Technical and Regulatory Considerations for Taking Liquid Biopsy to the Clinic: Validation of the JAX PlasmaMonitor

The standard of care in oncology has been genomic profiling of tumor tissue biopsies for the treatment and management of disease, which can prove to be quite challenging in terms of cost, invasiveness of procedure, and potential risk for the patient. As the number of available drugs in oncology continues to increase, so too does the demand for technologies and testing applications that can identify genomic alterations targetable by these new therapies. Liquid biopsies that use a blood draw from the diseased patient may offset the many disadvantages of the invasive procedure. However, as with any new technology or finding in the clinical field, the clinical utility of an analytical test such as that of the liquid biopsy has to be established. Here, we review the clinical testing space for liquid biopsy offerings and elucidate the technical and regulatory considerations to develop such an assay, using our recently validated PlasmaMonito

Classical Swine Fever Virus p7 Protein Interacts with Host Protein CAMLG and Regulates Calcium Permeability at the Endoplasmic Reticulum

We have previously shown that Classical Swine Fever Virus (CSFV) p7 is an essential nonstructural protein with a viroporin activity, a critical function in the progression of virus infection. We also identified p7 domains and amino acid residues critical for pore formation. Here, we describe how p7 specifically interacts with host protein CAMLG, an integral ER transmembrane protein involved in intracellular calcium release regulation and signal response generation. Detection of interaction as well as the identification of p7 areas mediating interaction with CAMLG was performed by yeast two-hybrid. p7-CAMLG interaction was further confirmed by confocal microscopy in eukaryotic cells, co-expressing both proteins. Mutant forms of p7 having substituted native residues identified as mediating interaction with CAMLG showed a decreased co-localization compared with the native forms of p7. Furthermore, it is shown that native p7, but not the mutated forms of p7 that fail to interact with CAMLG, efficiently mediates calcium permeability in the ER. Interestingly, viruses harboring some of those mutated forms of p7 have been previously shown to have a significantly decreased virulence in swine.ARS/USDA-University of Connecticut SCA# 58-1940-1-190 and ARS/USDA-University of the Basque Country NACA#8064-32000-056-18S

Association of the Host Immune Response with Protection Using a Live Attenuated African Swine Fever Virus Model

Citation: Carlson, J.; O’Donnell, V.; Alfano, M.; Velazquez Salinas, L.; Holinka, L.G.; Krug, P.W.; Gladue, D.P.; Higgs, S.; Borca, M.V. Association of the Host Immune Response with Protection Using a Live Attenuated African Swine Fever Virus Model. Viruses 2016, 8, 291.African swine fever (ASF) is a lethal hemorrhagic disease of swine caused by a double-stranded DNA virus, ASF virus (ASFV). There is no vaccine to prevent the disease and current control measures are limited to culling and restricting animal movement. Swine infected with attenuated strains are protected against challenge with a homologous virulent virus, but there is limited knowledge of the host immune mechanisms generating that protection. Swine infected with Pretoriuskop/96/4 (Pret4) virus develop a fatal severe disease, while a derivative strain lacking virulence-associated gene 9GL (Pret4Δ9GL virus) is completely attenuated. Swine infected with Pret4Δ9GL virus and challenged with the virulent parental virus at 7, 10, 14, 21, and 28 days post infection (dpi) showed a progressive acquisition of protection (from 40% at 7 dpi to 80% at 21 and 28 dpi). This animal model was used to associate the presence of host immune response (ASFV-specific antibody and interferon (IFN)-γ responses, or specific cytokine profiles) and protection against challenge. With the exception of ASFV-specific antibodies in survivors challenged at 21 and 28 dpi, no association between the parameters assessed and protection could be established. These results, encompassing data from 65 immunized swine, underscore the complexity of the system under study, suggesting that protection relies on the concurrence of different host immune mechanisms

Adult digit ratio (2D:4D) is not related to umbilical cord androgen or estrogen concentrations, their ratios or net bioactivity

Background: Ratio of second digit length to fourth digit length (2D:4D) has been extensively used in human and experimental research as a marker of fetal sex steroid exposure. However, very few human studies have measured the direct relationship between fetal androgen or estrogen concentrations and digit ratio. Aims: We investigated the relationships between both androgen and estrogen concentrations in umbilical cord blood and digit ratio in young adulthood. In addition we calculated measures of total serum androgen and total estrogen bioactivity and investigated their relationship to digit ratio. Study design: Prospective cohort study. Subjects: An unselected subset of the Western Australian Pregnancy Cohort (Raine) Study (159 female; 182 male). Outcome measures: Cord serum samples were collected immediately after delivery. Samples were assayed for androgen (testosterone, Δ4-androstenedione, dehydroepiandrosterone) and estrogen (estrone, estradiol, estriol, estetrol) concentrations using liquid-chromatography mass-spectrometry. Digit ratio measurements were taken from hand photocopies at age 19–22 years. Results: For both males and females, there were no significant correlations between digit ratio and any androgen or estrogen concentrations considered individually, the testosterone to estradiol ratio, total androgen bioactivity measure or ratio of androgen to estrogen bioactivity (all p > .05). In males, but not females, total estrogen bioactivity was negatively correlated with left hand digit ratio (r = − .172, p = .02), but this relationship was no longer significant when adjusted for variables known to affect sex steroid concentrations in cord blood. Conclusions: Our findings indicate that digit ratio is not related to fetal androgens or estrogens at late gestation

