BackgroundThe 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.ResultsWe 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.ConclusionsOur 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 materialThe online version of this article (10.1186/s12864-017-4342-x) contains supplementary material, which is available to authorized users.

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.

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.

Maturation for survival Although cells with defects in DNA replication usually die under stress conditions, some cells acquire new mutations and survive. Sun et al . identified an error-prone, stress-induced Okazaki fragment maturation pathway that induces tandem duplications and enables the survival of cells that have defects in removing the 5′ RNA-DNA flap during DNA replication. In these cells, stress conditions activate DUN1 signaling and induce conversion of the 5′ flap to a 3′ flap that can form secondary structures and be extended and ligated to the downstream DNA fragment, generating alternative duplication mutations similar to the ones in human cancers. The revealed information is analogous to the mechanism in cancer cell evolution and drug resistance. —DJ

14Aristolochic acid (AA) derived from traditional Chinese herbal remedies 15 has recently been statistically associated with human liver cancer; however, 16 the causal relationships between AA and liver cancer and the underlying 17 evolutionary process of AA-mediated mutagenesis during tumorigenesis 18 are obscure. Here, we subjected mice, including Pten-deficient ones, to 19 aristolochic acid I (AAI) alone or a combination of AAI and carbon 20 tetrachloride (CCl 4 ), which may induce liver injury. Significantly, AAI 21 promoted the development of liver cancer, including hepatocellular 22 carcinoma and intrahepatic cholangiocarcinoma, in a dose-dependent 23 manner, and it increased the incidence of liver cancer, together with CCl 4 24 or Pten deficiency. AAI could lead to DNA damage and AAI-DNA adducts 25 that initiate liver cancer via characteristic A>T transversions, as indicated 26 by the comprehensive genomic analysis, which revealed recurrent 27 mutations in Hras and some genes encoding components of the Ras/Raf, 28 PI3K, Notch, Hippo, Wnt, DNA polymerase family and the SWI/SNF 29 complex, some of which are also often found in human liver cancer. 30 Mutational signature analysis across human cancer types revealed that the 31 AA-related dominant signature was especially implicated in liver cancer in 32 China, based on very stringent criteria derived from the animal cancer form, 33 in which mutations of TP53 and JAK1 are prone to be significantly 34 enriched. Interestingly, AAI-mediated characteristic A>T mutations were 35 the earliest genetic event driving malignant subclonal evolution in mouse 36 and human liver cancer. In general, this study provides documented 37 evidence for AA-induced liver cancer with featured mutational processes 38 during malignant clonal evolution, laying a solid foundation for the 39 prevention and diagnosis of AA-associated human cancers, especially liver 40 cancer. 42 Aristolochic acid (AA) is present in plants in the genera Aristolochia, 43 Bragantia, Asarum and others 1 , which have been widely used in traditional 44 Chinese herbal remedies. AA is one of the most potent carcinogens known 45 to man, belonging to the Group I human carcinogens classified the by 46 International Agency for Research on Cancer (IARC). Aristolochic acid I 47 (AAI) and Ⅱ (AAII) are the major components of the AA mixture contained 48 in the plant extract of Aristolochia species 2 . AA is a genotoxic carcinogen 49 because its metabolite can bind purines to form AA-DNA adducts, 50 aristolactam (AL)-DNA adducts (dA-AL and dG-AL), which are specific 51 markers of exposure to aristolochic acids and induce DNA mutations with 52 characteristic adenine-to-thymine (A>T) transversions in vitro and in 53 vivo 2,3 . 54 The dA-AL-I (7-(deoxyadenosin-N6-yl) aristolactam I) adducts 55 induced by AAI can show long-term persistence in renal tissue 4 , which 56 may have led to the occurrence of aristolochic acid nephropathy (AAN) in 57 Belgian women who had taken weight-reducing pills containing 58 Aristolochia f...

Down syndrome (DS) is the most common form of intellectual disability associated with central nervous system abnormalities and results from an extra complete or partial copy of human chromosome 21. However, whether DNA hydroxymethylation is perturbed in a specific gene associated with DS phenotypes, or the alteration of DNA hydroxymethy-lation results in changes of gene expression in DS remains unidentified. The current study mapped 5‑methylcytosine and 5‑hydroxymethylcytosine at CpG islands of the PR domain containing 8 (PRDM8) in the peripheral blood of 16 DS and 19 normal samples by oxidative bisulfite-pyrosequencing. Furthermore, the association of the expression levels of the two transcripts and epigenetic modification in different genomic contexts of PRDM8 was analyzed. The results demonstrated hypermethylation and hyperhydroxymethylation at the internal promoter of PRDM8 in DS, and significantly increased the expression of PRDM8 transcript variant 2 in the DS patients (median 3.9 vs. 2.04; P=0.016), accompanied by a positive correlation between the expression of two PRDM8 transcripts and hydroxymethylation at the corresponding external and internal promoters in patients, although not in the controls. A similar association was observed between the expression of transcript variant 1 and intragenic methylation of PRDM8. Taken together, the results of the present study suggest a critical role for DNA hydroxymethylation and methylation in regulating abnormal PRDM8 overexpression in DS.

BackgroundA 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.ResultsWe 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.ConclusionsFor 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 materialThe 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.