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1.
Commun Biol ; 7(1): 824, 2024 Jul 06.
Article in English | MEDLINE | ID: mdl-38971948

ABSTRACT

The expression dysregulation of microRNAs (miRNA) has been widely reported during cancer development, however, the underling mechanism remains largely unanswered. In the present work, we performed a systematic integrative study for genome-wide DNA methylation, copy number variation and miRNA expression data to identify mechanisms underlying miRNA dysregulation in lower grade glioma. We identify 719 miRNAs whose expression was associated with alterations of copy number variation or promoter methylation. Integrative multi-omics analysis revealed four subtypes with differing prognoses. These glioma subtypes exhibited distinct immune-related characteristics as well as clinical and genetic features. By construction of a miRNA regulatory network, we identified candidate miRNAs associated with immune evasion and response to immunotherapy. Finally, eight prognosis related miRNAs were validated to promote cell migration, invasion and proliferation through in vitro experiments. Our study reveals the crosstalk among DNA methylation, copy number variation and miRNA expression for immune regulation in glioma, and could have important implications for patient stratification and development of biomarkers for immunotherapy approaches.


Subject(s)
Brain Neoplasms , DNA Copy Number Variations , DNA Methylation , Gene Expression Regulation, Neoplastic , Glioma , MicroRNAs , Humans , Glioma/genetics , Glioma/immunology , Glioma/pathology , MicroRNAs/genetics , MicroRNAs/metabolism , Brain Neoplasms/genetics , Brain Neoplasms/immunology , Brain Neoplasms/pathology , Epigenomics , Genomics , Gene Regulatory Networks , Cell Line, Tumor , Immune Evasion/genetics , Epigenesis, Genetic , Female , Male , Prognosis , Neoplasm Grading
2.
BMC Med Genomics ; 17(1): 111, 2024 Apr 27.
Article in English | MEDLINE | ID: mdl-38678264

ABSTRACT

BACKGROUND: Statistical epistasis, or "gene-gene interaction" in genetic association studies, means the nonadditive effects between the polymorphic sites on two different genes affecting the same phenotype. In the genetic association analysis of complex traits, nevertheless, the researchers haven't found enough clues of statistical epistasis so far. METHODS: We developed a statistical model where the statistical epistasis was presented as an extra linkage disequilibrium between the polymorphic sites of different risk genes. The power of statistical test for identifying the gene-gene interaction was calculated and then compared in different hypothesis scenarios. RESULTS: Our results show the statistical power increases with the increasing of interaction coefficient, relative risk, and linkage disequilibrium with genetic markers. However, the power of interaction discovery is much lower than that of regular single-site association test. When rigorous criteria were employed in statistical tests, the identification of gene-gene interaction became a very difficult task. Since the criterion of significance was given to be p-value ≤ 5.0 × 10-8, the same as that of many genome-wide association studies, there is little chance to identify the gene-gene interaction in all kind of circumstances. CONCLUSIONS: The lack of epistasis tends to be an inevitable result caused by the statistical principles of methods in the genetic association studies and therefore is the inherent characteristic of the research itself.


Subject(s)
Epistasis, Genetic , Genome-Wide Association Study , Linkage Disequilibrium , Humans , Models, Genetic , Polymorphism, Single Nucleotide , Models, Statistical
3.
Infect Genet Evol ; 113: 105479, 2023 09.
Article in English | MEDLINE | ID: mdl-37437767

ABSTRACT

In the worst future pandemic, effective vaccines and medicines could be unavailable for a long time. In such circumstances, it is necessary to evaluate whether a periodic screening can protect isolated communities and critical facilities and avoid a complete shutdown. In this study, we introduced an epidemiological model that included the essential parameters of infection transmission and screening. With varying parameters, we studied the dynamics of viral infection in the isolated communities. In the scenario with a periodic infection screening once per 3 days and a viral basic reproduction number 3.0, >85% of the infection waves have a duration <7 days and the infection size in each of the waves is generally <4 individuals when the efficiency of infection discovery is 0.9 in the screening. When the period of screening was elongated to once per 7 days, the cases of infection dramatically increased to 5 folds of that mentioned previously. Further, with a weak discovery efficiency of 0.7 and the aforementioned low screening frequency, the spread of infection would be out of control. Our study suggests that frequent periodic screening is capable of controlling a future epidemic in isolated communities without other measures.