Development of an Improved Live Attenuated Antigenic Marker CSF Vaccine Strain Candidate with an Increased Genetic Stability

Classical Swine Fever Virus (CSFV) is an extremely contagious, hemorrhagic and often fatal disease of pigs that causes serious socioeconomic impact on countries which experience outbreaks or are endemically infected. Current control measures utilized for CSFV are contingent upon the epidemiological status of the inflicted area and entail either prophylactic vaccination or non-vaccination, “stamping out”, protocol with the elimination of infected herds and culling of animals on neighboring farms. This latter practice results in less than satisfactory consequences, although once thought to be the answer to eradication of CSFV from a region, “stamping out” results in tremendous economic losses as well as the ethical objection to the potential killing of millions of healthy pigs. Marker vaccines also referred to as DIVA vaccines because they allow for differentiation between naturally infected and vaccinated animals (DIVA), could complement or replace the “stamping out” strategy. The use of a DIVA vaccine with an accompanying diagnostic test would make mass vaccination of susceptible pigs during and outbreak possible thereby preventing the rapid spread of the virus while allowing for identification of CSFV infected animal through serological surveillance. With the advent of reverse genetic technology, it is now possible to rationally design a CSFV vaccine that contains such markers. Recently, we reported the development of a live attenuated CSFV strain with two antigenic markers, named Flag T4v. During the vaccine assessment process, Flag T4v showed evidence of reverting back to the virulent phenotype of wild type CSFV. Analysis of the genome sequence from the recovered revertant virus revealed the presence of four non synonymous substitutions and a deletion of one of the antigenic epitopes compared to the parental Flag T4v genome. In order to improve the genetic stability of Flag T4v, the nucleotide codon sequence in these regions was modified as much as possible from its original sequence without compromising the wild type amino acid sequence by taking advantage of codon redundancy in an attempt to make viral reversion more difficult while maintaining both viral attenuation and reactivity of the antigenic markers. The newly developed virus, Flag T4Gv, was shown to be stably attenuated when assessed in a reversion to virulence test. In addition, Flag T4Gv was also shown to possess similar efficacy of Flag T4v in terms of protecting swine at early and late times post vaccination

Interaction of Structural Glycoprotein E2 of Classical Swine Fever Virus with Protein Phosphatase 1 Catalytic Subunit Beta (PPP1CB)

Classical swine fever virus (CSFV) E2 protein, the major virus structural glycoprotein, is an essential component of the viral envelope. E2 is involved in virus absorption, induction of a protective immune response and is critical for virulence in swine. Using the yeast two-hybrid system, we identified protein phosphatase 1 catalytic subunit beta (PPP1CB), which is part of the Protein Phosphatase 1 (PP1) complex, as a specific binding host partner for E2. We further confirmed the occurrence of this interaction in CSFV-infected swine cells by using two independent methodologies: Co-immunoprecipitation and Proximity Ligation Assay. In addition, we demonstrated that pharmacological activation of the PP1 pathway has a negative effect on CSFV replication while inhibition of the PP1 pathway or knockdown of PPP1CB by siRNA had no observed effect. Overall, our data suggests that the CSFV E2 and PPP1CB protein interact in infected cells, and that activation of the PP1 pathway decreases virus replication

Interaction of CSFV E2 protein with swine host factors as detected by yeast two-hybrid system.

E2 is one of the envelope glycoproteins of pestiviruses, including classical swine fever virus (CSFV) and bovine viral diarrhea virus (BVDV). E2 is involved in several critical functions, including virus entry into target cells, induction of a protective immune response and virulence in swine. However, there is no information regarding any host binding partners for the E2 proteins. Here, we utilized the yeast two-hybrid system and identified fifty-seven host proteins as positive binding partners which bound E2 from both CSFV and BVDV with the exception of two proteins that were found to be positive for binding only to CSFV E2. Alanine scanning of CSFV E2 demonstrated that the binding sites for these cellular proteins on E2 are likely non-linear binding sites. The possible roles of the identified host proteins are discussed as the results presented here will be important for future studies to elucidate mechanisms of host protein-virus interactions during pestivirus infection. However, due to the limitations of the yeast two hybrid system, the proteins identified is not exhaustive and each interaction identified needs to be confirmed by independent experimental approaches in the context of virus-infected cells before any definitive conclusion can be drawn on relevance for the virus life cycle

Technical and Regulatory Considerations for Taking Liquid Biopsy to the Clinic: Validation of the JAX PlasmaMonitor Assay

The standard of care in oncology has been genomic profiling of tumor tissue biopsies for the treatment and management of disease, which can prove to be quite challenging in terms of cost, invasiveness of procedure, and potential risk for the patient. As the number of available drugs in oncology continues to increase, so too does the demand for technologies and testing applications that can identify genomic alterations targetable by these new therapies. Liquid biopsies that use a blood draw from the diseased patient may offset the many disadvantages of the invasive procedure. However, as with any new technology or finding in the clinical field, the clinical utility of an analytical test such as that of the liquid biopsy has to be established. Here, we review the clinical testing space for liquid biopsy offerings and elucidate the technical and regulatory considerations to develop such an assay, using our recently validated PlasmaMonitor TM test