Biology subjects

Luo, K.

Publications and source records attributed to Luo, K..

44 records · Page 3Linked to original sources

bioRxiv2019

IFN-alpha and 5-Aza-2-deoxycytidine enhance the anti-tumor efficacy of a dendritic-cell targeting MIP3alpha-Gp100-Trp2 DNA vaccine by affecting T-cell recruitment and tumor microenvironment gene expression

BackgroundThe chemokine MIP-3 (CCL20) binds to CCR6 found on immature dendritic cells. DNA vaccines fusing MIP-3 to melanoma-associated antigens have shown improved efficacy and immunogenicity in the B16F10 model. To optimize the therapy, our laboratory has added agents designed to overcome immunoregulatory mechanisms of the tumor microenvironment. Here, we report that the combination of type-I interferon therapy (IFN) with 5-Aza-2-deoxycitidine (Aza) profoundly enhanced the therapeutic anti-melanoma efficacy of a MIP-3-Gp100-Trp2 DNA vaccine. MethodsThe current studies utilize the B16F10 syngeneic mouse melanoma model. The vaccine is administered intramuscularly (i.m.) followed by i.m. electroporation. Vaccinations are given thrice at one-week intervals beginning day 5 with CpG adjuvant given two days later as noted. Aza is given i.p. at 1mg/kg on days 5 and 12. IFN therapy is given in a series of one high followed by three low doses, beginning on days 5 and 12. Tumor sizes, growth, and survival were all assessed. Tumor microenvironment gene expression levels were explored by qRT-PCR. Tumor-infiltrating lymphocytes (TILs) were assessed by stimulating the purified lymphocyte fraction of tumors with vaccine antigens followed by intracellular cytokine staining flow cytometry. ResultsWe demonstrate that the addition of IFN and Aza treatments to mice vaccinated with the MIP-3-Gp100-Trp2 vaccine has led to significantly reduced tumor burden and overall increases in mouse survival, increasing median survival by 39% over vaccine and 86% over controls. Importantly, this increase in efficacy was dependent on the presence of all three components: vaccine, IFN, and Aza. The addition of Aza and IFN to the vaccine increased T-cell tumor infiltration and altered the proportion of CD8+T-cells. Also, IFN and vaccine induced durable changes in IFN-stimulated gene transcription. ConclusionsEfficient targeting of antigen to immature dendritic cells with a chemokine-fusion vaccine offers a potential alternative approach to classic and dendritic cell based vaccines currently undergoing clinical investigation. Combining this approach with IFN and Aza combination treatment significantly improved vaccine efficacy, with efficacy correlating with changes in TILs and in IFN -stimulated gene expression. Further potential therapy optimization currently undergoing investigation offers promise for this line of investigation to become a novel melanoma therapy.

immunology↗

bioRxiv2019

Comprehensive identification of survival-associated genes for cancers

Prognostic signature is important in estimating cancer risk, subtyping cancer, and planning treatment. A single gene as a prognostic marker would facilitate the development of a clinical test. Here we showed that the number of prognostic and diagnostic genes differ greatly across cancers. By considering both the survival difference and the fold change of expression in cancer, we revealed the prognostic genes for each cancer and found twenty two genes with both diagnostic and prognostic capacity. The universal prognostic genes (CDC20, CDCA8, ASPM, ERCC6L, and GTSE1) mainly function in the spindle assembly checkpoint, and show more statistical links to mutated pathways, suggesting that expression of these genes can be altered by mutations from many pathways. Briefly, we systematically identified the prognostic genes and revealed the associations between the prognostic genes and genes mutated in cancer. Keywords: Prognostic gene; Cancer; Mutation; Diagnosis

cancer biology↗

bioRxiv2018

Reorganization of 3D Genome Structure May Contribute to Gene Regulatory Evolution in Primates