Subject(s)
COVID-19 , Virus Diseases , Humans , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/prevention & control , SARS-CoV-2 , Pandemics/prevention & control , Mass Screening
4.
Front Mol Biosci ; 9: 1067406, 2022.
Article in English | MEDLINE | ID: mdl-36533073

ABSTRACT

DNA methylation is one of the most important epigenetic mechanisms that governing regulation of gene expression, aberrant DNA methylation patterns are strongly associated with human malignancies. Long non-coding RNAs (lncRNAs) have being discovered as a significant regulator on gene expression at the epigenetic level. Emerging evidences have indicated the intricate regulatory effects between lncRNAs and DNA methylation. On one hand, transcription of lncRNAs are controlled by the promoter methylation, which is similar to protein coding genes, on the other hand, lncRNA could interact with enzymes involved in DNA methylation to affect the methylation pattern of downstream genes, thus regulating their expression. In addition, circular RNAs (circRNAs) being an important class of noncoding RNA are also found to participate in this complex regulatory network. In this review, we summarize recent research progress on this crosstalk between lncRNA, circRNA, and DNA methylation as well as their potential functions in complex diseases including cancer. This work reveals a hidden layer for gene transcriptional regulation and enhances our understanding for epigenetics regarding detailed mechanisms on lncRNA regulatory function in human cancers.

5.
Mol Biol Evol ; 39(10)2022 10 07.
Article in English | MEDLINE | ID: mdl-36173765

ABSTRACT

As the most prevalent aboriginal group on Hainan Island located between South China and the mainland of Southeast Asia, the Li people are believed to preserve some unique genetic information due to their isolated circumstances, although this has been largely uninvestigated. We performed the first whole-genome sequencing of 55 Hainan Li (HNL) individuals with high coverage (∼30-50×) to gain insight into their genetic history and potential adaptations. We identified the ancestry enriched in HNL (∼85%) is well preserved in present-day Tai-Kadai speakers residing in South China and North Vietnam, that is, Bai-Yue populations. A lack of admixture signature due to the geographical restriction exacerbated the bottleneck in the present-day HNL. The genetic divergence among Bai-Yue populations began ∼4,000-3,000 years ago when the proto-HNL underwent migration and the settling of Hainan Island. Finally, we identified signatures of positive selection in the HNL, some outstanding examples included FADS1 and FADS2 related to a diet rich in polyunsaturated fatty acids. In addition, we observed that malaria-driven selection had occurred in the HNL, with population-specific variants of malaria-related genes (e.g., CR1) present. Interestingly, HNL harbors a high prevalence of malaria leveraged gene variants related to hematopoietic function (e.g., CD3G) that may explain the high incidence of blood disorders such as B-cell lymphomas in the present-day HNL. The results have advanced our understanding of the genetic history of the Bai-Yue populations and have provided new insights into the adaptive scenarios of the Li people.


Subject(s)
Ethnicity , Indigenous Peoples , Humans , China/epidemiology , Geography , Asia, Southeastern , Genetics, Population
6.
Environ Res ; 215(Pt 1): 114231, 2022 12.
Article in English | MEDLINE | ID: mdl-36087772

