Genetic and epigenetic changes in fibrosis-associated hepatocarcinogenesis in mice: Genetic and epigenetic changes in mouse hepatocarcinogenesis

Hepatocellular carcinoma (HCC) is one of the most prevalent cancers and is rising in incidence worldwide. The molecular mechanisms leading to the development of HCC are complex and include both genetic and epigenetic events. To determine the relative contribution of these alterations in liver tumorigenesis, we evaluated epigenetic modifications at both global and gene specific levels, as well as the mutational profile of genes commonly altered in liver tumors. A mouse model of fibrosis-associated liver cancer that was designed to emulate cirrhotic liver, a prevailing disease state observed in most humans with HCC, was used. Tumor and non-tumor liver samples from B6C3F1 mice treated with N-nitrosodiethylamine (DEN; a single ip injection of 1 mg/kg at 14 days of age) and carbon tetrachloride (CCl4; 0.2 ml/kg, 2 times/week ip starting at 8 weeks of age for 14 weeks), as well as corresponding vehicle control animals, were analyzed for genetic and epigenetic alterations. H-ras, Ctnnb1, and Hnf1α genes were not mutated in tumors in mice treated with DEN+CCl4. In contrast, the increased tumor incidence in mice treated with DEN+CCl4 was associated with marked epigenetic changes in liver tumors and non-tumor liver tissue, including demethylation of genomic DNA and repetitive elements, a decrease in histone 3 lysine 9 trimethylation (H3K9me3), and promoter hypermethylation and functional down-regulation of Riz1, a histone lysine methyltransferase tumor suppressor gene. Additionally, the reduction in H3K9me3 was accompanied by increased expression of long interspersed nucleotide elements (LINE) 1 and short interspersed nucleotide elements (SINE) B2, which is an indication of genomic instability. In summary, our results suggest that epigenetic events, rather than mutations in known cancer-related genes, play a prominent role in increased incidence of liver tumors in this mouse model of fibrosis-associated liver cancer

Assessing Vulnerability and Risk to Livelihoods in River Deltas Socio-ecological Systems: Alignment of the GDRI With Global Frameworks’ Indicators

Disasters have significant impacts on the progress towards achieving the Sustainable Development Goals (SDGs). However, the interlinkage between sustainable development and disaster risk reduction is not considered enough in risk assessment tools. A greater alignment with global frameworks would ease the monitoring while increasing the capacity to address data availability issues for indicator-based assessments. To bridge this gap, we use the Global Delta Risk Index (GDRI), which is composed of multiple components to assess risks to livelihoods: hazards, vulnerability, and exposure of social-ecological systems. The modular library of indicators of the GDRI has been further aligned with the Sustainable Development Goals (SDG) and the Sendai Framework for Disaster and Risk Reduction (SFDRR). To improve the accuracy of the risk assessment, the list of indicators has been weighted and scored through consultation with stakeholders. This research presents the initial results of a multi-hazard risk assessment that encompasses SDG and SFDRR indicators in three Asian river deltas: Ganges-Brahmaputra-Meghna, Mekong and Red River. This work aims at better informing risk management and supporting delta-level interventions to influence progress towards sustainability and resilience of river deltas

Aligning the Global Delta Risk Index with SDG and SFDRR global frameworks to assess risk to socio-ecological systems in river deltas

River deltas globally are highly exposed and vulnerable to natural hazards and are often over-exploited landforms. The Global Delta Risk Index (GDRI) was developed to assess multi-hazard risk in river deltas and support decision-making in risk reduction interventions in delta regions. Disasters have significant impacts on the progress towards the Sustainable Development Goals (SDGs). However, despite the strong interlinkage between disaster risk reduction and sustainable development, global frameworks are still developed in isolation and actions to address them are delegated to different institutions. Greater alignment between frameworks would both simplify monitoring progress towards disaster risk reduction and sustainable development and increase capacity to address data gaps in relation to indicator-based assessments for both processes. This research aims at aligning the GDRI indicators with the SDGs and the Sendai Framework for Disaster and Risk Reduction (SFDRR). While the GDRI has a modular indicator library, the most relevant indicators for this research were selected through a delta-specific impact chain designed in consultation with experts, communities and stakeholders in three delta regions: the Red River and Mekong deltas in Vietnam and the Ganges–Brahmaputra–Meghna (GBM) delta in Bangladesh and India. We analyse how effectively the 143 indicators for the GDRI match (or not) the SDG and SFDRR global frameworks. We demonstrate the interconnections of the different drivers of risk to better inform risk management and in turn support delta-level interventions towards improved sustainability and resilience of these Asian mega-deltas

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Human cancer cells retain modest levels of enzymatically active matriptase only in extracellular milieu following induction of zymogen activation.

