Biomedical subjects

Xiaohong Wu

Publications and source records attributed to Xiaohong Wu.

9 recordsLinked to original sources

PubMed2026

Large-scale pleiotropic analysis across cancers reveals shared genetic mechanisms and identifies novel functional genes.

Pleiotropic genetic loci have been increasingly reported in cancer, and identifying genetic variants with pleiotropic associations can reveal shared biological pathways influencing multiple cancers. Using summary statistics from genome-wide association studies for 37 cancer types (N = 433 836), we identified extensive genome-wide and local genetic correlations among cancers. Through pairwise pleiotropic analysis, we identified 75 243 significant pleiotropic single nucleotide polymorphisms (SNPs) across 372 cancer pairs, among which 3472 were lead SNPs with potential regulatory functions. Using FUMA and MAGMA, we identified 2527 pleiotropic risk loci and 4272 candidate pleiotropic genes. Notably, genes such as TERT (5p15.33), POU5F1B (8q24.21), and FANCA (16q24.3) exhibited widespread pleiotropy across multiple cancer types. Pathway enrichment analysis highlighted the critical roles of pigment synthesis, metabolism, and apoptosis in skin-related cancers, while cross-cancer enrichment analysis emphasized pathways related to apoptosis, chromatin structure, and intermediate filaments. We also identified 33 novel functional genes harboring previously unreported cancer risk variants. Drug-gene interaction analysis revealed several repositionable FDA-approved drugs. Importantly, drug sensitivity assays demonstrated that bosutinib and cobimetinib exhibited promising therapeutic potential in breast cancer cell lines. Finally, we developed the PleioCancer database (https://gonglab.hzau.edu.cn/PleioCancer/), providing a comprehensive resource for cancer pleiotropy research. These findings have important implications for carcinogenesis cancer, prevention and treatment.

Humans↗

PubMed2026

Genome-wide annotation of human multi-nucleotide variants reveals widespread functional differences from single nucleotide variants.

Multi-nucleotide variants (MNVs) represent a crucial yet underexplored category of genetic variation. Despite previous studies highlighting the prevalence and potential biological impact of MNVs in populations, comprehensive identification and detailed functional annotation of MNVs remain challenging. Here, we develop MNVAnno, a toolbox for rapid identification and annotation of complex MNVs, and utilize it to identify 3,984,258 MNVs from 700,134 human samples, expanding the human MNV list to 8,199,654. Our analysis reveals that MNVs can not only lead to distinct amino acid changes from their constituent single-nucleotide variants, but also significantly impact the function of non-coding regions. Furthermore, through genome-wide association studies, we identify some MNVs associated with multiple cancers, and establish the Human MNV Database to facilitate MNV research. Our study emphasizes the importance of MNV annotation, broadens the human MNV landscape, and opens avenues for exploring genetic variation in phenotypes and diseases.

Humans↗

PubMed2003

High accuracy genotyping directly from genomic DNA using a rolling circle amplification based assay.

BACKGROUND: Rolling circle amplification of ligated probes is a simple and sensitive means for genotyping directly from genomic DNA. SNPs and mutations are interrogated with open circle probes (OCP) that can be circularized by DNA ligase when the probe matches the genotype. An amplified detection signal is generated by exponential rolling circle amplification (ERCA) of the circularized probe. The low cost and scalability of ligation/ERCA genotyping makes it ideally suited for automated, high throughput methods. RESULTS: A retrospective study using human genomic DNA samples of known genotype was performed for four different clinically relevant mutations: Factor V Leiden, Factor II prothrombin, and two hemochromatosis mutations, C282Y and H63D. Greater than 99% accuracy was obtained genotyping genomic DNA samples from hundreds of different individuals. The combined process of ligation/ERCA was performed in a single tube and produced fluorescent signal directly from genomic DNA in less than an hour. In each assay, the probes for both normal and mutant alleles were combined in a single reaction. Multiple ERCA primers combined with a quenched-peptide nucleic acid (Q-PNA) fluorescent detection system greatly accellerated the appearance of signal. Probes designed with hairpin structures reduced misamplification. Genotyping accuracy was identical from either purified genomic DNA or genomic DNA generated using whole genome amplification (WGA). Fluorescent signal output was measured in real time and as an end point. CONCLUSIONS: Combining the optimal elements for ligation/ERCA genotyping has resulted in a highly accurate single tube assay for genotyping directly from genomic DNA samples. Accuracy exceeded 99 % for four probe sets targeting clinically relevant mutations. No genotypes were called incorrectly using either genomic DNA or whole genome amplified sample.

Chromosomes, Human, Pair 6↗

PubMed2003

Unbiased whole-genome amplification directly from clinical samples.