ABSTRACT

In this work, a novel co-precipitation coupled solvothermal procedure is proposed to prepare a SmMnOx catalyst (SmMnOx-CP + ST) with a reed flower-like structure for the selective catalytic reduction of NOx by NH3 (NH3-SCR). Over 90% NOx conversion and N2 selectivity was achieved at a low temperature range (25-200 °C), and 96% NOx conversion was achieved in the presence of 100 ppm SO2 at 75 °C. While the NH3-SCR of the SmMnOx catalysts prepared by co-precipitation (SmMnOx-CP) and solvothermal (SmMnOx-ST) methods performed much poorer than the SmMnOx-CP + ST catalyst. All catalysts were characterized by XRD, BET, SEM, XPS, H2-TPR, NH3-TPD, NOx-TPD, and FT-IR. The results revealed that the superior performance of the SmMnOx-CP + ST is due to the unique reed flower-like structure morphology, which endows the SmMnOx-CP + ST with the largest surface area, the strongest synergistic reaction of Sm and Mn, abundant surface oxygen species and surface active sites, and significantly enhances the redox ability. Furthermore, the amorphous reed flower-like structure showed strong short-range ordered interaction between the active components and weaken the formation of sulfates species. In addition, the highest content of Mn4+ and Mn3++Mn4+ greatly promotes the redox cycles of Sm2+↔Mn4+ and Sm2+↔Mn3+, and suppresses the production of sulfate species in the presence of SO2.


Subject(s)
Ammonia , Oxygen , Ammonia/chemistry , Catalysis , Oxidation-Reduction , Spectroscopy, Fourier Transform Infrared , Sulfates , Temperature
7.
Genomics Proteomics Bioinformatics ; 20(3): 446-454, 2022 06.
Article in English | MEDLINE | ID: mdl-35643191

ABSTRACT

MicroRNAs (miRNAs) are important regulators in gene expression. The dysregulation of miRNA expression is widely reported in the transformation from physiological to pathological states of cells. A large number of differentially expressed miRNAs (DEMs) have been identified in various human cancers by using high-throughput technologies, such as microarray and miRNA-seq. Through mining of published studies with high-throughput experiment information, the database of DEMs in human cancers (dbDEMC) was constructed with the aim of providing a systematic resource for the storage and query of the DEMs. Here we report an update of the dbDEMC to version 3.0, which contains two-fold more data entries than the second version and now includes also data from mice and rats. The dbDEMC 3.0 contains 3268 unique DEMs in 40 different cancer types. The current datasets for differential expression analysis have expanded to 9 generalized categories. Moreover, the current release integrates functional annotations of DEMs obtained by using experimentally validated targets. The annotations can be of great benefit to the intensive analysis of the roles of DEMs in cancer. In summary, dbDEMC 3.0 provides a valuable resource for characterizing molecular functions and regulatory mechanisms of DEMs in human cancers. The dbDEMC 3.0 is freely accessible at https://www.biosino.org/dbDEMC.


Subject(s)
Databases, Genetic , MicroRNAs , Neoplasms , Animals , Humans , Mice , Rats , Computational Biology , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Gene Regulatory Networks , MicroRNAs/genetics , MicroRNAs/metabolism , Neoplasms/genetics
8.
Cancer Discov ; 12(7): 1718-1741, 2022 07 06.
Article in English | MEDLINE | ID: mdl-35412588

ABSTRACT

The overall response rate for anti-PD-1 therapy remains modest in hepatocellular carcinoma (HCC). We found that a combination of IFNα and anti-PD-1-based immunotherapy resulted in enhanced antitumor activity in patients with unresectable HCC. In both immunocompetent orthotopic and spontaneous HCC models, IFNα therapy synergized with anti-PD-1 and the combination treatment led to significant enrichment of cytotoxic CD27+CD8+ T cells. Mechanistically, IFNα suppressed HIF1α signaling by inhibiting FosB transcription in HCC cells, resulting in reduced glucose consumption capacity and consequentially establishing a high-glucose microenvironment that fostered transcription of the T-cell costimulatory molecule Cd27 via mTOR-FOXM1 signaling in infiltrating CD8+ T cells. Together, these data reveal that IFNα reprograms glucose metabolism within the HCC tumor microenvironment, thereby liberating T-cell cytotoxic capacities and potentiating the PD-1 blockade-induced immune response. Our findings suggest that IFNα and anti-PD-1 cotreatment is an effective novel combination strategy for patients with HCC. SIGNIFICANCE: Our study supports a role of tumor glucose metabolism in IFNα-mediated antitumor immunity in HCC, and tumor-infiltrating CD27+CD8+ T cells may be a promising biomarker for stratifying patients for anti-PD-1 therapy. See related commentary by Kao et al., p. 1615. This article is highlighted in the In This Issue feature, p. 1599.


Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , CD8-Positive T-Lymphocytes , Carcinoma, Hepatocellular/metabolism , Glucose/metabolism , Glucose/pharmacology , Humans , Interferon-alpha/metabolism , Interferon-alpha/pharmacology , Interferon-alpha/therapeutic use , Liver Neoplasms/metabolism , Tumor Microenvironment
9.
Microbiol Spectr ; 10(2): e0083821, 2022 04 27.
Article in English | MEDLINE | ID: mdl-35230153

ABSTRACT

The complexity of genome-wide gene expression has not yet been adequately addressed due to a lack of comprehensive statistical analyses. In the present study, we introduce degree of freedom (DOF) as a summary statistic for evaluating gene expression complexity. Because DOF can be interpreted by a state-space representation, application of the DOF is highly useful for understanding gene activities. We used over 11,000 gene expression data sets to reveal that the DOF of gene expression in Saccharomyces cerevisiae is not greater than 450. We further demonstrated that various degrees of freedom of gene expression can be interpreted by different sequence motifs within promoter regions and Gene Ontology (GO) terms. The well-known TATA box is the most significant one among the identified motifs, while the GO term "ribosome genesis" is an associated biological process. On the basis of transcriptional freedom, our findings suggest that the regulation of gene expression can be modeled using only a few state variables. IMPORTANCE Yeast works like a well-organized factory. Each of its components works in its own way, while affecting the activities of others. The order of all activities is largely governed by the regulation of gene expression. In recent decades, biologists have recognized many regulations for yeast genes. However, it is not known how closely the regulation links each gene together to make all components of the cell work as a whole. In other words, biologists are very interested in how many independent control factors are needed to operate an artificial "cell" that works the same as a real one. In this work, we suggested that only 450 control factors were sufficient to represent the regulation of all 5800 yeast genes.


Subject(s)
Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Gene Expression , Gene Expression Regulation, Fungal , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism
11.
J Proteomics ; 253: 104454, 2022 02 20.
Article in English | MEDLINE | ID: mdl-34922012

ABSTRACT

Oral squamous cell carcinoma (OSCC) is a common pernicious tumor in the head and neck regions. However, the function of tumor extracellular matrix (ECM) has not been elucidated. A tissue engineering method was applied for remodeling ECM through decellularization. The cellular components were removed, and the biological composition was mostly preserved. Proteomics was performed to analyze the characterization between normal and tumor ECM. According to LC-MS/MS results, 26 proteins just showed in tumor ECM, and 14 proteins only showed in late-stage tumor ECM. KEGG pathway analysis showed that most variant proteins were linked to metabolic regulation and tumor immunity (such as SCC-Ag1, LOX). To affirm the influence of tumor ECM on the progression of OSCC, tumor cells and macrophages were co-cultured with ECM scaffold. Marked differences in proliferation, apoptosis, and migration of OSCC cells were observed between tumor and normal ECM. Tumor ECM polarized macrophages towards an anti-inflammatory phenotype (higher IL-10 and CD68, and relatively lower CD86 and IL1-ß). Collectively, these findings suggest that tumor ECM served as a permissive role in OSCC progression. SIGNIFICANCE: The variation between OSCC ECM and normal ECM confirm tumor ECM plays a significant role in OSCC deterioration, which is conducive to exploring the occurrence and progression mechanisms of OSCC, and further improving the curative effect of this disease.


Subject(s)
Carcinoma, Squamous Cell , Head and Neck Neoplasms , Mouth Neoplasms , Cell Line, Tumor , Cell Movement , Cell Proliferation , Chromatography, Liquid , Extracellular Matrix/metabolism , Head and Neck Neoplasms/metabolism , Humans , Mouth Neoplasms/metabolism , Squamous Cell Carcinoma of Head and Neck/metabolism , Tandem Mass Spectrometry , Tumor Microenvironment
12.
Biotechnol Biofuels ; 14(1): 236, 2021 Dec 14.
Article in English | MEDLINE | ID: mdl-34906221

ABSTRACT

BACKGROUND: Kluyveromyces marxianus is a promising cell factory for producing bioethanol and that raised a demand for a high yield of heterologous proteins in this species. Expressions of heterologous proteins usually lead to the accumulation of misfolded or unfolded proteins in the lumen of the endoplasmic reticulum (ER) and then cause ER stress. To cope with this problem, a group of ER stress response target genes (ESRTs) are induced, mainly through a signaling network called unfolded protein response (UPR). Characterization and modulation of ESRTs direct the optimization of heterologous expressions. However, ESRTs in K. marxianus have not been identified so far. RESULTS: In this study, we characterized the ER stress response in K. marxianus for the first time, by using two ER stress-inducing reagents, dithiothreitol (DTT) and tunicamycin (TM). Results showed that the Kar2-Ire1-Hac1 pathway of UPR is well conserved in K. marxianus. About 15% and 6% of genes were upregulated during treatment of DTT and TM, respectively. A total of 115 upregulated genes were characterized as ESRTs, among which 97 genes were identified as UPR target genes and 37 UPR target genes contained UPR elements in their promoters. Genes related to carbohydrate metabolic process and actin filament organization were identified as new types of UPR target genes. A total of 102 ESRTs were overexpressed separately in plasmids and their effects on productions of two different lignocellulolytic enzymes were systematically evaluated. Overexpressing genes involved in carbohydrate metabolism, including PDC1, PGK and VID28, overexpressing a chaperone gene CAJ1 or overexpressing a reductase gene MET13 substantially improved secretion expressions of heterologous proteins. Meanwhile, overexpressing a novel gene, KLMA_50479 (named ESR1), as well as overexpressing genes involved in ER-associated protein degradation (ERAD), including HRD3, USA1 andYET3, reduced the secretory expressions. ESR1 and the aforementioned ERAD genes were deleted from the genome. Resultant mutants, except the yet3Δ mutant, substantially improved secretions of three different heterologous proteins. During the fed-batch fermentation, extracellular activities of an endoxylanase and a glucanase in hrd3Δ cells improved by 43% and 28%, respectively, compared to those in wild-type cells. CONCLUSIONS: Our results unveil the transcriptional scope of the ER stress response in K. marxianus and suggest efficient ways to improve productions of heterologous proteins by manipulating expressions of ESRTs.

