant decreases in both fed and fasting serum insulin levels in mice treated with ginsenoside Re. With 12 days of ginsenoside treatment, glucose tolerance of ob/ob mice increased significantly, and the area under the curve for glucose decreased by 17.8% (P<0.05 compared to vehicle treatment). The hypoglycemic effect of the ginsenoside persisted even at 3 days of treatment cessation (blood glucose levels: 198+/-13.1 with ginsenoside treatment vs. 253+/-20.3 mg/dl with vehicle, P<0.01). There were no significant changes in body weight or body temperature. Preliminary microarray analysis revealed differential expression of skeletal muscle genes associated with lipid metabolism and muscle function. The results suggest that ginsenoside Re may prove to be useful in treating type 2 diabetes.

Analysis of Variance↗