Panel Of Subtypes Research Articles

ONC201(TIC10) Induces TRAIL and Cell Death In Preclinical Models Of Pediatric Lymphoma

Background The outcome for pediatric Non-Hodgkin Lymphomas (NHL) using conventional treatment standards is still inferior compared to other childhood malignancies, particularly in advanced stage and relapsed disease. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is an endogenous protein that induces apoptosis selectively in cancer cells by binding to death receptors. Previous TRAIL-targeting strategies have had limited potential due to unfavorable biodistribution and pharmacokinetics. Our laboratory identified a small molecule, ONC201(TIC10), which induces p53 independent TRAIL gene transcription and TRAIL-dependent cell death and overcomes the most critical efficacy-limiting drug properties of available TRAIL-based therapies. Selective advantages of ONC201 include longer half-life, stimulation of TRAIL and death receptor expression, stability, lower production cost, and ability to cross the intact blood-brain barrier. Our lab has reported that ONC201 is orally active, has potent anti-tumor effects in several preclinical animal cancer models including prolonging survival in lymphoma bearing Eu-myc transgenic mice, exhibits synergy with several antitumor agents (Allen JE et al, Sci Transl Med.,2013) and is being developed into a first-in-man study in advanced cancer patients in early 2014. Objective Assess monoagent activity and mechanism of action of ONC201 in pediatric lymphoma. Derive preclinical rationale to evaluate ONC201 as a novel targeted therapy for pediatric lymphoma as a monoagent or in combination in clinical trials. Methods A diverse sub-type panel of human lymphoma cell lines [Ramos, Raji and Daudi (Burkitt's lymphoma); Karpas299 (T-cell NHL); UPN2 and Granta (Mantle Cell lymphoma)] was selected to assess lymphoma sensitivity to ONC201. Luminescent cell viability assay was used to generate inhibition curves at 72 hours post-treatment with ONC201 yielding IC50's. Caspase-based Apoptosis assay was performed on cells treated with low micromolar dose ranges of ONC201 and data generated via flow cytometry at 72 hours post-treatment. Surface TRAIL expression was analyzed via FACS (Fluorescence-activated cell-sorting) at 60 hours post-treatment. Inhibition of ONC201-induced Apoptosis was demonstrated using Pan-caspase inhibitor (Z-VAD-FMK) at 72 hour post-treatment. Western blot analysis of representative cell lines from the three sub-types (Ramos, Karpas299 and UPN2) at 48 hour post-treatment with ONC201 for AKT and ERK was used to validate the mechanism of induction of apoptosis of lymphoma cells by ONC201. Results Cell viability assays demonstrated sharp dose-response curves at 72 hours post-treatment with ONC201. Quantitative analysis of these relationships yielded ONC201 IC50 values in the range of 1.3 to 5.06 uM, which is comparable to reported activity of ONC201 in other tumor types. Sub-G1 analysis by flow cytometry revealed significant levels of apoptosis at 72 hours post-treatment in a dose-dependent manner (Fig.1) with substantial increase in sub-G1 content (range 1.8-fold to 4.15-fold) in comparison with that of untreated cells. Treatment with ONC201 revealed increase in surface TRAIL expression in a dose dependent manner across the representative cell lines. ONC201 induced apoptosis was demonstrably inhibited using Pan-caspase inhibitor. Western blot analysis of representative cell lines from the three sub-types (Ramos, Karpas299 and UPN2) at 48 hour post-treatment with ONC201 confirmed dual inhibition of Akt and ERK as potential mechanism of induction of apoptosis of lymphoma cells by ONC201. Conclusion ONC201 is a first-in-class therapy that has apoptotic activity in human lymphoma cells at low micromolar concentrations and promotes up-regulation of TRAIL. ONC201 is promising as a monoagent and may be enhanced by combination with approved therapies to improve the standard of care for pediatric NHL. We are currently assessing in vitro synergistic tumor cell-killing by standard chemotherapeutic agents used to treat lymphoma in combination with ONC201. We plan to translate our work in vivo using xenograft mice models. The ultimate goal of this project is to provide the preclinical rationale for a potential phase Ib trial of ONC201 as a combination therapy in pediatric lymphoma. Disclosures: Allen: ONCOCEUTICS: Employment; ONCOCEUTICS: Equity Ownership. El-Deiry:ONCOCEUTICS: Equity Ownership.

