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The aristolochic acids (AAs), derived from Aristolochia and Asarum species used widely in herbal medicines, are closely associated with liver cancer. The major AA derivatives are aristolochic acid I (AAI) and II (AAII), which can bind DNA covalently to form AA-DNA adducts after metabolic activation in vivo. Among all these AA-DNA adducts, 7-(deoxyadenosine-N6-yl) aristolactam I (dA-AL-I) is the most abundant and persistent DNA lesion in patients. However, the direct evidence indicating AA exposure in human liver cancer is still missing. Here, we analyzed dA-AL-I adduct, the direct biomarker of AAI exposure, by ultra-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UPLC-TQ/MS) in 209 liver cancer patients. Also, DNA samples from mice treated with/without AAI were used as positive and negative controls. dA-AL-I adduct was present in 110 of 209 (52.6%) patients, indicating that these patients were exposed to AAI prior to their clinical investigations and also had a worse prognosis. The relative high AA exposure rate and worse prognosis in our cohort of patients emphasize the significance to increase public awareness to avoid the use of herbal medicine containing AAs or their derivatives.

Background and aims Aristolochic acid (AA) exposure has been statistically associated with human liver cancers. However, direct evidence of AA exposure-induced liver cancer is absent. This study aims to establish a direct causal relationship between AA exposure and liver cancers based on a mouse model and then explores the AA-mediated genomic alterations that could be implicated in human cancers with AA-associated mutational signature. Approach and results We subjected mice, including phosphatase and tensin homolog (Pten)-deficient ones, to aristolochic acid I (AAI) alone or a combination of AAI and CCl4 . Significantly, AAI exposure induced mouse liver cancers, including hepatocellular carcinoma (HCC) and combined HCC and intrahepatic cholangiocarcinoma, in a dose-dependent manner. Moreover, AAI exposure also enhanced tumorigenesis in these CCl4 -treated or Pten-deficient mice. AAI led to DNA damage and AAI-DNA adduct that could initiate liver cancers through characteristic adenine-to-thymine transversions, as indicated by comprehensive genomic analysis, which revealed recurrent mutations in Harvey rat sarcoma virus oncogene. Interestingly, an AA-associated mutational signature was mainly implicated in human liver cancers, especially from China. Moreover, we detected the AAI-DNA adduct in 25.8% (16/62) of paratumor liver tissues from randomly selected Chinese patients with HCC. Furthermore, based on phylogenetic analysis, the characteristic mutations were found in the initiating malignant clones in the AA-implicated mouse and human liver cancers where the mutations of tumor protein p53 and Janus kinase 1 were prone to be significantly enriched in the AA-affected human tumors. Conclusions This study provides evidence for AA-induced liver cancer with the featured mutational processes during malignant clonal evolution, laying a solid foundation for the prevention and diagnosis of AA-associated human cancers, especially liver cancers.

Background A major facilitator superfamily transporter Dehp2 was recently shown to be playing an important role in transport and biodegradation of haloacids in Paraburkholderia caribensis MBA4, and Dehp2 is phylogenetically conserved in Burkholderia sensu lato. Results We designed both Burkholderia sensu stricto-specific and Paraburkholderia-specific qPCR assays based on dehp2 and 16S rRNA, and validated the qPCR assays in 12 bacterial strains. The qPCR assays could detect single species of Burkholderia sensu stricto or Paraburkholderia with high sensitivity and discriminate them in mixtures with high specificity over a wide dynamic range of relative concentrations. At relatively lower cost compared with sequencing-based approach, the qPCR assays will facilitate discrimination of Burkholderia sensu stricto and Paraburkholderia in a large number of samples. Conclusions For the first time, we report the utilization of a haloacids transporter gene for discriminative purpose in Burkholderia sensu lato. This enables not only quick decision on proper handling of putative pathogenic samples in Burkholderia sensu stricto group but also future exploitation of relevant species in Paraburkholderia group for haloacids biodegradation purposes. Electronic supplementary material The online version of this article (10.1186/s12866-019-1411-0) contains supplementary material, which is available to authorized users.