A growing body of evidence supports the notion that variation in gene regulation plays a crucial role in both speciation and adaptation. However, a comprehensive functional understanding of the mechanisms underlying regulatory evolution remains elusive. In primates, one of the crucial missing pieces of information towards a better understanding of regulatory evolution is a comparative annotation of interactions between distal regulatory elements and promoters. Chromatin conformation capture technologies have enabled genome-wide quantifications of such distal 3D interactions. However, relatively little comparative research in primates has been done using such technologies. To address this gap, we used Hi-C to characterize 3D chromatin interactions in induced pluripotent stem cells (iPSCs) from humans and chimpanzees. We also used RNA-sequencing to collect gene expression data from the same lines. We generally observed that lower-order, pairwise 3D genomic interactions are conserved in humans and chimpanzees, but higher order genomic structures, such as TADs, are not as conserved. Inter-species differences in 3D genomic interactions are often associated with gene expression differences between the species. To provide additional functional context to our observations, we considered previously published chromatin data from human iPSCs. We found that inter-species differences in 3D genomic interactions, which are also associated with gene expression differences between the species, are enriched for both active and repressive marks. Overall, our data demonstrates that, as expected, an understanding of 3D genome reorganization is key to explaining regulatory evolution.

genomics↗

bioRxiv2018

Characterization and mechanism of lead and zinc biosorption by growing Verticillium insectorum J3

Verticillium insectorum J3 was isolated from a local lead-zinc deposit tailing, and its biosorption characteristics and reaction to the toxicities of different Pb(II) and Zn(II) concentrations were investigated. SEM, FTIR, a pH test and a desorption experiment were carried out to identify a possible mechanism. The biosorption of J3 presented an inhibition trend at low concentrations (25-75 mg L-1) and promotion at high concentrations (100-300 mg L-1). J3 absorbed Pb(II) prior to Zn(II) and produced alkaline substances, while mycelial and pellet morphology modifications were important for the removal of Pb(II) and Zn(II) under different stressful conditions (SEM results). Both intracellular accumulation and extracellular absorption may contribute to the removal of Pb(II) at lower concentrations (25-50 mg L-1), although mainly extracellular biosorption occurred at higher concentrations (75-300 mg L-1). However, Zn(II) bioaccumulation occurred at all concentrations assayed. Verticillium insectorum J3 may have evolved active defenses to alleviate the toxicity of heavy metals and proved to be a highly efficient biosorbent, especially for Pb(II) at high concentrations. This study is a useful reference for the development of biotreatment technologies to mitigate heavy metal waste.

microbiology↗

bioRxiv2018

Population based hospitalization burden of laboratory-confirmed hand, foot and mouth disease caused by multiple enterovirus serotypes in southern China

BackgroundHand, foot and mouth disease (HFMD) is spread widely across Asia, and the hospitalization burden is as yet not well understood. Here, we estimated serotype-specific and age-specific hospitalization rates of HFMD in Southern China.\n\nMethodsWe enrolled pediatric patients admitted to 3/3 county-level hospitals and 3/23 township level hospitals in Anhua county, Hunan (CN) with HFMD, and collected samples to identify enterovirus serotypes by RT-PCRs between October 2013 and September 2016. The information of other eligible but un-enrolled patients were retrospectively collected from the same six hospitals. Monthly number of hospitalizations for all causes was collected from each of 23 township level hospitals to extrapolate hospitalizations associated with HFMD among these.\n\nResultsDuring the three years, an estimated 3,236 pediatric patients were hospitalized with lab-confirmed HFMD, and among these only one patient was severe. The mean hospitalization rates were 660 (95% CI: 638-684) per 100,000 person-years for lab-confirmed HFMD, with higher rates among CV-A16 and CV-A6 associated HFMD (213 vs 209 per 100,000 person-years), and lower among EV-A71, CV-A10 and other enteroviruses associated HFMD (134, 39 and 66 per 100,000 person-years, p<0.001). Children aged 12-23 months had the highest hospitalization rates (3,594/100,000 person-years), followed by those aged 24-35 months (1,828/100,000 person-years) and 6-11 months (1,572/100,000 person-years). Compared with other serotypes, CV-A6-associated hospitalizations were evident at younger ages.\n\nConclusionsOur study indicates a substantial hospitalization burden associated with non-severe HFMD in a rural county in southern China. Future mitigation policies should take into account the disease burden identified, and optimize interventions for HFMD.

epidemiology↗

bioRxiv2017

Guanosine monophosphate reductase 1 is a potential therapeutic target for Alzheimer’s disease