Complexes of neutralizing and non-neutralizing affinity matured Fabs with a mimetic of the internal trimeric coiled-coil of HIV-1 gp41.

A series of mini-antibodies (monovalent and bivalent Fabs) targeting the conserved internal trimeric coiled-coil of the N-heptad repeat (N-HR) of HIV-1 gp41 has been previously constructed and reported. Crystal structures of two closely related monovalent Fabs, one (Fab 8066) broadly neutralizing across a wide panel of HIV-1 subtype B and C viruses, and the other (Fab 8062) non-neutralizing, representing the extremes of this series, were previously solved as complexes with 5-Helix, a gp41 pre-hairpin intermediate mimetic. Binding of these Fabs to covalently stabilized chimeric trimers of N-peptides of HIV-1 gp41 (named (CCIZN36)3 or 3-H) has now been investigated using X-ray crystallography, cryo-electron microscopy, and a variety of biophysical methods. Crystal structures of the complexes between 3-H and Fab 8066 and Fab 8062 were determined at 2.8 and 3.0 Å resolution, respectively. Although the structures of the complexes with the neutralizing Fab 8066 and its non-neutralizing counterpart Fab 8062 were generally similar, small differences between them could be correlated with the biological properties of these antibodies. The conformations of the corresponding CDRs of each antibody in the complexes with 3-H and 5-Helix are very similar. The adaptation to a different target upon complex formation is predominantly achieved by changes in the structure of the trimer of N-HR helices, as well as by adjustment of the orientation of the Fab molecule relative to the N-HR in the complex, via rigid-body movement. The structural data presented here indicate that binding of three Fabs 8062 with high affinity requires more significant changes in the structure of the N-HR trimer compared to binding of Fab 8066. A comparative analysis of the structures of Fabs complexed to different gp41 intermediate mimetics allows further evaluation of biological relevance for generation of neutralizing antibodies, as well as provides novel structural insights into immunogen design.

Cross‐neutralization studies with salmonid alphavirus subtype 1–6 strains: results with sera from experimental studies and natural infections

The serological reactivity between strains of each of the six currently genetically defined subtypes of salmonid alphavirus (SAV) was examined by comparison of homologous and heterologous virus neutralization titres on sera from experimentally infected fish. With the exception of the level of SAV subtype 6 neutralization by heterologous sera, good cross-neutralization was detected between all subtypes, albeit with variation in geometric mean titres when each subtype-specific serum set was tested against the panel of virus subtypes. A similar pattern was evident with field sera, except that heterologous neutralization of the SAV6 strain was more evident. In only 23% of available pairwise comparisons was the homologous titre recorded with an experimentally derived serum fourfold or greater than the heterologous titre, and in only two instances was this difference demonstrated in both directions. No virus strains consistently met the old serology-based criteria (Sub-committee on Inter-relationships Among Catalogued Alphaviruses) to be considered separate subtypes within an alphavirus species. Only when testing with an SAV subtype-2-specific monoclonal antibody was a major difference between homologous and heterologous neutralization capacity evident. These results provide new direct or indirect information in terms of SAV classification, vaccine efficacy and the selection and validation of reagents for serological and immunological diagnostic purposes.

Nanoplasmonic quantitative detection of intact viruses from unprocessed whole blood.

Infectious diseases such as HIV and hepatitis B pose an omnipresent threat to global health. Reliable, fast, accurate, and sensitive platforms that can be deployed at the point-of-care (POC) in multiple settings, such as airports and offices, for detection of infectious pathogens are essential for the management of epidemics and possible biological attacks. To the best of our knowledge, no viral load technology adaptable to the POC settings exists today due to critical technical and biological challenges. Here, we present for the first time a broadly applicable technology for quantitative, nanoplasmonic-based intact virus detection at clinically relevant concentrations. The sensing platform is based on unique nanoplasmonic properties of nanoparticles utilizing immobilized antibodies to selectively capture rapidly evolving viral subtypes. We demonstrate the capture, detection, and quantification of multiple HIV subtypes (A, B, C, D, E, G, and subtype panel) with high repeatability, sensitivity, and specificity down to 98 ± 39 copies/mL (i.e., HIV subtype D) using spiked whole blood samples and clinical discarded HIV-infected patient whole blood samples validated by the gold standard, i.e., RT-qPCR. This platform technology offers an assay time of 1 h and 10 min (1 h for capture, 10 min for detection and data analysis). The presented platform is also able to capture intact viruses at high efficiency using immuno-surface chemistry approaches directly from whole blood samples without any sample preprocessing steps such as spin-down or sorting. Evidence is presented showing the system to be accurate, repeatable, and reliable. Additionally, the presented platform technology can be broadly adapted to detect other pathogens having reasonably well-described biomarkers by adapting the surface chemistry. Thus, this broadly applicable detection platform holds great promise to be implemented at POC settings, hospitals, and primary care settings.