Preparation of genomic DNA from clinical samples is a bottleneck in genotyping and DNA sequencing analysis and is frequently limited by the amount of specimen available. We use Multiple Displacement Amplification (MDA) to amplify the whole genome 10,000-fold directly from small amounts of whole blood, dried blood, buccal cells, cultured cells, and buffy coats specimens, generating large amounts of DNA for genetic testing. Genomic DNA was evenly amplified with complete coverage and consistent representation of all genes. All 47 loci analyzed from 44 individuals were represented in the amplified DNA at between 0.5- and 3.0-fold of the copy number in the starting genomic DNA template. A high-fidelity DNA polymerase ensures accurate representation of the DNA sequence. The amplified DNA was indistinguishable from the original genomic DNA template in 5 SNP and 10 microsatellite DNA assays on three different clinical sample types for 20 individuals. Amplification of genomic DNA directly from cells is highly reproducible, eliminates the need for DNA template purification, and allows genetic testing from small clinical samples. The low amplification bias of MDA represents a dramatic technical improvement in the ability to amplify a whole genome compared with older, PCR-based methods.

Blood Cells↗

PubMed2003

Up-regulation of transforming growth factor-beta 1 in the spleen of aniline-treated rats.

Aniline exposure produces selective toxicity to the spleen, leading to a variety of sarcomas in rats following chronic exposure. Fibrosis appears to be an important preneoplastic lesion of the spleen. However, early molecular events leading to splenic fibrosis are not known. Earlier studies have shown that aniline exposure in rats leads to excessive deposition of iron and increased lipid peroxidation in the spleen, which may produce changes in the expression of fibrogenic cytokines, such as transforming growth factor-beta 1 (TGF-beta 1), leading to splenic fibrosis. Therefore, this study was designed to establish whether aniline exposure leads to induction/overexpression of TGF-beta 1 and association of such induction with lipid peroxidation (oxidative stress) in the spleen. To achieve this, male Sprague-Dawley rats were given 1 mmol/kg/day aniline hydrochloride in water by gavage for 7 days, while controls received water only. Aniline treatment resulted in significant increases in spleen weight (97%), spleen-to-body weight ratios (104%), and splenocyte population (25%). Malondialdehyde-protein adducts, quantitated by a competitive ELISA, showed a 56% increase in the spleen of aniline-treated rats. TGF-beta 1, measured in the supernatants of cultured splenocytes by an ELISA specific for TGF-beta 1, showed a significant increase (60%) in the total TGF-beta 1 from aniline-treated rats. These increases were further confirmed by Western blot analysis, which showed approximately 2.5-fold increase in cell-associated TGF-beta 1 protein expression in aniline-treated rats. Furthermore, determination of TGF-beta 1 mRNA expression showed a 4-fold increase in the spleens of aniline-treated rats. These results suggest an association between formation of MDA-protein adducts and overexpression of TGF-beta 1 as a result of aniline insult, which together could promote splenic injury and fibrogenesis.

Aniline Compounds↗

PubMed2003

Cocaine affinity decreased by mutations of aromatic residue phenylalanine 105 in the transmembrane domain 2 of dopamine transporter.

Dopamine transporter (DAT) is a major target of cocaine, one of the most abused drugs. Major efforts have been focused on defining residues in DAT involved in cocaine binding. We have isolated the Drosophila melanogaster DAT (dDAT) cDNA, which is 10-fold less sensitive to cocaine than the mammalian DATs. Replacing transmembrane domain 2 (TM2) of mouse DAT (mDAT) with dDAT sequence reduced cocaine sensitivity. The reciprocal construct exhibited increased cocaine sensitivity. Switching residue 105 in TM2, a phenylalanine conserved in all mammalian DATs, to methionine, the corresponding residue in dDAT, resulted in a functional transporter with cocaine sensitivity 4-fold lower. Replacing F105 with alanine, leucine, isoleucine, serine, threonine, asparagine, or glutamine resulted in transporters with low transport activity. In contrast, changing F105 to the other aromatic residues tyrosine or tryptophan retained more than 75% transport activity and high cocaine sensitivity. Most significantly, the reciprocal construct, switching the methionine in dDAT at the corresponding residue to phenylalanine, increased cocaine sensitivity 3-fold. Finally, the mDAT mutant with a cysteine at this position had normal transport activity but exhibited cocaine sensitivity that was 15-fold lower. These results suggest that F105 in mDAT contributes to high-affinity cocaine binding. The functional cocaine-insensitive mutants provide tools for the study of the mechanism of cocaine addiction.

Animals↗

PubMed2002

Protein adducts of malondialdehyde and 4-hydroxynonenal in livers of iron loaded rats: quantitation and localization.

Pathophysiological mechanisms for hepatocellular injury, fibrosis and/or cirrhosis in hepatic iron overload are poorly understood. An increase in intracellular transit pool of iron can catalyze peroxidation of lipids to produce reactive aldehydes such as malondialdehyde (MDA) and 4-hydroxynonenal (HNE). Covalent binding of such lipid aldehydes with proteins may cause impairment in cellular function and integrity. This investigation was focused on quantitative determination of MDA and HNE-protein adducts, and to establish a correlation between iron deposition and formation and localization of MDA and HNE-protein adducts, using immunohistochemistry. To achieve iron overload, male SD rats were fed a 2.5% carbonyl iron-supplemented diet for six weeks, while control animals received standard diet. Total iron as well as low molecular weight chelatable iron (LMWC-Fe) in the hepatic tissue of rats fed the iron supplemented diet increased significantly ( approximately 14- and approximately 15-fold, respectively). Quantitative ELISA for MDA-and HNE-protein adducts showed remarkable increases of 186 and 149%, respectively, in the liver homogenates of rats fed the iron-supplemented diet. Sections of liver stained for iron showed striking iron deposits in periportal (zone 1) hepatocytes, which was less dramatic in midzonal (zone 2) cells. Livers from iron-loaded rats showed strong, diffuse staining for both MDA and HNE adducts, which was highly pronounced in centrilobular (zone 3) hepatocytes, but was also evident in midzonal cells (zone 2). The demonstration of greater formation of both MDA and HNE-protein adducts provides evidence of iron-catalyzed lipid peroxidation in vivo. Although in this model of iron overload there was no evidence of tissue injury, our results provide an account of some of the initiating factors or early molecular events in hepatocellular damage that may lead to the pathological manifestations seen in chronic iron overload.

Aldehydes↗

PubMed2002

Comprehensive human genome amplification using multiple displacement amplification.

Fundamental to most genetic analysis is availability of genomic DNA of adequate quality and quantity. Because DNA yield from human samples is frequently limiting, much effort has been invested in developing methods for whole genome amplification (WGA) by random or degenerate oligonucleotide-primed PCR. However, existing WGA methods like degenerate oligonucleotide-primed PCR suffer from incomplete coverage and inadequate average DNA size. We describe a method, termed multiple displacement amplification (MDA), which provides a highly uniform representation across the genome. Amplification bias among eight chromosomal loci was less than 3-fold in contrast to 4-6 orders of magnitude for PCR-based WGA methods. Average product length was >10 kb. MDA is an isothermal, strand-displacing amplification yielding about 20-30 microg product from as few as 1-10 copies of human genomic DNA. Amplification can be carried out directly from biological samples including crude whole blood and tissue culture cells. MDA-amplified human DNA is useful for several common methods of genetic analysis, including genotyping of single nucleotide polymorphisms, chromosome painting, Southern blotting and restriction fragment length polymorphism analysis, subcloning, and DNA sequencing. MDA-based WGA is a simple and reliable method that could have significant implications for genetic studies, forensics, diagnostics, and long-term sample storage.

Blotting, Southern↗

PubMed2002

The protective effects of tetrahydrocurcumin on oxidative stress in cholesterol-fed rabbits.

Tetrahydrocurcumin (THC) is an antioxidative substance which is derived from curcumin by hydrogenation. Curcumin is the main component of turmeric and is responsible for the yellow color of curried foods.First, LDL derived from a normal human volunteer was incubated in the presence of an antioxidant with 10 microM CuSO(4) at 37 degrees C for 2 hours.All antioxidants tested (THC, curcumin, probucol, and alpha-tocopherol) dose-dependently (1-10 microM) inhibited the oxidative modification of LDL. Probucol was the strongest, followed by THC, alpha-tocopherol, and curcumin.Next, in order to evaluate the antioxidative activity of THC in vivo, we fed rabbits diets containing 1% cholesterol with or without 0.5% THC and examined their effects on oxidative stress and atherosclerosis. Animals were divided into two groups: the control group rabbits (n = 12) were fed a normal chow diet and the experimental group (n = 12) was fed a diet containing 0.5% THC for one week.Then, 1% cholesterol was added to the diets and the animals were allowed to feed further for either 6 (n = 4 for each group) or 12 weeks (n = 8 for each group). Although serum cholesterol levels rapidly increased after starting the high cholesterol diet, no difference was observed between the control and THC groups.TBARS formation in the absence of added copper ion was inhibited in the LDL separated from THC-treated animals compared with that from control animals.THC treatment tended to inhibit the area covered with atherosclerotic lesions compared with the control, although this was not significant (28.8 +/- 17.5% vs. 40.0 +/- 23.7%, p = 0.2). Formation of N(epsilon)-(hexanoyl) lysine, 4-hydroxynonenal and dityrosine in liver and kidney also had a tendency to be inhibited by THC treatment. Although free THC was not detected in serum and liver, THC was detected in samples treated with beta-glucuronidase and sulfatase, suggesting that THC is present as a conjugate with glucuronic acid or sulfate. In conclusion, the present results suggest that curcuminoids, particularly THC, which are contained in turmeric, may be useful as a functional food factor.

Animals↗