Keng Po Lai

A positive role for c-Abl in Atm and Atr activation in DNA damage response

DNA damage triggers Atm- and/or Atr-dependent signaling pathways to control cell cycle progression, apoptosis, and DNA repair. However, how Atm and Atr are activated is not fully understood. One of the downstream targets of Atm is non-receptor tyrosine kinase c-Abl, which is phosphorylated and activated by Atm. The current view is that c-Abl relays pro-apoptotic signals from Atm to p73 and p53. Here we show that c-Abl deficiency resulted in a broad spectrum of defects in cell response to genotoxic stress, including activation of Chk1 and Chk2, activation of p53, nuclear foci formation, apoptosis, and DNA repair, suggesting that c-Abl might also act upstream of the DNA damage-activated signaling cascades in addition to its role in p73 and p53 regulation. Indeed, we found that c-Abl is required for proper activation of both Atm and Atr. c-Abl is bound to the chromatin and shows enhanced interaction with Atm and Atr in response to DNA damage. c-Abl can phosphorylate Atr on Y291 and Y310 and this phosphorylation appears to have a positive role in Atr activation under genotoxic stress. These findings suggest that Atm-mediated c-Abl activation in cell response to double-stranded DNA breaks might facilitate the activation of both Atm and Atr to regulate their downstream cellular events.

S6K1 is a multifaceted regulator of Mdm2 that connects nutrient status and DNA damage response

p53 mediates DNA damage‐induced cell‐cycle arrest, apoptosis, or senescence, and it is controlled by Mdm2, which mainly ubiquitinates p53 in the nucleus and promotes p53 nuclear export and degradation. By searching for the kinases responsible for Mdm2 S163 phosphorylation under genotoxic stress, we identified S6K1 as a multifaceted regulator of Mdm2. DNA damage activates mTOR‐S6K1 through p38α MAPK. The activated S6K1 forms a tighter complex with Mdm2, inhibits Mdm2‐mediated p53 ubiquitination, and promotes p53 induction, in addition to phosphorylating Mdm2 on S163. Deactivation of mTOR‐S6K1 signalling leads to Mdm2 nuclear translocation, which is facilitated by S163 phosphorylation, a reduction in p53 induction, and an alteration in p53‐dependent cell death. These findings thus establish mTOR‐S6K1 as a novel regulator of p53 in DNA damage response and likely in tumorigenesis. S6K1–Mdm2 interaction presents a route for cells to incorporate the metabolic/energy cues into DNA damage response and links the aging‐controlling Mdm2–p53 and mTOR‐S6K pathways.

Deep sequencing of small RNA transcriptome reveals novel non-coding RNAs in hepatocellular carcinoma.

BACKGROUND & AIMS Small non-coding RNAs (ncRNA) are increasingly recognized to play important roles in tumorigenesis. With the advent of deep sequencing, efforts have been put forth to profile the miRNome in a number of human malignancies. However, information on ncRNA in hepatocellular carcinoma (HCC), especially the non-microRNA transcripts, is still lacking. METHODS Small RNA transcriptomes of two HCC cell lines (HKCI-4 and HKCI-8) and an immortalized hepatocyte line (MIHA) were examined using Illumina massively parallel sequencing. Dysregulated ncRNAs were verified in paired HCC tumors and non-tumoral livers (n=73) by quantitative reverse transcription-polymerase chain reaction. Clinicopathologic correlations and in vitro functional investigations were further carried out. RESULTS The combined bioinformatic and biological analyses showed the presence of ncRNAs and the involvement of a new PIWI-interacting RNA (piRNA), piR-Hep1, in liver tumorigenesis. piR-Hep1 was found to be upregulated in 46.6% of HCC tumors compared to the corresponding adjacent non-tumoral liver. Silencing of piR-Hep1 inhibited cell viability, motility, and invasiveness, with a concomitant reduction in the level of active AKT phosphorylation. In the analysis of miRNA, we showed for the first time, the abundant expression of miR-1323 in HCC and its distinct association in tumors arising from a cirrhotic background. Furthermore, miR-1323 overexpression in cirrhotic HCC correlated with poorer disease-free and overall survivals of patients (p<0.009). CONCLUSIONS Our study demonstrated the value of next-generation sequencing in dissecting the ncRNome in cancer. The comprehensive definition of transcriptome unveils virtually all types of ncRNAs and provides new insight into liver carcinogenetic events.