13.
J Nanobiotechnology ; 19(1): 342, 2021 Oct 26.
Article in English | MEDLINE | ID: mdl-34702291

ABSTRACT

BACKGROUND: Jaw bones are the most common organs to be invaded by oral malignancies, such as oral squamous cell carcinoma (OSCC), because of their special anatomical relationship. Various serious complications, such as pathological fractures and bone pain can significantly decrease the quality of life or even survival outcomes for a patient. Although chemotherapy is a promising strategy for bone invasion treatment, its clinical applications are limited by the lack of tumor-specific targeting and poor permeability in bone tissue. Therefore, it is necessary to develop a smart bone and cancer dual targeting drug delivery platform. RESULTS: We designed a dual targeting nano-biomimetic drug delivery vehicle Asp8[H40-TPZ/IR780@(RBC-H)] that has excellent bone and cancer targeting as well as immune escape abilities to treat malignancies in jaw bones. These nanoparticles were camouflaged with a head and neck squamous cell carcinoma WSU-HN6 cell (H) and red blood cell (RBC) hybrid membrane, which were modified by an oligopeptide of eight aspartate acid (Asp8). The spherical morphology and typical core-shell structure of biomimetic nanoparticles were observed by transmission electron microscopy. These nanoparticles exhibited the same surface proteins as those of WSU-HN6 and RBC. Flow cytometry and confocal microscopy showed a greater uptake of the biomimetic nanoparticles when compared to bare H40-PEG nanoparticles. Biodistribution of the nanoparticles in vivo revealed that they were mainly localized in the area of bone invasion by WSU-HN6 cells. Moreover, the Asp8[H40-TPZ/IR780@(RBC-H)] nanoparticles exhibited effective cancer growth inhibition properties when compared to other TPZ or IR780 formulations. CONCLUSIONS: Asp8[H40-TPZ/IR780@(RBC-H)] has bone targeting, tumor-homing and immune escape abilities, therefore, it is an efficient multi-targeting drug delivery platform for achieving precise anti-cancer therapy during bone invasion.


Subject(s)
Bone and Bones/metabolism , Drug Delivery Systems/methods , Nanoparticles/chemistry , Photochemotherapy/methods , Photothermal Therapy/methods , Animals , Biomimetic Materials/chemistry , Biomimetic Materials/pharmacology , Cell Hypoxia/drug effects , Cell Line, Tumor , Cell Survival/drug effects , Erythrocyte Membrane/chemistry , Erythrocyte Membrane/metabolism , Female , Head and Neck Neoplasms/metabolism , Humans , Mice , Mice, Nude , Theranostic Nanomedicine
14.
Comput Struct Biotechnol J ; 19: 3930-3937, 2021.
Article in English | MEDLINE | ID: mdl-34377361

ABSTRACT

Studies of gut microbiota explore their complicated connections between individuals of different characteristics by applying different metrics to abundance data obtained from fecal samples. Although classic metrics are capable to quantify differences between samples, the microbiome of fecal sample is not a good surrogate for the gut microbiome of individuals because the microbial populations of the distal colon does not adequately represent that of the entire gastrointestinal tract. To overcome the deficiency of classic metrics in which the differences can be measured between the samples analyzed, but not the corresponding populations, we propose a metric for representing composition differences in the gut microbiota of individuals. Our investigation shows this metric outperforms traditional measures for multiple scenarios. For gut microbiota in diverse geographic populations, this metric presents more explainable data variance than others, not only in regular variance analysis but also in principle component analysis and partition analysis of biologic characteristics. With time-series data, the metric further presents a strong correlation with the time interval of serial sampling. Our findings suggest that the metric is robust and powerfully detects the intrinsic variations in gut microbiota. The metric holds promise for revealing more relations between gut microbiota and human health.

15.
ACS Omega ; 6(26): 17103-17112, 2021 Jul 06.
Article in English | MEDLINE | ID: mdl-34250367

ABSTRACT

Novel highly stereoselective syntheses of (+)-streptol and (-)-1-epi-streptol starting from naturally abundant (-)-shikimic acid were described in this article. (-)-Shikimic acid was first converted to the common key intermediate by 11 steps in 40% yield. It was then converted to (+)-streptol by three steps in 72% yield, and it was also converted to (-)-1-epi-streptol by one step in 90% yield. In summary, (+)-streptol and (-)-1-epi-streptol were synthesized from (-)-shikimic acid by 14 and 12 steps in 29 and 36% overall yields, respectively.