Abstract LB-307: TRAIL-inducing agent -TIC10 and combinatorial therapeutics in pediatric lymphoma: a targeted approach.

Abstract Despite significant progress in 5-year survival rates for Non-Hodgkin's Lymphoma (NHL) using conventional treatment standards, there is still a need for improved therapies especially for children and adolescents with advanced-stage disease and for those who relapse after conventional therapy. TRAIL (TNF-related apoptosis-inducing ligand) is an endogenous protein that induces apoptosis selectively in cancer cells by binding to death receptors DR4 or DR5. Our laboratory identified a small molecule, TIC10, that induces TRAIL gene transcription and TRAIL-dependent cell death and overcomes the most critical efficacy-limiting drug properties of available TRAIL-based therapies. Selective advantages of TIC10 include longer half-life, stimulation of TRAIL and death receptor expression, stability, lower production cost, and ability to cross the intact blood-brain barrier. Our lab has reported that TIC10 is orally active and has potent anti-tumor effects in several preclinical models, including prolonging survival of lymphoma-bearing Eu-myc transgenic mice. We hypothesize that TIC10 induces apoptosis in human lymphoma cell lines. We selected a diverse sub-type panel of lymphoma cell lines [BJAB, Daudi, Ramos and Raji (Burkitt's lymphoma); Karpas299 (T-cell NHL), and UPN2 (Mantle Cell lymphoma)] to assess lymphoma sensitivity to TIC10. Cell viability assays demonstrated sharp dose-response curves in all of the above cell lines at 72 hours post-treatment. Quantitative analysis of these relationships yielded TIC10 IC50 values in the range of 1.3 to 2.9 uM, which is comparable to the reported activity of TIC10 in other tumor types. Using low micromolar dose ranges, Daudi and Ramos cell lines were treated with TIC10 and sub-G1 analysis by flow cytometry revealed that TIC10 induced significant levels of apoptosis of both the treated cell lines at 72 hours post-treatment in a dose-dependent manner [Daudi cells: untreated cells: 9.4%; increase in sub-G1 content to 39% (4.3 fold); Ramos cells: untreated cells: 41.4%; increase in sub-G1 content to 72.1% (1.74 fold)]. These preliminary findings suggest that TIC10 induces apoptosis in human lymphoma cell lines at low micromolar concentrations. Our lab has previously established that TIC10 synergizes with several approved antitumor agents such as taxanes and sorafenib in other tumor types. We further hypothesize that TIC10 will have synergistic cytotoxic effects in lymphoma in combination with standard chemotherapeutic agents used to treat lymphoma. We have established monoagent dose-response relationships for gemcitabine, etoposide, doxorubicin and vincristine in the above mentioned lymphoma panel of cell lines. In conclusion, TIC10 is a first-in-class therapy that has apoptotic activity in human lymphoma cells that is promising as a monoagent and may be enhanced by combination with approved therapies to improve the standard of care in this setting. Citation Format: Mala K. Talekar, Joshua E. Allen, Wafik S. El-Deiry. TRAIL-inducing agent -TIC10 and combinatorial therapeutics in pediatric lymphoma: a targeted approach. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-307. doi:10.1158/1538-7445.AM2013-LB-307

Mucosal Tissue Tropism and Dissemination of HIV-1 Subtype B Acute Envelope-Expressing Chimeric Virus