Beckground：The series of human Metastatic Hepatocellular Carcinoma (MHCC) cell lines MHCC97 with a continuously enlarged metastatic capabilities have been widely used as a metastatic model in cancer research. However, their genomic features have not been thoroughly investigated so far. This study aims to reveal the genetic events that could drive metastatic clonal evolution through uncovering their genomic aberrations, together with methylomic and transcriptomic alteration.Results： We investigated the karyotypes on MHCC97L and HCCLM6 HCC cell lines with lower and the highest metastatic capability respectively, and interrogated their complete repertoire of genomic features by performing whole genome sequencing (WGS), whole exome sequencing (WES) and single-nucleotide polymorphism (SNP) genotyping. Mutations including single nucleotide variant (SNV), copy number variation (CNV) and structural variant (SV) were called. In addition, the methylome profiles were analyzed via Illumina Infinium HumanMethylation450 Bead Chip and the transcriptome profiles were analyzed via RNA sequencing (RNA-Seq). The karyotypic examination revealed that MHCC97L cells are more heterogenous than the HCCLM6 cells. The clonal analysis on the two cell lines revealed that a minor subclone with the mutations predisposed to metastatic potential within the MHCC97L become the dominant one within the HCCLM6 cell population. The amplification of CAV1, CAV2 and MET, together with STAT1 deep deletion and DELC1 promoter hypermethylation could be the earlier key drivers occurred in the MHCC97L cells. Subsequently, extra CCL4, CCL26 and TWIST2 amplification, along with the c.1061T>G in SMAD5 and c.1373A>G in RNF169 mutations and deregulatory promoter methylation in the HCCLM6 cells, aggravate the metastatic capability.Conclusions： Our results revealed that HCCLM6 cells might be derived from a minor subclone within the MHCC97L cell population, where the genetic events, including MET, CAV1 and CAV2 amplification, together with the extra mutations, amplification and deregulatory promoter methylation of some genes, drive the clonal expansion and evolution of those cells with the metastatic capability.

Brg1/SMARCA4 serves as the ATPase and the helicase catalytic subunit for the multi-component SWI/SNF chromatin remodeling complex, which plays a pivotal role in governing chromatin structure and gene transcription. However, the upstream signaling pathways regulating Brg1 protein stability and its physiological contribution to carcinogenesis remain largely elusive. Here we report that Brg1 is a bona fide ubiquitin substrate of SCFFBW7. We reveal that CK1δ phosphorylates Brg1 at Ser31/Ser35 residues to facilitate the binding of Brg1 to FBW7, leading to ubiquitination-mediated degradation. In keeping with a tumor suppressive role of FBW7 in human gastric cancer, we find an inverse correlation between FBW7 and Brg1 expression in human gastric cancer clinical samples. Mechanistically, we find that stabilization of Brg1 in gastric cancer cells suppresses E-cadherin expression, subsequently promoting gastric cancer metastasis. Hence, this previously unknown FBW7/Brg1 signaling axis provides the molecular basis and the rationale to target Brg1 in FBW7-compromised human gastric cancers.