16.
J Gen Virol ; 102(7)2021 07.
Article in English | MEDLINE | ID: mdl-34292864

ABSTRACT

Hepatitis B virus surface antigen (HBsAg) encoded by the S gene is highly expressed during the replication cycle of hepatitis B virus (HBV). However, the frequent usage of tryptophan in HBsAg, which leads to a high cost of biosynthesis, is inconsistent with the high expression level of this protein. Tryptophan-truncated mutation of HBsAg, that is, a tryptophan to stop codon mutation resulting in truncated HBsAg, might help to maintain its high expression with lower biosynthetic cost. We aimed to investigate the prevalence of tryptophan-truncated S quasispecies in treatment-naïve patients with chronic hepatitis B (CHB) by applying CirSeq as well as a site-by-site algorithm developed by us to identify variants at extremely low frequencies in the carboxyl terminus of HBsAg. A total of 730 mutations were identified in 27 patients with CHB, varying from seven to 56 mutations per sample. The number of synonymous mutations was much higher than that of nonsynonymous mutations in the reverse transcriptase (RT) coding region and vice versa in the S coding region, implying that the evolutionary constraints on the RT and S genes might be different. We showed that 25 (92.6 %) of 27 patients had at least one S-truncated mutation, most of which were derived from tryptophan, indicating a high prevalence of tryptophan-truncated S mutations in treatment-naïve patients with CHB. In terms of the RT gene, 21 (77.8 %) patients had pre-existing drug-resistant mutations, while no truncated mutations were detected. Our findings that tryptophan-truncated S quasispecies and drug-resistant RT mutants were highly prevalent in treatment-naïve patients with CHB provide new insights into the composition of the HBV population, which might help optimize the treatment and management of patients with CHB.


Subject(s)
Hepatitis B Surface Antigens/genetics , Hepatitis B virus/genetics , Hepatitis B, Chronic/virology , Mutation , Tryptophan/genetics , Adolescent , Adult , Algorithms , Amino Acid Motifs , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Codon , Drug Resistance, Viral , Evolution, Molecular , Female , Genes, Viral , Hepatitis B Surface Antigens/chemistry , Hepatitis B virus/chemistry , Hepatitis B virus/drug effects , Hepatitis B, Chronic/drug therapy , Humans , Male , Middle Aged , Quasispecies , RNA-Directed DNA Polymerase/genetics , Sequence Analysis, DNA , Young Adult
17.
Nucleic Acids Res ; 49(11): 6364-6374, 2021 06 21.
Article in English | MEDLINE | ID: mdl-34057476

ABSTRACT

DNA-hydrolyzing DNAs represent an attractive type of DNA-processing catalysts distinctive from the protein-based restriction enzymes. The innate DNA property has enabled them to readily join DNA-based manipulations to promote the development of DNA biotechnology. A major in vitro selection strategy to identify these DNA catalysts relies tightly on the isolation of linear DNAs processed from a circular single-stranded (ss) DNA sequence library by self-hydrolysis. Herein, we report that by programming a terminal hybridization stem in the library, other than the previously reported classes (I & II) of deoxyribozymes, two new classes (III & IV) were identified with the old selection strategy to site-specifically hydrolyze DNA in the presence of Zn2+. Their representatives own a catalytic core consisting of ∼20 conserved nucleotides and a half-life of ∼15 min at neutral pH. In a bimolecular construct, class III exhibits unique broad generality on the enzyme strand, which can be potentially harnessed to engineer DNA-responsive DNA hydrolyzers for detection of any target ssDNA sequence. Besides the new findings, this work should also provide an improved approach to select for DNA-hydrolyzing deoxyribozymes that use various molecules and ions as cofactors.


Subject(s)
DNA, Catalytic/chemistry , DNA, Catalytic/metabolism , Bioengineering , DNA, Catalytic/classification , DNA, Single-Stranded/analysis , Zinc
18.
EBioMedicine ; 68: 103399, 2021 Jun.
Article in English | MEDLINE | ID: mdl-34044218