Human immunodeficiency virus type 1 (HIV-1) transmission results from infection with one or a small number of variants from the donor quasispecies. Transmitted/founder (T/F) viruses have recently been identified from acutely infected patients, but the way in which they interact with primary targets of HIV-1 infection is poorly understood. We have conducted a biological characterization of a panel of subtype B T/F acute and chronic envelope (Env)-expressing chimeric virus in primary human target cells and mucosal tissues. Both acute and chronic Envs preferentially replicated in peripheral blood mononuclear cells (PBMC) and a CD4 T-cell line compared to monocyte-derived macrophages, or dendritic cells (DC). In a model of trans infection from monocyte-derived dendritic cells to T cells, chimeric virus from acute Envs achieved significantly lower titers compared to chronic Envs. Challenge of primary human mucosal tissues revealed significantly higher levels of replication in chronic Env-expressing virus in rectal tissue compared to cervical and penile tissues and enhanced replication in tonsillar tissue relative to acute Envs. In agreement with data from the DC to T-cell trans infection assay, chronic Env-chimeric virus pools were transmitted more efficiently by migratory cells from cervical and penile tissues to CD4(+) T cells than individual acute Env chimeras. These data indicate that virus with HIV-1 Envs of transmitted acute infections preferentially replicate in T cells rather than macrophages or dendritic cells and are less efficiently transmitted from antigen-presenting cells to CD4 T cells than chronic Envs. Such properties together with chemokine (C-C motif) receptor 5 (CCR5) use may confer an advantage for transmission.

Characterization of V1V2-specific antibodies present in broadly neutralizing plasma isolated from HIV-1 infected individuals

Background Recent studies of antibodies in human plasma from HIV1-infected and immunized individuals have revealed an important role for the V1/V2 region of gp120 in an antiviral response, and recent evidence that protection in the RV144 vaccine trial correlated with the presence of V1/ V2-specific antibodies suggests that the V1V2 region is an important target for candidate HIV-1 vaccines. However, the function of V1V2-specific antibodies is not well understood. In this study we present data about the development, subtype specificity, and neutralization activity of such antibodies present in plasma from several hundred infected North American and African subjects. Methods Human plasma from infected individuals were screened for neutralization activity versus a panel of subtype B, subtype C, and other Tier 2 pseudoviruses, and were titrated for binding activity against the consensus subtype B, C and A/E V1/V2 fusion glycoproteins, expressed via fusion to a fragment of the MuLV gp70 sequence. This system expresses V1/V2 domains in their native glycosylated and conformational forms. V1V2-specific antibodies were isolated from selected plasma by immunoaffinity chromatography on gp70-V1/V2 antigen columns, and characterized for neutralizing activity against various HIV-1 pseudoviruses. Results Most (>80%) of the HIV-1 infected subjects possessed robust levels of V1/V2 binding activity versus the three antigens. Interestingly, the development of V1/V2-reactive antibodies tracked with the development of autologous neutralizing antibodies in several subjects infected with subtype C viruses. Immunoaffinity-purified V1/V2specific antibodies from selected broadly neutralizing plasma samples also possessed broad neutralization activities, with IC50s generally in the 1-20 μg/ml range. Conclusion

Anti-HIV-1 Activity of a New Scorpion Venom Peptide Derivative Kn2-7

For over 30 years, HIV/AIDS has wreaked havoc in the world. In the absence of an effective vaccine for HIV, development of new anti-HIV agents is urgently needed. We previously identified the antiviral activities of the scorpion-venom-peptide-derived mucroporin-M1 for three RNA viruses (measles viruses, SARS-CoV, and H5N1). In this investigation, a panel of scorpion venom peptides and their derivatives were designed and chosen for assessment of their anti-HIV activities. A new scorpion venom peptide derivative Kn2-7 was identified as the most potent anti-HIV-1 peptide by screening assays with an EC50 value of 2.76 µg/ml (1.65 µM) and showed low cytotoxicity to host cells with a selective index (SI) of 13.93. Kn2-7 could inhibit all members of a standard reference panel of HIV-1 subtype B pseudotyped virus (PV) with CCR5-tropic and CXCR4-tropic NL4-3 PV strain. Furthermore, it also inhibited a CXCR4-tropic replication-competent strain of HIV-1 subtype B virus. Binding assay of Kn2-7 to HIV-1 PV by Octet Red system suggested the anti-HIV-1 activity was correlated with a direct interaction between Kn2-7 and HIV-1 envelope. These results demonstrated that peptide Kn2-7 could inhibit HIV-1 by direct interaction with viral particle and may become a promising candidate compound for further development of microbicide against HIV-1.

