Characterization of mutants and splice variants of hepatitis B virus isolated from South African black hepatocellular carcinoma patients

Ph.D. thesis, Faculty of Health Sciences,University of the Witwatersrand, 2009Hepatitis B virus (HBV) infection is endemic in Africa. As many as 98% of black Africans are infected during their lives and about 10% (65 million) have chronic HBV infection, which is the cause of 70-80% of all hepatocellular carcinoma (HCC) cases. Despite this high prevalence of HBV and the high incidence of HCC in Africa, relatively few complete HBV genomes from African HCC cases have been deposited in international data bases. In order to gain a clearer understanding of the role of genetic variants and mutants in the development of HCC, the complete genomes of HBV isolated from southern African HCC patients were amplified and molecularly characterized. HBV DNA was extracted from the serum forty HBsAgpositive HCC patients. Twenty six complete genomes were successfully amplified, cloned and sequenced from nine HCC patients. Phylogenetic analyses of the complete genomes and the individual open reading frames of HBV isolates from the HCC patients, led to the classification of all the isolates within subgenotype A1. No isolates belonging to subgenotype A2 and genotype D were identified, even though these genotypes/subgenotypes have been shown to circulate in South Africa. Three patients contained the uncommon combination of serological subtype ayw1 in the subgenotype A1 strain. This combination has been found previously in South Africa and the Phillipines. Seventy-eight percent of the patients carried HBV strains with the double basic core promoter (BCP) mutation (1762T/1764A), previously shown to reduce HBeAg expression. Furthermore, complete genome sequence analysis has revealed a complex combination of mutations, which include at least three or five of these residues 1753C1762T1764A1766T1768A1809T1812T occurring as the dominant HBV strains isolated from 5/9 HCC patients. These mutations have previously been shown to regulate gene expression at various levels, to enhance viral replication and simultaneously decrease HBeAg expression. All five HBV genomes isolated from one patient contained novel complex BCP rearrangements, which introduced 2 HNF1 and 1 putative HNF3 transcription factor binding sites. These mutations can enhance viral replication and simultaneously abolish HBeAg expression at a transcriptional level. Furthermore, truncated core proteins would be expressed from 4/5 isolates and none would express wild-type HBx. Several mutations were identified in the pre-S/S genes of 2/5 isolates, which would result in the expression of novel 3’ truncated medium surface proteins (MHBst) and large surface proteins (LHBst). The majority of the mutations would contribute to hepatocyte pathogenesis and transformation by activating cell proliferating pathways. Two patients also contained rare HBV variants not previously identified in HBV strains from southern Africa. These included an HBV splice variant and a poly (dA) variant from patient 10 and patient 6, respectively. These variants occurred in combination with other isolates within the respective patients. The envelope genes were characterised in a total of 18 HCC patients, the pre-S gene of HBV contained deletions in 72% of the patients. Deletions across pre- S1/pre-S2, pre-S2 initiation codon mutations with internal deletions, and S gene nonsense mutations were prevalent. Mutated envelope proteins have been shown to accumulate within the hepatocyte endoplasmic reticulum (ER) and are a characteristic histopathological hallmark of HCC known as ground glass hepatocytes. HBV induced ER stress has been shown to dysregulate several cell cycle regulatory pathways, which contribute to HCC. In addition several novel LHBst and MHBst have been described. These potential transactivators require further investigation. The HBV mutations described in this study have been associated with increased risk for HCC. Despite the obvious heterogeneity HBV displays within and between patients, there are common characteristics shared between the HBV variants which emerge during the development of HCC. These include the BCP and pre-C (1753C1762T1764A1766T1768A1809T1812T) mutations and the pre-S/S mutations. These mutations are able to affect HBV replication and gene expression, and may work synergistically to promote liver dysfunction and HCC

The gene-rich genome of the scallop Pecten maximus.

BACKGROUND: The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management. FINDINGS: Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species. CONCLUSIONS: The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid

The genome sequence of the Eurasian river otter, Lutra lutra Linnaeus 1758 [version 1; peer review: 2 approved]

We present a genome assembly from an individual male Lutra lutra (the Eurasian river otter; Vertebrata; Mammalia; Eutheria; Carnivora; Mustelidae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled

The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758.

We present a genome assembly from an individual female Aquila chrysaetos chrysaetos (the European golden eagle; Chordata; Aves; Accipitridae). The genome sequence is 1.23 gigabases in span. The majority of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the W and Z sex chromosomes

The genome sequence of the Eurasian river otter, Lutra lutra Linnaeus 1758.

We present a genome assembly from an individual male Lutra lutra (the Eurasian river otter; Vertebrata; Mammalia; Eutheria; Carnivora; Mustelidae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled

The genome sequence of the brown trout, Salmo trutta Linnaeus 1758

publishedVersio

Computational approaches for network-based integrative multi-omics analysis

Advances in omics technologies allow for holistic studies into biological systems. These studies rely on integrative data analysis techniques to obtain a comprehensive view of the dynamics of cellular processes, and molecular mechanisms. Network-based integrative approaches have revolutionized multi-omics analysis by providing the framework to represent interactions between multiple different omics-layers in a graph, which may faithfully reflect the molecular wiring in a cell. Here we review network-based multi-omics/multi-modal integrative analytical approaches. We classify these approaches according to the type of omics data supported, the methods and/or algorithms implemented, their node and/or edge weighting components, and their ability to identify key nodes and subnetworks. We show how these approaches can be used to identify biomarkers, disease subtypes, crosstalk, causality, and molecular drivers of physiological and pathological mechanisms. We provide insight into the most appropriate methods and tools for research questions as showcased around the aetiology and treatment of COVID-19 that can be informed by multi-omics data integration. We conclude with an overview of challenges associated with multi-omics network-based analysis, such as reproducibility, heterogeneity, (biological) interpretability of the results, and we highlight some future directions for network-based integration

Exploring South Africa’s southern frontier: A 20-year vision for polar research through the South African National Antarctic Programme

Antarctica, the sub-Antarctic islands and surrounding Southern Ocean are regarded as one of the planet’s last remaining wildernesses, ‘insulated from threat by [their] remoteness and protection under the Antarctic Treaty System’1 . Antarctica encompasses some of the coldest, windiest and driest habitats on earth. Within the Southern Ocean, sub-Antarctic islands are found between the Sub-Antarctic Front to the north and the Polar Front to the south. Lying in a transition zone between warmer subtropical and cooler Antarctic waters, these islands are important sentinels from which to study climate change.2 A growing body of evidence3,4 now suggests that climatically driven changes in the latitudinal boundaries of these two fronts define the islands’ short- and long-term atmospheric and oceanic circulation patterns. Consequently, sub-Antarctic islands and their associated terrestrial and marine ecosystems offer ideal natural laboratories for studying ecosystem response to change.5 For example, a recent study6 indicates that the shift in the geographical position of the oceanic fronts has disrupted inshore marine ecosystems, with a possible impact on top predators. Importantly, biotic responses are variable as indicated by different population trends of these top predators.7,8 When studied collectively, these variations in species’ demographic patterns point to complex spatial and temporal changes within the broader sub-Antarctic ecosystem, and invite further examination of the interplay between extrinsic and intrinsic drivers

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy