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Biomedical subjects

Xin Cheng

Publications and source records attributed to Xin Cheng.

At least 19 recordsLinked to original sources
PubMed2026

Discovery of antimicrobial peptides from incomplete biosynthetic gene clusters to combat multidrug-resistant bacteria.

The escalating crisis of multidrug-resistant bacteria necessitates innovative antibiotic discovery platforms. Conventional antimicrobial peptide (AMP) mining often relies on complete biosynthetic gene clusters (BGCs), leaving fragmented genomic resources underexplored. Here, we present an evolution-inspired approach to reconstruct and predict AMPs from partial BGCs. Applying this strategy to 954 Paenibacillus genomes identifies five polymyxin-like peptides, NP001-NP005, with broad in vitro activity. Crucially, in murine models of polymyxin-resistant infection, NP001 reduced bacterial burdens by up to 1,000-fold in a thigh infection model and improved survival (50% vs. 0%) in a lethal peritonitis model. Structural simulations and biophysical assays revealed that NP001 maintains high affinity for bacterial membranes and effectively binds to MCR-1-modified lipid A, a key colistin-resistance mechanism. Moreover, Leu at position 10 of NP001 plays a key role in antibacterial activity against MCR-1-resistant bacteria. Our work establishes a generalizable framework for AMP discovery and introduces a promising therapeutic candidate, NP001, which effectively counteracts polymyxin-resistant pathogens.

Multigene Family↗
PubMed2025

Endogenous fine-mapping and prioritization of functional regulatory elements in complex genetic loci.

Most genetic loci linked to polygenic traits are in non-coding regions, with complex regulation and linkage disequilibrium (LD), complicating causal variant and gene prioritization. We used multiplexed single-cell CRISPR interference and activation perturbations to investigate cis-regulatory element (CRE) and gene expression relationships within tight LD in the endogenous chromatin context. We demonstrated the prevalence of multiple causality in perfect LD (pLD) for independent expression quantitative trait loci (eQTLs) and uncovered fine-grained genetic effects on gene expression within pLD, which are difficult to decipher using traditional eQTL fine-mapping or existing computational methods. We found that over one-third of the causal CREs lack classical epigenetic markers prior to perturbation, and we functionally validated one of these hidden regulatory mechanisms. Leveraging Multiome single-cell epigenetic and sequence perturbations, we highlighted the regulatory plasticity of the human genome. Our study will guide the exploration of missing causal mechanisms underlying molecular trait regulation and disease development.

Humans↗
PubMed2007

An osteoprotegerin-like peptidomimetic inhibits osteoclastic bone resorption and osteolytic bone disease in myeloma.

Multiple myeloma is a B-cell malignancy characterized by the uncontrolled growth of plasma cells in the bone marrow and the development of osteolytic bone disease. Myeloma cells express the receptor activator of nuclear factor kappaB ligand (RANKL), induce RANKL expression in the bone marrow, and down-regulate expression of the decoy receptor osteoprotegerin, thereby promoting bone resorption. Targeting this system in myeloma has clear therapeutic potential. However, osteoprotegerin also binds tumor necrosis factor-related apoptosis inducing ligand (TRAIL) and prevents TRAIL-induced apoptosis of myeloma cells. Whether or not osteoprotegerin can bind TRAIL and prevent apoptosis in vivo and the relative importance of osteoprotegerin binding to TRAIL and RANKL are unclear. In the present study, we have investigated the ability of an osteoprotegerin-like peptidomimetic (OP3-4), designed to block the RANKL/RANK interaction, to inhibit osteoclastic bone resorption and TRAIL-induced apoptosis in vitro and myeloma bone disease in vivo. OP3-4 inhibited osteoclast formation (P < 0.01) and bone resorption (P < 0.01) in vitro. However, OP3-4 had no effect on TRAIL-induced apoptosis of RPMI 8226 myeloma cells. Treatment of 5T2MM myeloma-bearing mice with OP3-4 decreased osteoclast number and the proportion of bone surface covered by osteoclasts (P < 0.05). Treatment also prevented the tumor-induced decrease in cancellous bone area and the development of osteolytic lesions (P < 0.05). OP3-4 also reduced tumor burden when compared with the control (P < 0.05). These data suggest that OP3-4 and the selective inhibition of RANKL, but not TRAIL activity, are effective in preventing myeloma bone disease and offer a novel therapeutic approach to treating this aspect of myeloma. [Cancer Res 2007;67(1):202-8].