UCLA1, a Synthetic Derivative of a gp120 RNA Aptamer, Inhibits Entry of Human Immunodeficiency Virus Type 1 Subtype C

Entry of human immunodeficiency virus type 1 (HIV-1) into cells is mediated by the virion surface envelope (Env) glycoproteins, making it a desirable target for antiretroviral entry inhibitors. We previously isolated a family of gp120 binding RNA aptamers and showed that they neutralized the infectivity of HIV-1. In this study, we assessed the activity of a shortened synthetic derivative of the B40 aptamer, called UCLA1, against a large panel of HIV-1 subtype C viruses. UCLA1 tightly bound to a consensus HIV-1 subtype C gp120 and neutralized isolates of the same subtype with 50% inhibitory concentrations (IC(50)s) in the nanomolar range. The aptamer had little toxicity in tests with cell lines and primary cells. Furthermore, it exhibited high therapeutic indices, suggesting that it may be effective at very low doses. Mapping of UCLA1 binding sites on gp120 revealed eight amino acid residues that modulated neutralization resistance. This included residues within the coreceptor binding site, at the base of the V3 loop, and in the bridging sheet within the conserved V1/V2 stem-loop of gp120. The aptamer was also shown to have synergistic effects with T20, a gp41 fusion inhibitor, and IgG1b12 (b12), an anti-CD4 binding site monoclonal antibody. These results suggest that UCLA1 may be suitable for development as a potent HIV-1 entry inhibitor.

Pilot Studies for Development of an HIV Subtype Panel for Surveillance of Global Diversity

The continued global spread and evolution of HIV diversity pose significant challenges to diagnostics and vaccine strategies. NIAID partnered with the FDA, WRAIR, academia, and industry to form a Viral Panel Working Group to design and prepare a panel of well-characterized current and diverse HIV isolates. Plasma samples that had screened positive for HIV infection and had evidence of recently acquired infection were donated by blood centers in North and South America, Europe, and Africa. A total of 80 plasma samples were tested by quantitative nucleic acid tests, p24 antigen, EIA, and Western blot to assign a Fiebig stage indicative of approximate time from initial infection. Evaluation of viral load using FDA-cleared assays showed excellent concordance when subtype B virus was tested, but lower correlations for subtype C. Plasma samples were cocultivated with phytohemagglutinin (PHA)-stimulated peripheral blood mononuclear cells (PBMCs) from normal donors to generate 30 viral isolates (50-80% success rate for samples with viral load >10,000 copies/ml), which were then expanded to 10(7)-10(9) virus copies per ml. Analysis of env sequences showed that sequences derived from cultured PBMCs were not distinguishable from those obtained from the original plasma. The pilot collection includes 30 isolates representing subtypes B, C, B/F, CRF04_cpx, and CRF02_AG. These studies will serve as a basis for the development of a comprehensive panel of highly characterized viral isolates that reflects the current dynamic and complex HIV epidemic, and will be made available through the External Quality Assurance Program Oversight Laboratory (EQAPOL).

Measuring Enzymatic HIV-1 Susceptibility to Two Reverse Transcriptase Inhibitors as a Rapid and Simple Approach to HIV-1 Drug-Resistance Testing

Simple and cost-effective approaches for HIV drug-resistance testing are highly desirable for managing increasingly expanding HIV-1 infected populations who initiate antiretroviral therapy (ART), particularly in resource-limited settings. Non-nucleoside reverse trancriptase inhibitor (NNRTI)-based regimens with an NRTI backbone containing lamivudine (3TC) or emtricitabine (FTC) are preferred first ART regimens. Failure with these drug combinations typically involves the selection of NNRTI- and/or 3TC/FTC- resistant viruses. Therefore, the availability of simple assays to measure both types of drug resistance is critical. We have developed a high throughput screening test for assessing enzymatic resistance of the HIV-1 RT in plasma to 3TC/FTC and NNRTIs. The test uses the sensitive “Amp-RT” assay with a newly-developed real-time PCR format to screen biochemically for drug resistance in single reactions containing either 3TC-triphosphate (3TC-TP) or nevirapine (NVP). Assay cut-offs were defined based on testing a large panel of subtype B and non-subtype B clinical samples with known genotypic profiles. Enzymatic 3TC resistance correlated well with the presence of M184I/V, and reduced NVP susceptibility was strongly associated with the presence of K103N, Y181C/I, Y188L, and G190A/Q. The sensitivity and specificity for detecting resistance were 97.0% and 96.0% in samples with M184V, and 97.4% and 96.2% for samples with NNRTI mutations, respectively. We further demonstrate the utility of an HIV capture method in plasma by using magnetic beads coated with CD44 antibody that eliminates the need for ultracentifugation. Thus our results support the use of this simple approach for distinguishing WT from NNRTI- or 3TC/FTC-resistant viruses in clinical samples. This enzymatic testing is subtype-independent and can assist in the clinical management of diverse populations particularly in resource-limited settings.