Identification and Expression Profiling of MicroRNAs in the Brain, Liver and Gonads of Marine Medaka (Oryzias melastigma) and in Response to Hypoxia

The marine medaka (Oryzias melastigma) has been increasingly used as a fish model for detecting environmental stresses and chemical contaminants in the marine environment. Recent mammalian studies have shown that environmental stresses can alter the expression profiles of microRNAs (miRNAs), leading to transgenerational effects. Here, we use high-throughput Illumina RNA sequencing (RNA-Seq) for miRNA transcriptome analysis of brain, liver, and gonads from sexually mature male and female marine medaka. A total of 128,883,806 filtered sequence reads were generated from six small RNA libraries, identifying a total of 2,125,663 non-redundant sequences. These sequences were aligned and annotated to known animal miRNAs (miRBase) using the BLAST method. A total of 223 distinct miRNA types were identified, with the greatest number expressed in brain tissue. Our data suggested that 55 miRNA types from 34 families are common to all tested tissues, while some of the miRNAs are tissue-enriched or sex-enriched. Quantitative real-time PCR analysis further demonstrated that let-7a, miR-122, and miR-9-3p were downregulated in hypoxic female medaka, while miR-2184 was specifically upregulated in the testis of hypoxic male fish. This is the first study to identify miRNAs in O. melastigma using small RNA deep sequencing technology. Because miRNA expression is highly conserved between marine medaka and other vertebrates, marine medaka may serve as a good model for studies on the functional roles of miRNAs in hypoxia stress response and signaling in marine fish.

Histone deacetylase inhibitor-induced cellular apoptosis involves stanniocalcin-1 activation

Our previous studies have demonstrated the involvement of HIF-1 and p53 in the regulation of stanniocalcin-1 (STC1) gene transcription in human cancer cells. In this study, we reported that the treatment of human colon adenoma HT29 cells with a histone deacetylase (HDAC) inhibitor (i.e. trichostatin A, TSA) induced both cellular apoptosis and STC1 expression. The activation of STC1 expression was also observed in other TSA-treated human cancer cells (i.e. SKOV3, CaCo-2, Jurkat and CNE-2 cells). STC1 mRNA was rapidly induced within 4 h in TSA-treated HT29 cells, and was found to be transcriptionally regulated and was independent of new protein synthesis as revealed by ActD and CHX treatment respectively. The induction was correlated with increased cellular levels of acetyl histone H3 and H4 and acetyl NFkappaB. Chromatin immunoprecipitation (ChIP) assay showed the increased binding of acetyl histone H3 and H4 to STC1 promoter in the TSA-treated cells. A cotreatment of HT29 cells with a NFkappaB inhibitor (parthenolide) significantly inhibited the TSA-induced cellular levels of acetyl NFkappaB p65 and abolished the stimulation of STC1 gene expression. ChIP assay also demonstrated that TSA treatment increased while TSA/parthenolide cotreatment decreased NFkappaB p65 binding to STC1 gene promoter. In the STC1-luciferase promoter construct (1 kb) study, the data implied that the promoter can be activated by TSA treatment. Interestingly, the promoter region contains 2 putative NFkappaB binding sites. Consistent with the STC1mRNA expression data, TSA/parthenolide cotreatment also significantly inhibited the TSA-induced STC1 promoter-driven luciferase activity. Importantly, TSA-induced apoptotic process was found to be significantly reduced by the silencing of STC1 expression. This is the first study to show that histone hyper-acetylation and the recruitment of activated NFkappaB stimulated STC1 gene expression. In addition, our results support the notion that STC1 is a pro-apoptotic factor.