Animals↗
PubMed2006

Test for detection of disease-associated prion aggregate in the blood of infected but asymptomatic animals.

We have developed a sensitive in vitro assay for detecting disease-associated prion aggregates by combining an aggregation-specific enzyme-linked immunosorbent assay (AS-ELISA) with the fluorescent amplification catalyzed by T7 RNA polymerase technique (FACTT). The new assay, named aggregation-specific FACTT (AS-FACTT), is much more sensitive than AS-ELISA and could detect prion aggregates in the brain of mice as early as 7 days after an intraperitoneal inoculation of PrP(Sc). However, AS-FACTT was still unable to detect prion aggregates in blood of infected mice. To further improve the detection limit of AS-FACTT, we added an additional prion amplification step (Am) and developed a third-generation assay, termed Am-A-FACTT. Am-A-FACTT has 100% sensitivity and specificity in detecting disease-associated prion aggregates in blood of infected mice at late but still asymptomatic stages of disease. At a very early stage, Am-A-FACTT had a sensitivity of 50% and a specificity of 100%. Most importantly, Am-A-FACTT also detects prion aggregates in blood of mule deer infected with the agent causing a naturally occurring prion disease, chronic wasting disease. Application of this assay to cattle, sheep, and humans could safeguard food supplies and prevent human contagion.

Animals↗
PubMed2006

Unexpected reactions of [60]fullerene involving tertiary amines and insight into the reaction mechanisms.

Thermal reactions of [60]fullerene with amino acid ester hydrochlorides and triethylamine in o-dichlorobenzene at reflux afforded pyrrolidinofullerene derivatives containing the CH(3)CH moiety and originating from triethylamine through an unusual C-N bond cleavage. Detailed investigation of these thermal reactions resulted in the discovery of unprecedented reactions between C(60) and tertiary amines and of reactions of C(60) with tertiary amines and aldehydes, giving cyclopentafullerene derivatives with high stereoselectivity. Plausible reaction mechanisms for the product formation involving the uncommon C-N bond cleavage of tertiary amines were proposed on the basis of extensive experimental results.

Amines↗
PubMed2006

A sensitive and high-throughput assay to detect low-abundance proteins in serum.

The ability to detect antigens immunologically is limited by the affinity of the antibodies and the amount of antigens. We have now succeeded in creating a modular, facile amplification system, termed fluorescent amplification catalyzed by T7 polymerase technique (FACTT). Such a system can detect protein targets specifically at subfemtomolar levels ( approximately 0.08 fM). We describe here the detection of Her2 (also known as Neu) from rodent and human sera. FACTT is adaptable to high-throughput screening and automation and provides a practical method to enhance current ELISAs in medical practice.

Animals↗
PubMed2006

Endometrial and ovarian F-18 FDG uptake in serial PET studies and the value of delayed imaging for differentiation.

PURPOSE: This study was designed to characterize the physiological endometrial and ovarian F-18 FDG uptake through analysis of clinical patients with serial PET follow ups (group 1) or who underwent delayed imaging (group 2). METHODS: Group 1 had 24 patients (14 premenopausal and 10 postmenopausal). Each patient underwent 2 to 4 serial FDG PET studies and summed to 57 studies. Group 2 included 15 premenopausal patients with delayed imaging 3 hours after injection. Ten of them showed endometrial uptake, and 8 showed intense uptake in 10 ovaries. Visual and semiquantitative methods were applied for analysis. RESULTS: By analysis of serial PET studies, endometrial and ovarian uptake showed some specific characteristics. Surrounded by a relatively low-uptake uterine wall, the inverted cone-shaped endometrium showed 2 peaks of uptake, one in early menstruation and the other in midcycle. The ovarian uptake was more prominent in the midcycle, and the foci of uptake had an ovoid shape and located at the left and/or right side superior-posterior to the bladder. For the postmenopausal and amenorrhea women (35 studies), only one study in a woman within 1 year of menopause showed mild endometrial and ovarian uptake. Compared with the imaging 1 hour after injection, the standardized uptake value increased in 2 of 10 endometria and 4 of 10 ovaries in the delayed imaging. CONCLUSION: Physiological endometrial and ovarian uptake can be identified on PET alone by their specific shape and position as well as their relation to the menstrual state, whereas delayed imaging was of little value for differentiation in this preliminary study.