Alzheimers disease (AD) is a severe neurodegenerative disorder. Identification of differentially expressed genes in AD would help to find biomarker and therapeutic target. Here, we carried out an analysis to identify the age-independent and AD-specific genes. We found that genes MET, WIF1 and NPTX2 are down regulated in AD. WIF1 and MET are in signaling of WNT and MET, regulating the activity of GSK3{beta}, thus in AD. Importantly, we found gene GMPR shows a gradual increase in AD progress. A logistic model based on GMPR exhibits a good capacity in classifying AD cases. GMPRs product GMPR1 links with AMPK and adenosine receptor pathways, thus associating phosphorylation of Tau in AD. This allows GMPR1 to be a therapeutic target. Therefore, we screened five possible inhibitors to GMPR1 by docking GMPR1 with 1174 approved drugs. Among them, lumacaftor is ideal due to its high affinity and light molecular weight. We then tested the effect of lumacaftor on AD model mice. After twenty days of oral administration, {beta}-Amyloid accumulation is slowed down and phosphorylation of Tau is almost eliminated in the treated mice, showing a satisfying effect. In conclusion, the elevated expression level of GMPR tightly associates with AD progress and leads to AD phenotype probably through AMPK and adenosine receptor pathways; and one of therapeutic strategies is to inhibit GMPRs product with lumacaftor.\n\nSignificance StatementWe found the elevated expression level of GMPR tightly associates with AD progress and leads to AD phenotype probably through AMPK and adenosine receptor pathways; and the therapeutic strategy targeting GMPR1 with lumacaftor shows a satisfying result.

bioinformatics↗

bioRxiv2017

Silencing Of Transposable Elements May Not Be A Major Driver Of Regulatory Evolution In Primate Induced Pluripotent Stem Cells

Transposable elements (TEs) comprise a substantial proportion of primate genomes. The regulatory potential of TEs can result in deleterious effects, especially during development. It has been suggested that, in pluripotent stem cells, TEs are targeted for silencing by KRAB-ZNF proteins, which recruit the TRIM28-SETDB1 complex, to deposit the repressive histone modification H3K9me3. TEs, in turn, can acquire mutations that allow them to evade detection by the host, and hence KRAB-ZNF proteins need to rapidly evolve to counteract them. To investigate the short-term evolution of TE silencing, we profiled the genome-wide distribution of H3K9me3 in induced pluripotent stem cells from ten human and seven chimpanzee individuals. We performed chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) for H3K9me3, as well as total RNA sequencing. We focused specifically on cross-species H3K9me3 ChIP-seq data that mapped to four million orthologous TEs. We found that, depending on the TE class, 10-60% of elements are marked by H3K9me3, with SVA, LTR and LINE elements marked most frequently. We found little evidence of inter-species differences in TE silencing, with as many as 80% of orthologous, putatively silenced, TEs marked at similar levels in humans and chimpanzees. Our data suggest limited species-specificity of TE silencing across six million years of primate evolution. Interestingly, the minority of TEs enriched for H3K9me3 in one species are not more likely to be associated with gene expression divergence of nearby orthologous genes. We conclude that orthologous TEs may not play a major role in driving gene regulatory divergence between humans and chimpanzees.

genomics↗

bioRxiv2016

Chimeric Genes Revealed in the Polyploidy Fish Hybrids of Carassius cuvieri (Female) x Megalobrama amblycephala (Male)

The genomes of newly formed natural or artificial polyploids may experience rapid gene loss and genome restructuring. In this study, we obtained tetraploid hybrids (4n=148, 4nJB) and triploid hybrids (3n=124, 3nJB) derived from the hybridization of two different subfamily species Carassius cuvieri ([female], 2n = 100, JCC) and Megalobrama amblycephala ([male], 2n = 48, BSB). Some significant morphological and physiological differences were detected in the polyploidy hybrids compared with their parents. To reveal the molecular traits of the polyploids, we compared the liver transcriptomes of 4nJB, 3nJB and their parents. The results indicated high proportion chimeric genes (31 > %) and mutated orthologous genes (17 > %) both in 4nJB and 3nJB. We classified 10 gene patterns within three categories in 4nJB and 3nJB orthologous gene, and characterized 30 randomly chosen genes using genomic DNA to confirm the chimera or mutant. Moreover, we mapped chimeric genes involved pathways and discussed that the phenotypic novelty of the hybrids may relate to some chimeric genes. For example, we found there is an intragenic insertion in the K+ channel kcnk5b, which may be related to the novel presence of the barbels in 4nJB. Our results indicated that the genomes of newly formed polyploids experienced rapid restructuring post-polyploidization, which may results in the phenotypic and phenotypic changes among the polyploidy hybrid offspring. The formation of the 4nJB and 3nJB provided new insights into the genotypic and phenotypic diversity of hybrid fish resulting from distant hybridization between subfamilies.

developmental biology↗