The type 2 transmembrane serine protease matriptase is broadly expressed in human carcinomas and hematological cancers. The proteolytic activity of matriptase is a potential target of drugs and imaging probes. We assessed the fate of active matriptase following the induction of matriptase zymogen activation. Exposing eight human carcinoma cells to pH 6.0 buffer induced robust matriptase zymogen activation followed by rapid inhibition of the nascent active matriptase by hepatocyte growth factor activator inhibitor (HAI)-1. Consequently, no enzymatically active matriptase was detected in these cells. Some active matriptase is, however, rapidly shed to the extracellular milieu by these carcinoma cells. The lack of cell-associated active matriptase and the shedding of active matriptase were also observed in two hematological cancer lines. Matriptase shedding is correlated closely with the induction of matriptase activation, suggesting that matriptase activation and shedding are kinetically coupled. The coupling allows a proportion of active matriptase to survive HAI-1 inhibition by rapid shedding from cell surface. Our study suggests that cellular free, active matriptase is scarce and might not be an effective target for in vivo imaging and drug development

Aloe vera Non-Decolorized Whole Leaf Extract-Induced Large Intestinal Tumors in F344 Rats Share Similar Molecular Pathways with Human Sporadic Colorectal Tumors

ABSTRACT Aloe vera is one of the most commonly used botanicals for various prophylactic and therapeutic purposes. Recently, NTP/NCTR has demonstrated a dose-dependent increase in large intestinal tumors in F344 rats chronically exposed to Aloe barbadensis Miller (Aloe vera) non-decolorized whole leaf extract (AVNWLE) in drinking water. The morphological and molecular pathways of AVNWLE-induced large intestinal tumors in the F344 rats were compared to human colorectal cancer (hCRC) literature. Defined histological criteria were used to compare AVNWLEinduced large intestinal tumors with hCRC. The commonly mutated genes (Kras, Ctnnb1, and Tp53) and altered signaling pathways (MAPK, WNT, and TGF-b) important in hCRC were evaluated within AVNWLE-induced large intestinal tumors. Histological evaluation of the large intestinal tumors indicated eight of twelve adenomas (Ads) and four of twelve carcinomas (Cas). Mutation analysis of eight Ads and four Cas identified point mutations in exons 1 and 2 of the Kras gene (two of eight Ads, two of four Cas), and in exon 2 of the Ctnnb1 gene (three of eight Ads, one of four Cas). No Tp53 (exons 5-8) mutations were found in Ads or Cas. Molecular pathways important in hCRC such as MAPK, WNT, and TGF-b signaling were also altered in AVNWLE-induced Ads and Cas. In conclusion, the AVNWLE-induced large intestinal tumors in F344 rats share several similarities with hCRC at the morphological and molecular levels

Human prostate cancer cell do not retain free, enzymatically active matriptase.

<p><i>A</i>. The human prostate cancer cells, DU145 (DU), PC3 (PC3), and LNCaP (LN) were exposed to pH 6.0 (or control) buffer to induce matriptase activation. Cell lysates from pH 6-exposed cells (A, lanes 2, 4, and 6) and the non-activation control cells (N, lanes 1, 3, and 5) were analyzed for total matriptase species (left) using the mAb M24 and activated matriptase using the mAb M69 (right). <i>B</i>, <i>C</i>, and <i>D</i>. The human prostate cancer cells, DU145 (<i>B</i>), PC3 (<i>C</i>), and LNCaP (<i>D</i>) were treated with pH 6.0 buffer to induce matriptase activation. After neutralization, the combination of the cell and the shed fractions (combine), the cells fractions alone (cell), and the shed fraction alone (shed) were analyzed for tryptic activity. RFU stands for relative fluorescent units.</p

Matriptase shedding is tightly coupled with zymogen activation.

<p><i>A.</i> HaCaT human keratinocytes were treated with pH 6.0 buffer (A) or PBS as a non-activation control (N) for 20 min. The cell lysates (Cell) and the shed fractions (Shed) were analyzed for total matriptase (Total MTP) using the mAb M24 and activated matriptase (Activated MTP) using mAb M69. <i>B.</i> HaCaT human keratinocytes were treated with pH 6.0 buffer to induce matriptase activation and shed fractions were collected at the indicated times thereafter and analyzed for matriptase using the mAb M24.</p

MCF breast cancer cells don't retain enzymatically active matriptase.

<p><i>A.</i> MCF7 human breast cancer cells were incubated with a pH 6 buffer to induce matriptase zymogen activation (<i>A.</i> right, Act.) or with the pH 6 buffer supplemented with 150 mM NaCl as a non-activation control (<i>A.</i> left, Non-act.). Cell lysates were prepared, and samples retained for analysis (lanes 1 and 4). The remaining cell lysates were subjected to immunodepletion with the active matriptase-specific mAb M69 immobilized on Sepharose beads to deplete the activated matriptase, predominantly the 120-kDa complex (lanes 2 and 5, and D). The antibody-bound activated matriptase was recovered by a pH 2.4 buffer elution followed by pH neutralization (Lane 3, E). These samples were then analyzed for matriptase species by SDS-PAGE (without boiling the samples or using reducing agents) and Western blot using the total matriptase mAb M24. <i>B.</i> The cells, the immunodepleted lysates, and the eluates were assayed tryptic activity by cleavage of a synthetic fluorogenic substrate with Arg as P1 site. For the tryptic assay, the cells remained intact in the absence of Triton X-100. NA stands for non-activation; L for loading of immunodepletion, D for immunodepleted fraction; E for eluted fraction; A for activation; RFU for relative fluorescent unit.</p