Clinical Value of Multiomics-Based Biomarker Signatures in Inflammatory Bowel Diseases:Challenges and Opportunities

Inflammatory bowel diseases (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), are complex and heterogeneous diseases characterized by a multifactorial etiology, therefore demanding a multimodal approach to disentangle the main pathophysiological components driving disease onset and progression. Adoption of a systems biology approach is increasingly advocated with the advent of multi-omics profiling technologies, aiming to improve disease classification, to identify disease biomarkers and to accelerate drug discovery for patients with IBD. However, clinical translation of multi-omics-derived biomarker signatures is lagging behind, since there are several obstacles that need to be addressed in order to realize clinically useful signatures. Multi-omics integration and IBD-specific identification of molecular networks, standardization and clearly defined outcomes, strategies to tackle cohort heterogeneity, and external validation of multi-omics-based signatures are critical aspects. While striving for personalized medicine in IBD, careful consideration of these aspects is however needed to adequately match biomarker targets (e.g. the gut microbiome, immunity or oxidative stress) with their corresponding utilities (e.g. early disease detection, endoscopic and clinical outcome). Theory-driven disease classifications and predictions are still governing clinical practice, while this could be improved by adopting an unbiased, data-driven approach relying on molecular data structures integrated with patient and disease characteristics. In the foreseeable future, the main challenge will lie in the complexity and impracticality of implementing multi-omics-based signatures into clinical practice. Still, this could be achieved by developing easy-to-use, robust and cost-effective tools incorporating omics-derived predictive signatures and through the design and execution of prospective, longitudinal, biomarker-stratified clinical trials

Chromosomal targeting of replicating plasmids in the yeast Hansenula polymorpha

Using an optimized transformation protocol we have studied the possible interactions between transforming plasmid DNA and the Hansenula polymorpha genome. Plasmids consisting only of a pBR322 replicon, an antibiotic resistance marker for Escherichia coli and the Saccharomyces cerevisiae LEU2 gene were shown to replicate autonomously in the yeast at an approximate copy number of 6 (copies per genome equivalent). This autonomous behaviour is probably due to an H. polymorpha replicon-like sequence present on the S. cerevisiae LEU2 gene fragment. Plasmids replicated as multimers consisting of monomers connected in a head-to-tail configuration. Two out of nine transformants analysed appeared to contain plasmid multimers in which one of the monomers contained a deletion. Plasmids containing internal or flanking regions of the genomic alcohol oxidase gene were shown to integrate by homologous single or double cross-over recombination. Both single- and multi-copy (two or three) tandem integrations were observed. Targeted integration occurred in 1-22 % of the cases and was only observed with plasmids linearized within the genomic sequences, indicating that homologous linear ends are recombinogenic in H. polymorpha. In the cases in which no targeted integration occurred, double-strand breaks were efficiently repaired in a homology-independent way. Repair of double-strand breaks was precise in 50-68% of the cases. Linearization within homologous as well as nonhomologous plasmid regions stimulated transformation frequencies up to 15-fold

Experimental Infection of Rabbits with Newly Excysted Metacercariae of Japanese Fasciola Sp. and American Fasciola Hepatica by Portal Vein Route

日本産およびアメリカ産脱嚢幼肝蛭を家兎の門脈内に移入・感染させ,各種変化について検索した。幼肝蛭は感染後3時間で肝実質内に認められ,その後感染経過に伴い肝病変は漸次増大した。アメリカ産肝蛭では胆管への定着と虫卵排出も認められた。また,日本産肝蛭についても感染後虫体は漸次成長することが認められた。沈降抗体の出現時期は,感染後21-28日であった。幼肝蛭は血行によって肝臓に達してもよく発育し,感染が成立することが明らかとなった。 / Rabbits were experimentally infected with newly excysted metacercariae of the Japanese Fasciola sp. and the American Fasciola hepatica by portal vein route. At early stages of the infection, histopathological changes of the liver of rabbits infected with either F. sp. or F. hepatica were tract lesions characterized by haemorrhages, necrosis, cellular infiltration, and so on. The tract lesions grew larger and more numerous with the progress of the infection. At the 77th day of infection, increases of connective tissue around the intrahepatic bile ducts and in thickness of the wall of the bile ducts were noted. Precipitating antibodies were first detected at the 28th and 21st days of infection in sera of the rabbits infected with F. sp. and F. hepatica, respectively. Fluke eggs were first detected at the 63rd day in feces of the rabbits infected with F. hepatica, and were not detected even at the 77th day in the case of F. sp. Fluke eggs recovered from the infected rabbits were measured the maximum length of 15.9mm and 16.2mm, for F. sp. and F. hepatica, respectively. The infection of rabbits with F. sp. and F. hepatica by the vein route was successful

How does hepatic lipid accumulation lead to lipotoxicity in non-alcoholic fatty liver disease?

BACKGROUND: Non-alcoholic fatty liver disease (NAFLD), characterized as excess lipid accumulation in the liver which is not due to alcohol use, has emerged as one of the major health problems around the world. The dysregulated lipid metabolism creates a lipotoxic environment which promotes the development of NAFLD, especially the progression from simple steatosis (NAFL) to non-alcoholic steatohepatitis (NASH). PURPOSEAND AIM: This review focuses on the mechanisms of lipid accumulation in the liver, with an emphasis on the metabolic fate of free fatty acids (FFAs) in NAFLD and presents an update on the relevant cellular processes/mechanisms that are involved in lipotoxicity. The changes in the levels of various lipid species that result from the imbalance between lipolysis/lipid uptake/lipogenesis and lipid oxidation/secretion can cause organellar dysfunction, e.g. ER stress, mitochondrial dysfunction, lysosomal dysfunction, JNK activation, secretion of extracellular vesicles (EVs) and aggravate (or be exacerbated by) hypoxia which ultimately lead to cell death. The aim of this review is to provide an overview of how abnormal lipid metabolism leads to lipotoxicity and the cellular mechanisms of lipotoxicity in the context of NAFLD