Variable epitope libraries: New vaccine immunogens capable of inducing broad human immunodeficiency virus type 1-neutralizing antibody response

The extreme antigenic variability of human immunodeficiency virus (HIV) leads to immune escape of the virus, representing a major challenge in the design of effective vaccine. We have developed a novel concept for immunogen construction based on introduction of massive mutations within the epitopes targeting antigenically variable pathogens and diseases. Previously, we showed that these immunogens carrying large combinatorial libraries of mutated epitope variants, termed as variable epitope libraries (VELs), induce potent, broad and long lasting CD8+IFN-γ+ T-cell response. Moreover, we demonstrated that these T cells recognize more than 50% of heavily mutated variants (5 out of 10 amino acid positions were mutated in each epitope variant) of HIV-1 gp120 V3 loop-derived cytotoxic T lymphocyte epitope (RGPGRAFVTI) in mice. The constructed VELs had complexities of 10000 and 12500 individual members, generated as plasmid DNA or as M13 phage display combinatorial libraries, respectively, and with structural composition RGPGXAXXXX or XGXGXAXVXI, where X is any of 20 natural amino acids. Here, we demonstrated that sera from mice immunized with these VELs are capable of neutralizing 5 out of 10 viral isolates from Tier 2 reference panel of subtype B envelope clones, including HIV-1 isolates which are known to be resistant to neutralization by several potent monoclonal antibodies, described previously. These data indicate the feasibility of the application of immunogens based on VEL concept as an alternative approach for the development of molecular vaccines against antigenically variable pathogens.

Evaluation of the Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 Test and Identification of Rare Polymorphisms Potentially Affecting Assay Performance

We evaluated the FDA-approved Roche Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) HIV-1 viral load assay for sensitivity, reproducibility, linearity, HIV-1 subtype detection, and correlation to the Roche Amplicor HIV-1 monitor test, version 1.5 (Amplicor). The limit of detection calculated by probit analysis was 23.8 copies/ml using the 2nd International WHO Standard and 30.8 copies/ml using Viral Quality Assurance (VQA) standard material. Serial dilutions of six patient samples were used to determine inter- and intra-assay reproducibility and linearity, which were very good (<8% coefficient of variation [CV]; between approximately 1.7 and 7.0 log(10) copies/ml). Subtype detection was evaluated in the CAP/CTM, Amplicor, and Bayer Versant HIV-1 bDNA 3.0 (Versant) assays using a commercially available panel. Versant averaged 0.829 log(10) copies/ml lower than CAP/CTM and Amplicor averaged 0.427 log(10) copies/ml lower than CAP/CTM for the subtype panel. Correlation with samples previously tested by Amplicor was excellent (R(2) = 0.884; average difference [Amplicor value minus CAP/CTM value], 0.008 log(10) copies/ml). Of the 305 HIV samples tested, 7 samples generated CAP/CTM titers between 1.0 and 2.75 log(10) copies/ml lower than those for Amplicor. Three of these samples revealed primer and probe mismatches that could account for the discrepancies. Otherwise, the CAP/CTM assay exhibits excellent sensitivity, dynamic range, reproducibility, and correlation with Amplicor in an automated format.

Generation of a Family-specific Phage Library of Llama Single Chain Antibody Fragments That Neutralize HIV-1

Recently, we described llama antibody fragments (VHH) that can neutralize human immunodeficiency virus, type 1 (HIV-1). These VHH were obtained after selective elution of phages carrying an immune library raised against gp120 of HIV-1 subtype B/C CN54 with soluble CD4. We describe here a new, family-specific approach to obtain the largest possible diversity of related VHH that compete with soluble CD4 for binding to the HIV-1 envelope glycoprotein. The creation of this family-specific library of homologous VHH has enabled us to isolate phages carrying similar nucleotide sequences as the parental VHH. These VHH displayed varying binding affinities and neutralization phenotypes to a panel of different strains and subtypes of HIV-1. Sequence analysis of the homologs showed that the C-terminal three amino acids of the CDR3 loop were crucial in determining the specificity of these VHH for different subtype C HIV-1 strains. There was a positive correlation between affinity of VHH binding to gp120 of HIV-1 IIIB and the breadth of neutralization of diverse HIV-1 envelopes. The family-specific approach has therefore allowed us to better understand the interaction of the CD4-binding site antibodies with virus strain specificity and has potential use for the bioengineering of antibodies and HIV-1 vaccine development.