Aristolochic acid (AA) derived from traditional Chinese herbal remedies has recently been statistically associated with human liver cancer; however, the causal relationships between AA and liver cancer and the underlying evolutionary process of AA-mediated mutagenesis during tumorigenesis are obscure. Here, we subjected mice, including Pten-deficient ones, to aristolochic acid I (AAI) alone or a combination of AAI and carbon tetrachloride (CCl4), which may induce liver injury. Significantly, AAI promoted the development of liver cancer, including hepatocellular carcinoma and intrahepatic cholangiocarcinoma, in a dose-dependent manner, and it increased the incidence of liver cancer, together with CCl4 or Pten deficiency. AAI could lead to DNA damage and AAI-DNA adducts that initiate liver cancer via characteristic A>T transversions, as indicated by the comprehensive genomic analysis, which revealed recurrent mutations in Hras and some genes encoding components of the Ras/Raf, PI3K, Notch, Hippo, Wnt, DNA polymerase family and the SWI/SNF complex, some of which are also often found in human liver cancer. Mutational signature analysis across human cancer types revealed that the AA-related dominant signature was especially implicated in liver cancer in China, based on very stringent criteria derived from the animal cancer form, in which mutations of TP53 and JAK1 are prone to be significantly enriched. Interestingly, AAI-mediated characteristic A>T mutations were the earliest genetic event driving malignant subclonal evolution in mouse and human liver cancer. In general, this study provides documented evidence for AA-induced liver cancer with featured mutational processes during malignant clonal evolution, laying a solid foundation for the prevention and diagnosis of AA-associated human cancers, especially liver cancer.

As the rapid-changing inTrichodermataxonomy, an efficient identification ofTrichodermaspecies is an urgent issue forTrichoderma-based research. In this study, based on the current taxonomy ofTrichoderma, we constructed curated databases including 338 ITS sequences, 435 TEF1 sequences, 415 RPB2 sequences and 28 phenotypic characters. In addition, a polyphasic identification system (PIST) was developed. Within PIST, the resolution ability of molecular and phenotype characters could be combined for species identification in a step-by-step way. Compared with other identification systems, the involvedTrichodermaspecies were extended from 88 to 252 species and 175 from 188 testedTrichodermaspecies could be identified within PIST. In most tested cases, three nucleotide markers and phenotypic characters showed improved identification performance. The TEF1 sequences have superior resolution than other characters.ImportanceThe genusTrichodermais important to human society with a wide application in industry, agriculture and environment bio-remediation. Thus, a quick and accurate identification ofTrichodermaspp. is paramount since it is usually the first step to conduct aTrichoderma-based scientific research and is an obstruction especially for those researchers as nematologist, chemists, nutritionist and the like, lacking of taxonomic knowledge of fungi.

Background The differentiation and maturation trajectories of fetal liver stem/progenitor cells (LSPCs) are not fully understood at single-cell resolution, and a priori knowledge of limited biomarkers could restrict trajectory tracking. Results We employed marker-free single-cell RNA-Seq to characterize comprehensive transcriptional profiles of 507 cells randomly selected from seven stages between embryonic day 11.5 and postnatal day 2.5 during mouse liver development, and also 52 Epcam-positive cholangiocytes from postnatal day 3.25 mouse livers. LSPCs in developing mouse livers were identified via marker-free transcriptomic profiling. Single-cell resolution dynamic developmental trajectories of LSPCs exhibited contiguous but discrete genetic control through transcription factors and signaling pathways. The gene expression profiles of cholangiocytes were more close to that of embryonic day 11.5 rather than other later staged LSPCs, cuing the fate decision stage of LSPCs. Our marker-free approach also allows systematic assessment and prediction of isolation biomarkers for LSPCs. Conclusions Our data provide not only a valuable resource but also novel insights into the fate decision and transcriptional control of self-renewal, differentiation and maturation of LSPCs. Electronic supplementary material The online version of this article (10.1186/s12864-017-4342-x) contains supplementary material, which is available to authorized users.

Supplemental figures. Figure S1. Single-cell qPCR analysis of mouse fetal liver cells. Figure S2. Quality control of single-cell RNA-Seq analysis of mouse fetal liver cells. Figure S3. Grouping of fetal liver cells from E11.5 to E16.5. Figure S4. Validation of single-cell RNA-Seq results by immunofluorescence and qPCR. Figure S5. Dynamic developmental process of mouse LSPCs at single-cell resolution. Figure S6. Comparison of the gene expression patterns of some marker genes between mouse and human for cholangiocyte and hepatoblast. Figure S7. Assessment and prediction of LSPC biomarkers. Figure S8. Validation of some markers for LSPC isolation via flow cytometric analysis. (PDF 2895Â kb)