ABSTRACT

BACKGROUND: Disruption of DNA methylation (DNAm) is one of the key signatures of cancer, however, detailed mechanisms that alter the DNA methylome in cancer remain to be elucidated. METHODS: Here we present a novel integrative analysis framework, called MeLncTRN (Methylation mediated LncRNA Transcriptional Regulatory Network), that integrates genome-wide transcriptome, DNA methylome and copy number variation profiles, to systematically identify the epigenetically-driven lncRNA-gene regulation circuits across 18 cancer types. FINDING: We show that a significant fraction of the aberrant DNAm and gene expression landscape in cancer is associated with long noncoding RNAs (lncRNAs). We reveal distinct types of regulation between lncRNA modulators and target genes that are operative in either only specific cancers or across cancers. Functional studies identified a common theme of cancer hallmarks that lncRNA modulators may participate in. The coupled lncRNA gene interactions via DNAm also serve as markers for classifications of cancer subtypes with different prognoses. INTERPRETATION: Our study reveals a vital layer of DNAm and associated expression regulation for many cancer-related genes and we also provide a valuable database resource for interrogating epigenetically mediated lncRNA-gene interactions in cancer. FUNDING: National Natural Science Foundation of China [91959106, 31871255].


Subject(s)
Computational Biology/methods , DNA Methylation , Neoplasms/genetics , RNA, Long Noncoding/genetics , DNA Copy Number Variations , Databases, Genetic , Epigenesis, Genetic , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Gene Regulatory Networks , Humans , Prognosis , Sequence Analysis, RNA
19.
Biol Open ; 10(2)2021 02 09.
Article in English | MEDLINE | ID: mdl-33495209

ABSTRACT

Human pigmentation is a highly diverse and complex trait among populations and has drawn particular attention from both academic and non-academic investigators for thousands of years. Previous studies detected selection signals in several human pigmentation genes, but few studies have integrated contribution from multiple genes to the evolution of human pigmentation. Moreover, none has quantified selective pressures on human pigmentation over epochs and between populations. Here, we dissect dynamics and differences of selective pressures during different periods and between distinct populations with new approaches. We use genotype data of 19 genes associated with human pigmentation from 17 publicly available datasets and obtain data for 2346 individuals of six representative population groups from across the world. Our results quantify the strength of natural selection on light pigmentation not only in modern Europeans (0.0259/generation) but also in proto-Eurasians (0.00650/generation). Our results also suggest that several derived alleles associated with human dark pigmentation may be under positive directional selection in some African populations. Our study provides the first attempt to quantitatively investigate the dynamics of selective pressures during different time periods in the evolution of human pigmentation.This article has an associated First Person interview with the first author of the article.


Subject(s)
Biological Evolution , Selection, Genetic , Skin Pigmentation , Algorithms , Databases, Genetic , Genetic Variation , Genetics, Population , Humans , Models, Genetic , Multifactorial Inheritance , Polymorphism, Single Nucleotide , Skin Pigmentation/genetics
20.
RSC Adv ; 11(47): 29702-29710, 2021 Sep 01.
Article in English | MEDLINE | ID: mdl-35479555

ABSTRACT

A mild, efficient and eco-friendly method for the oxidation of 1-Bn-DHIQs to 1-Bz-DHIQs without concomitant excessive oxidation of 1-Bz-DHIQs to 1-Bz-IQs is very important for the syntheses of 1-Bz-DHIQ alkaloids and analogues. In this article, we developed a novel Cu(ii)-catalyzed and acid-promoted highly regioselective oxidation of tautomerizable C(sp3)-H bonds adjacent to the C-1 positions of various 1-Bn-DHIQs. It was observed that when 0.2 equiv. of Cu(OAc)2·2H2O was used as the catalyst, 3.0 equiv. of AcOH was used as the additive and air (O2) was used as a clean oxidant, various 1-Bn-DHIQs could be efficiently oxidized to corresponding 1-Bz-DHIQs at 25 °C in DMSO. Especially, almost no concomitant excessive oxidation of 1-Bz-DHIQs to 1-Bz-IQs was observed during the above reaction. In addition, this method was successfully applied in the first total synthesis of the alkaloid canelillinoxine.

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