Hypoxia causes transgenerational impairments in reproduction of fish

Hypoxia is amongst the most widespread and pressing problems in aquatic environments. Here we demonstrate that fish (Oryzias melastigma) exposed to hypoxia show reproductive impairments (retarded gonad development, decrease in sperm count and sperm motility) in F1 and F2 generations despite these progenies (and their germ cells) having never been exposed to hypoxia. We further show that the observed transgenerational reproductive impairments are associated with a differential methylation pattern of specific genes in sperm of both F0 and F2 coupled with relevant transcriptomic and proteomic alterations, which may impair spermatogenesis. The discovered transgenerational and epigenetic effects suggest that hypoxia might pose a dramatic and long-lasting threat to the sustainability of fish populations. Because the genes regulating spermatogenesis and epigenetic modifications are highly conserved among vertebrates, these results may also shed light on the potential transgenerational effects of hypoxia on other vertebrates, including humans.

Overexpression of ZFX confers self-renewal and chemoresistance properties in hepatocellular carcinoma.

Zinc finger protein X‐linked (ZFX) is a zinc finger protein of Zfy family, which is highly conserved in vertebrates. This transcriptional regulator is not only highly expressed in embryonic stem cells (ESC) and hematopoietic stem cells, but is also upregulated in a number of human cancers where it is functional related to cell proliferation and survival. Hepatocellular carcinoma (HCC) is highly aggressive cancer that commonly resistant to most chemotherapies and displays stemness characteristics. In this study, we examined the expression of ZFX in HCC and its possible functional implications in liver tumorigenesis. Quantitative RT‐PCR analysis showed common overexpressions of ZFX in 51.8% HCC tumors when compared with their adjacent nonmalignant liver (n = 43/83; p = 0.004). Inline with the pluripotency role of ZFX, we found silencing of ZFX readily inhibited self‐renewal capability (p = 0.0022), colony formation ability (p < 0.0001) and cell proliferation (p < 0.0001) through G0/G1 cell cycle arrest of HCC cells (p = 0.0038). In addition, suppression of ZFX sensitized HCC cells to chemotherapeutic agent cisplatin (p < 0.0001). Further investigations suggested that ZFX bind on the promoter of two important mediators, namely Nanog and SOX‐2, activating their expressions in HCC (p < 0.0001). Moreover, in vivo xenograft study demonstrated that overexpression of ZFX would promote the tumor growth (p = 0.031). Taken together, our results show, for the first time, commonly overexpressions of ZFX in HCC, where it likely contributes to the stemness and pluripotent behavior of this highly malignant cancer.

Bisphenol A alters gut microbiome: Comparative metagenomics analysis.

Mounting evidence has shown that an alteration of the gut microbiota is associated with diet, and plays an important role in animal health and metabolic diseases. However, little is known about the influence of environmental contaminants on the gut microbial community. Bisphenol A (BPA), which is widely used for manufacturing plastic products, has recently been classified as an environmental obesogen. Although many studies have demonstrated the metabolic-disrupting effects of BPA on liver and pancreatic functions, the possible effects of this synthetic compound on the metabolic diversity of the intestinal microbiota is unknown. Using 16S rRNA gene sequencing analysis on caecum samples of CD-1 mice, the present study aimed to test the hypothesis that dietary BPA intake may influence the gut microbiota composition and functions, an important attributing factor to development of the metabolic syndrome. A high-fat diet (HFD) and high-sucrose diet (HSD) were included as the positive controls for comparing the changes in the intestinal microbial profiles. Our results demonstrated a significant reduction of species diversity in the gut microbiota of BPA-fed mice. Alpha and beta diversity analyses showed that dietary BPA intake led to a similar gut microbial community structure as that induced by HFD and HSD in mice. In addition, comparative analysis of the microbial communities revealed that both BPA and a HFD favored the growth of Proteobacteria, a microbial marker of dysbiosis. Consistently, growth induction of the family Helicobacteraceae and reduction of the Firmicutes and Clostridia populations were observed in the mice fed BPA or a HFD. Collectively, our study highlighted that the effects of dietary BPA intake on the shift of microbial community structure were similar to those of a HFD and HSD, and revealed microbial markers for the development of diseases associated with an unstable microbiota.