Complex Mosaic Composition of Near Full-Length Genomes of Two NED (NIH-ENVA-DOD) Subtype Panel HIV Type 1 Strains, BCF-Dioum and BCF-Kita, Originating from the Democratic Republic of Congo (DRC)

Sequence characterization of the near full-length genomes of HIV-1 isolates BCF-Dioum and BCF-Kita, originating from the Democratic Republic of Congo (DRC), was continued. These NED panel isolates, contributed by F. Brun-Vezinet (ENVA-France), were first identified as subtypes G and H, respectively. Our earlier analyses of portions of their pol genes showed that both were likely to be intersubtype recombinants of different composition. This study analyzed the remainder of each genome, confirming them to be complex recombinants. The BCF-Dioum genome resembles CRF06_cpx strains found in West Africa, composed of subtypes A/G/J/K. The BCF-Kita genome is a unique complex recombinant A-F-G-H-K-U strain. These data support previous observations of the complexity of strains originating from the DRC. BCF-Dioum may be a suitable strain for standards and reagents since it matches a defined circulating recombinant form. Studies and reagents made from BCF-Kita should take into account its complex genome.

Human papillomavirus in early laryngeal carcinoma

To examine the role of HPV status in the etiology, prognosis, and treatment of head and neck squamous cell carcinoma in early larynx malignancies. Retrospective. Thirty-eight cases of T1 or carcinoma in situ (CIS) laryngeal lesions were examined for the presence of human papilloma virus (HPV) using an inclusive polymerase chain reaction (PCR)/hybridization technique capable of identifying 37 HPV subtypes. HPV DNA was detected in 6 (16%) of the 38 lesions, representing HPV types 16, 26, 31, 39, and 52, and p16 tumor suppressor protein expression was confirmed in 10 representative cases. This HPV prevalence is higher than that noted in many previous laryngeal cancer studies, possibly due to the relatively large panel of subtypes screened for in this study. Identification of HPV-26, which has been associated with uterine cervical cancer, in an early laryngeal cancer specimen represents the first evidence of this subtype in a laryngeal carcinoma. Consistent with reports focusing on head and neck squamous cell carcinoma (HNSCC) arising from other subsites within the upper aerodigestive tract, patients with HPV-positive laryngeal carcinomas were of younger age and were somewhat less likely to have a history of tobacco use, although the latter of the two findings did not reach statistical significance. Our findings emphasize the presence of a broad spectrum of HPV types in a relevant proportion of early laryngeal cancers, and together with evidence of an association of HPV tumor status with a more favorable clinical course, provide a rationale for the routine HPV testing of small larynx lesions.

Evaluation of the Abbott m 2000 RealTi m e Human Immunodeficiency Virus Type 1 (HIV-1) Assay for HIV Load Monitoring in South Africa Compared to the Roche Cobas AmpliPrep-Cobas Amplicor, Roche Cobas AmpliPrep-Cobas TaqMan HIV-1, and BioMerieux NucliSENS EasyQ HIV-1 Assays

The implementation of antiretroviral therapy demands the need for increased access to viral load (VL) monitoring. Newer real-time VL testing technologies are faster and have larger dynamic ranges and fully automated extraction to benefit higher throughputs in resource-poor environments. The Abbott RealTime human immunodeficiency virus type 1 (HIV-1) assay was evaluated as a new option for testing for HIV-1 subtype C in South Africa, and its performance was compared to the performance of existing assays (the Cobas AmpliPrep-Cobas TaqMan HIV-1, version 1, assay; the AmpliPrep-Cobas Monitor standard HIV-1 assay; and the NucliSENS EasyQ-EasyMag HIV-1 assay) in a high-throughput laboratory. The total precision of the RealTime HIV-1 assay was acceptable over all viral load ranges. This assay compared most favorably with the Cobas AmpliPrep-Cobas TaqMan HIV-1 assay (R(2) = 0.904), with a low standard deviation of difference being detected (0.323 copies/ml). The bias against comparator assays ranged from -0.001 copies/ml to -0.228 copies/ml. Variability in the reporting of VLs for a 20-member subtype panel compared to the variability of other assays was noted with subtypes G and CRF02-AG. The RealTime HIV-1 assay can test 93 samples per day with minimal manual preparation, less staff, and the minimization of contamination through automation. This assay is suitable for HIV-1 subtype C VL quantification in South Africa.