Adolescent↗
PubMed2005

The synthetic genetic interaction spectrum of essential genes.

The nature of synthetic genetic interactions involving essential genes (those required for viability) has not been previously examined in a broad and unbiased manner. We crossed yeast strains carrying promoter-replacement alleles for more than half of all essential yeast genes to a panel of 30 different mutants with defects in diverse cellular processes. The resulting genetic network is biased toward interactions between functionally related genes, enabling identification of a previously uncharacterized essential gene (PGA1) required for specific functions of the endoplasmic reticulum. But there are also many interactions between genes with dissimilar functions, suggesting that individual essential genes are required for buffering many cellular processes. The most notable feature of the essential synthetic genetic network is that it has an interaction density five times that of nonessential synthetic genetic networks, indicating that most yeast genetic interactions involve at least one essential gene.

Gene Expression Regulation, Fungal↗
PubMed2005

Disabling TNF receptor signaling by induced conformational perturbation of tryptophan-107.

We have disabled TNF receptor (TNFR) function by inducing allosteric modulation of tryptophan-107 (W107) in the receptor. The allosteric effect operates by means of an allosteric cavity found a short distance from a previously identified loop involved in ligand binding. Occupying this cavity by small molecules leads to perturbation of distal W107 and disables functions of the TNFR, a molecule not known to undergo conformational change upon binding TNF-alpha. TNF-alpha-induced NF-kappaB and p38 kinase activities and clinical symptoms of collagen-induced arthritis in mice were all diminished. Thus, disabling receptor function by induced conformational changes of active binding surfaces represents an innovative paradigm in structure-based drug design.

Allosteric Site↗
PubMed2005

Single C59N molecule as a molecular rectifier.

We report a new kind of experimental realization of a molecular rectifier, which is based on a single azafullerene C59N molecule in a double-barrier tunnel junction via the single electron tunneling effect. An obvious rectifying effect is observed. The positive onset voltage is about 0.5-0.7 V, while the negative onset voltage is about 1.6-1.8 V. Theoretical analyses show that the half-occupied molecular orbital of the C59N molecule and the asymmetric shift of the molecular Fermi level when the molecule is charged are responsible for the molecular rectification.

Journal Article↗
PubMed2004

Fas-disabling small exocyclic peptide mimetics limit apoptosis by an unexpected mechanism.

Fas ligand- (FasL) mediated apoptosis is an important element of tissue-specific organ damage. We have developed biologically active small exocyclic peptide mimetics that disable apoptotic functions of Fas. The most effective mimetic binds to both its receptor and FasL with comparable affinity. In vitro, the most effective antagonist blocked FasL-induced cytotoxicity completely and specifically. In vivo, the antagonistic mimetic also prevented Concanavilin A (Con A) induced hepatitis, a CD4(+) T cell-mediated animal model of liver injury. Although current approaches prevent Fas receptor signaling by excluding FasL binding to Fas, the small molecule mimetics reported here disable Fas by promoting a defective Fas-FasL receptor complex. This event desensitizes FasL-mediated apoptosis by inhibiting extracellular signal regulated kinase activity and up-regulating NF-kappaB.

Amino Acid Sequence↗
PubMed2004

Selective addition to [60]fullerene of two different radicals generated from Mn(III)-based radical reaction.

Reaction of [60]fullerene in toluene with diethyl methylmalonate (3a), diethyl ethylmalonate (3b), diethyl bromomalonate (3c), triethyl methanetricarboxylate (3d) and ethyl cyanoacetate (3e) in the presence of manganese(III) acetate dihydrate afforded benzyl-substituted unsymmetrical 1,4-adducts 4a-4e. Dibenzylated 1,4-adduct 5 and methanofullerene 6 were also obtained in the case of 3d and 3e, respectively. A possible reaction mechanism for the formation of the 1,4-adducts 4a-4e is proposed.