Dioxin-like components in human breast milk collected from Hong Kong and Guangzhou

The H4IIE rat hepatoma cell line was employed as a cell model to screen 7-ethoxyresorufin O-deethylase (EROD)-TCDD equivalents (EROD-TEQ) of human breast milk samples collected from Hong Kong and Guangzhou, China. The screening methods employed a 96-well plate spectrofluorometer-EROD assay. For cell-line validation, our results demonstrated a dose-dependent increase in the Ah receptor-mediated response (i.e., CYP1A1 mRNA and EROD) of the cells upon exposure to a number of known Ah receptor agonists, including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), 2,3,7,8-tetrachlorodibenzothiophene, benzo[a]pyrene, and beta-naphthaflavone. TCDD induced CYP1A1 mRNA and EROD was in a close positive correlation (r=0.98). For the screening of dioxin-like compounds, breast milk samples collected during lactation weeks 3-5 were used. One hundred (from Hong Kong) and 48 (from Guangzhou) breast milk samples were assayed, of which 65% and 68% of the samples, respectively, showed detectable dioxin-like activities using the H4IIE cell EROD screening method. For sixty-five samples from Hong Kong the mean EROD-TEQ values ranged from 58.1 to 96.5 pg/g of milk fat for those aged 21-36 years while 32 samples from Guangzhou had mean values of 98.8-202.1 pg/g of milk fat. In comparisons of the EROD-TEQ values for different age groups from both cities, there were no significant differences (P<0.05). However, the mean and median EROD-TEQ values of the Guangzhou population were in general higher than those of the Hong Kong population. The results of the present study indicate that it is feasible to use the H4IIE cell-line as a model for screening dioxin-like compounds in human breast milk. In addition, the method is rapid and cost-effective, particularly for a routine and high-throughput sample screening analysis, compared to the costly and time-intensive chemical analytical techniques.

GEF‐H1 over‐expression in hepatocellular carcinoma promotes cell motility via activation of RhoA signalling

The interstitial chromosome (chr.) 1q21‐q22 region is frequently amplified in human cancers, where it has been reported to carry prognostic significance for patients. We attempted to delineate chr. 1q21‐q22 for affected gene(s) in hepatocellular carcinoma (HCC) by array‐CGH and detected copy number gains of ρ‐guanine nucleotide exchange factor‐H1 (GEF‐H1) as most significant event. Gene expression evaluation in the HCC cohort indicated common up‐regulations of GEF‐H1 in 64% tumours compared to adjacent non‐tumoural liver (64/100; paired t‐test p < 0.0001). Moreover, GEF‐H1 over‐expressions correlated with microvascular invasion and advanced‐stage tumours (p < 0.05). High GEF‐H1 levels also predict shorter disease‐free and overall survival of HCC patients (p < 0.03). Functional knock‐down of GEF‐H1 by RNAi indicated marked reduction in cell invasion through matrigel and an inhibition of cell migration (p < 0.035), but an effect on cell viability was not apparent. More interestingly, a mesenchymal‐epithelial transition (MET) was readily observed in GEF‐H1 knock‐down cells, where a concomitant re‐expression of epithelial markers (E‐cadherin and cytokeratin 18) and cell adhesion proteins (α‐catenin and γ‐catenin) was found but down‐regulation of mesenchymal features (N‐cadherin, vimentin and fibronectin). This phenotype was accompanied by reduced filamentous actin polymerizations and diminution of the stress fibre formation. In addition, reduced active form of GTP‐RhoA, together with its downstream effectors, including cleaved ROCK1 and phosphorylated MLC2, were also detected in GEF‐H1‐depleted cells. Taken together, our findings underscore a potent oncogenic role for GEF‐H1 in promoting the metastatic potentials of HCC, possibly through activation of RhoA signalling and the EMT phenomenon. Copyright