The Maturation Inhibitor Bevirimat (PA-457) can be Active in Patients Carrying HIV type-1 non-B Subtypes and Recombinants

Bevirimat (PA-457) is the first candidate of a new family of antiretroviral drugs, the maturation inhibitors. Its action is based on disruption of the protease cleavage of the Gag precursor region. Six resistance mutations have been described and analysed in virus from both treatment-naive and protease inhibitor (PI)-experienced patients, but only in the subtype B of HIV type-1 (HIV-1) virus. Thus, genotypic resistance in non-B subtypes still requires analysis. HIV-1 sequences of different subtypes (54 B, 81 non-B and recombinants) were analysed for the presence of resistance mutations to bevirimat, located within the capsid (CA) protein and spacer peptide 1 (SP1) cleavage site. No resistance mutations were found, although polymorphisms appeared in some CA-SP1 residues. The C-terminal CA protein and the N-terminal SP1 presented high conservation, whereas C-terminal SP1 was highly variable in sequence and length, with unknown influence in resistance acquisition. The results of the present study confirm an absolute conservation of the residues involved in bevirimat in vitro resistance in a large panel of HIV-1 subtypes and recombinants from both treatment-naive and PI-experienced patients. Treatment alone seemed to increase the polymorphisms account in CRF02_AG recombinant sequences; however, the influence of natural polymorphisms needs to be explored.

Performance of a Novel Human Immunodeficiency Virus (HIV) Type 1 Total Nucleic Acid-Based Real-Time PCR Assay Using Whole Blood and Dried Blood Spots for Diagnosis of HIV in Infants

The new Cobas AmpliPrep/Cobas TaqMan HIV-1 Qual test offers advanced automation for the detection of human immunodeficiency virus type 1 (HIV-1) RNA and DNA in dried blood spots (DBS) and whole blood. An analytical evaluation using an HIV-1 secondary standard yielded limits of detection of 514, 710, and 1,090 HIV RNA copies/ml for EDTA plasma, whole blood, and DBS, respectively. The precision and reproducibility of HIV-1 detection was equivalent for DBS and whole blood. Inclusivity was demonstrated for a reference panel of HIV-1 subtypes A to N. A clinical evaluation of the Cobas AmpliPrep/Cobas TaqMan HIV-1 Qual test was performed at a center for routine diagnostics in Johannesburg, South Africa, using 1,013 clinical specimens from HIV-1 exposed children. The Amplicor HIV-1 DNA test v1.5 with the MagNApure DNA isolation procedure was used as the reference method. A total of 995 valid results for whole blood with both methods yielded 691 and 303 concordant negative and positive results for the Cobas AmpliPrep/Cobas TaqMan HIV-1 Qual test, respectively. For the 800 valid DBS specimen results, 495 and 300 concordant negative and positive results were obtained, respectively. The resulting clinical specificities and sensitivities of the new test were 100% and 99.7% for whole blood and DBS, respectively. The new test was characterized by its robustness, enhanced automation, and improved sample throughput. The Cobas AmpliPrep/Cobas TaqMan HIV-1 Qual test will support early, reliable diagnosis of HIV in children in routine laboratory settings.

Induction of Broad Cross-Subtype-Specific HIV-1 Immune Responses by a Novel Multivalent HIV-1 Peptide Vaccine in Cynomolgus Macaques

One of the major obstacles in the design of an effective vaccine against HIV-1 is its antigenic variation, which results in viral escape from the immune system. Through a bioinformatics approach, we developed an innovative multivalent HIV-1 vaccine comprised of a pool of 176 lipidated and nonlipidated peptides representing variable regions of Env and Gag proteins. The potency and breadth of the candidate vaccine against a panel of HIV-1 subtypes was evaluated in nonhuman primate (cynomolgus macaques) and humanized mouse (HLA-A2.1) models. The results demonstrate strong immunogenicity with both breadth (humoral and cellular immunity) and depth (immune recognition of widely divergent viral sequences) against heterologous HIV-1 subtypes A-F.