Background Aberrant DNA methylation occurs frequently in cancer. The aim of this study was to identify novel methylation markers in lung cancer in Xuanwei, China, through integrated genome-wide DNA methylation and gene expression studies. Methods Differentially methylated regions (DMRs) and differentially expressed genes (DEGs) were detected on 10 paired lung cancer tissues and noncancerous lung tissues by methylated DNA immunoprecipitation combined with microarray (MeDIP-chip) and gene expression microarray analyses, respectively. Integrated analysis of DMRs and DEGs was performed to screen out candidate methylation-related genes. Both methylation and expression changes of the candidate genes were further validated and analyzed. Results Compared with normal lung tissues, lung cancer tissues expressed a total of 6,899 DMRs, including 5,788 hypermethylated regions and 1,111 hypomethylated regions. Integrated analysis of DMRs and DEGs identified 45 tumor-specific candidate genes: 38 genes whose DMRs were hypermethylated and expression was downregulated, and 7 genes whose DMRs were hypomethylated and expression was upregulated. The methylation and expression validation results identified 4 candidate genes (STXBP6, BCL6B, FZD10, and HSPB6) that were significantly hypermethylated and downregulated in most of the tumor tissues compared with the noncancerous lung tissues. Conclusions This integrated analysis of genome-wide DNA methylation and gene expression in lung cancer in Xuanwei revealed several genes regulated by promoter methylation that have not been described in lung cancer before. These results provide new insight into the carcinogenesis of lung cancer in Xuanwei and represent promising new diagnostic and therapeutic targets.
Tubercidin (TBN), an adenosine analog with potent antimycobacteria and antitumor bioactivities, highlights an intriguing structure, in which a 7-deazapurine core is linked to the ribose moiety by an N-glycosidic bond. However, the molecular logic underlying the biosynthesis of this antibiotic has remained poorly understood. Here, we report the discovery and characterization of the TBN biosynthetic pathway from Streptomyces tubercidicus NBRC 13090 via reconstitution of its production in a heterologous host. We demonstrated that TubE specifically utilizes phosphoribosylpyrophosphate and 7-carboxy-7-deazaguanine for the precise construction of the deazapurine nucleoside scaffold. Moreover, we provided biochemical evidence that TubD functions as an NADPH-dependent reductase, catalyzing irreversible reductive deamination. Finally, we verified that TubG acts as a Nudix hydrolase, preferring Co2+ for the maintenance of maximal activity, and is responsible for the tailoring hydrolysis step leading to TBN. These findings lay a foundation for the rational generation of TBN analogs through synthetic biology strategy, and also open the way for the target-directed search of TBN-related antibiotics.
Non-heme Fe2+ and 2-oxoglutarate (Fe2+/2OG)-dependent halogenases are a promising platform for biocatalytic halogenations owing to their ability to functionalize unactivated sp3 C–H bonds. To date, however, relatively few Fe2+/2OG-dependent halogenases have been identified that act on small stand-alone molecules. AdaV, a member of the carrier-protein-independent halogenases, selectively modifies the unactivated C2′ of the dAMP in 2′-chloropentostatin biosynthesis. In this study, we report the X-ray crystallographic structures of the AdaV complex with its substrate and various AdaV variants. The combined crystallographic and biochemical data clarify the molecular mechanism of AdaV for its substrate specificity and stereoselectivity. Moreover, we have engineered the AdaVQ203A/AdaVV269A variant to produce a mixture of halogenated and hydroxylated products and further engineered AdaVQ203A&V269A&G196D/E variants to merely keep hydroxylation activity. Remarkably, we have also proposed a dual-controlling mechanism for AdaV catalysis, in which G196 plays an important role in halogenation by creating an iron coordination site for chloride binding, while Q203&V269 serve to orient the Fe(III)-OH intermediate to constrain the oxygen rebounding onto the radical substrate. These results greatly expand the enzymatic repertoire regarding halogenated natural product biosynthesis and open the way for the rational and rapid discovery of more AdaV-related enzymes as toolkits for further synthetic biology uses.
Objective To investigate the efficacy and toxicity of fludarabine combined with intermediate-dose cytarabine on relapsed refractory acute myeloid leukemia (AML).Methods Forty-nine patients with relapsed or refractory AML were divided into modified FLAG group and CAG group.Modified FLAG group:G-CSF 200 μg·m-2·d-1 on days 0-5; fludarabine 30 mg·m-2·d-1 on days 1-5; Ara-C 1 g·m-2·d-1on days 1-5.CAG group:Ara-C 10 mg·m-2·12 h-1 on days 1-14,aclarubicin 20 mg/d on days 1-4,G-CSF 200 μg·m-2·d-1 on days 0-14.Results In modified FLAG group,the complete response (CR) rate was 43 ％(10/23) and the partial response (PR) rate was 21％ (5/23),so the overall response(OR) rate was 64 ％.However,in CAG group,CR rate and PR rate were 23 ％ (6/26) and 19 ％ (5/26),respectively,and OR rate was 42 ％.There was statistical difference between the two groups (P ＜ 0.05).The main toxicities of these two groups were myelosupression and infection.The infection rate were 70 ％ (16/23) in modified FLAG group and 54 ％ (14/26) in CAG group.There was no statistical difference between the two groups (P ＞ 0.05).Conclusions Fludarabine and intermediate-dose cytarabine are effective in treating relapsed refractory AML.The treatment produces the significant effect in strengthening control of infection measures and shortening the time of bone marrow suppression.CAG regimen has less adverse effects and could be utilized in stratified and personalized treatment for individuals with relapsed refractory AML.
Key words:
Leukemia, myeloid, acute; Fludarabine; Cytarabine; Efficacy
Abstract Epidemic diseases and antibiotic resistance are urgent threats to global health, and human is confronted with an unprecedented dilemma to conquer them by expediting development of new natural product related drugs. C -nucleoside antibiotics, a remarkable group of microbial natural products with diverse biological activities, feature a heterocycle base linked with a ribosyl moiety via an unusual C -glycosidic bond, and have played significant roles in healthcare and for plant protection. Elucidating how nature biosynthesizes such a group of antibiotics has provided the basis for engineered biosynthesis as well as targeted genome mining of more C -nucleoside antibiotics towards improved properties. In this review, we mainly summarize the recent advances on the biosynthesis of C -nucleoside antibiotics, and we also tentatively discuss the future developments on rationally accessing C -nucleoside diversities in a more efficient and economical way via synthetic biology strategies.
FOR-A and PRF-A are C -nucleoside antibiotics known for their unusual chemical structures and remarkable biological activities. Deciphering the enzymatic mechanism for the construction of a C -nucleoside scaffold during FOR-A/PRF-A biosynthesis will not only expand the biochemical repertoire for novel enzymatic reactions but also permit target-oriented genome mining of FOR-A/PRF-A-related C -nucleoside antibiotics. Moreover, the availability of FOR-A/PRF-A biosynthetic gene clusters will pave the way for the rational generation of designer FOR-A/PRF-A derivatives with enhanced/selective bioactivity via synthetic biology strategies.
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