Journal Article↗
PubMed2004

Global mapping of the yeast genetic interaction network.

A genetic interaction network containing approximately 1000 genes and approximately 4000 interactions was mapped by crossing mutations in 132 different query genes into a set of approximately 4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to identify components of the same pathway. The genetic network exhibited dense local neighborhoods; therefore, the position of a gene on a partially mapped network is predictive of other genetic interactions. Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.

Amino Acid Sequence↗
PubMed2004

[Effect of S-2-(3-aminopropylamino) ethyl phosphorothioic acid on apoptosis and proliferation inhibition of HL-60 cell line].

To study the effects of S-2-(3-aminopropylamino) ethyl phosphorothioic acid (WR-2721, amifostine) on proliferation inhibition and apoptosis of HL-60 human leukemia cell line, the cell apoptosis rate of HL-60 was determined by annexin V/PI double staining method. Cell proliferation and chemotherapy sensitivity were analyzed with XTT assay, and the changes of cell cycle were observed through flow cytometry. The results showed that WR-2721 could significantly inhibit HL-60 cell proliferation. After treatment (30 min, 37 degrees C) with WR-2721, the sensitivity of HL-60 cells to VP16 was enhanced, and the IC(50) descended from 52.5 micro g/ml to 40.5 microg/ml. After 72 hours treatment of HL-60 cells with WR-2721, the early apoptotic cells (annexin V-FITC positive/PI negative) were increased from (5.5 +/- 1.9)% to (48.5 +/- 8.4)% (P < 0.001), late apoptotic cells (annexin V-FITC positive/PI positive) were increased from (1.2 +/- 0.5)% to (39.0 +/- 4.0)% (P < 0.001), and HL-60 cells were arrested in G(2)-M phase. In conclusion, WR-2721 treatment can enhance HL-60 cell chemotherapy sensitivity to VP16, inhibit proliferation, induce apoptosis and accumulation of cells in G(2)-M phase.

Amifostine↗
PubMed2004

[Construction, expression and bioactivity characterization of targeting toxin DT-VEGF].

Tumor rapid growth depends on neovascularization. Vascular endothelial growth factor, the main mediator during the occurrence and formation of vascularization, has specific receptors whose expression rate shows difference of orders of magnitude between tumor and the normal tissue, so it can be used to transport toxin molecules to the proliferative tumor endothelial and kill cancer cells. In our experiment, we constructed fusion protein DT-VEGF by linking diphtheria toxin's forward 389 amino acids's gene and VEGF165 via a linker. DT-VEGF is expressed in E. coli and purified. Our experiment proves in can kill vascular endothelial cells specifically, and the inhibition of neovascularization of chicken chorionic membrane is also confirmed.

Angiogenesis Inhibitors↗
PubMed2003

Disabling of receptor activator of nuclear factor-kappaB (RANK) receptor complex by novel osteoprotegerin-like peptidomimetics restores bone loss in vivo.

The tumor necrosis factor family ligand, tumor necrosis factor-related activation-induced cytokine (TRANCE), and its receptors, receptor activator of nuclear factor-kappaB (RANK) and osteoprotegerin (OPG), are known to be regulators of development and activation of osteoclasts in bone remodeling. Sustained osteoclast activation that occurs through TRANCE-RANK causes osteopenic disorders such as osteoporosis and contributes to osteolytic metastases. Here, we report a rationally designed small molecule mimic of osteoprotegerin to inhibit osteoclast formation in vitro and limit bone loss in an animal model of osteoporosis. One of the mimetics, OP3-4, significantly inhibited osteoclast formation in vitro (IC(50) = 10 microm) and effectively inhibited total bone loss in ovariectomized mice at a dosage of 2 mg/kg/day. Unlike soluble OPG receptors, which preclude TRANCE binding to RANK, OP3-4 shows the ability to modulate RANK-TRANCE signaling pathways and alters the biological functions of the RANK-TRANCE receptor complex by facilitating a defective receptor complex. These features suggest that OPG-derived small molecules can be used as a probe to understand complex biological functions of RANK-TRANCE-OPG receptors and also can be used as a platform to develop more useful therapeutic agents for inflammation and bone disease.

Amino Acid Sequence↗