Robert G Whalen

• Doctor of Philosophy
• CSO at Maxygen LLC

Previously, VLPs bearing JR-FL strain HIV-1 Envelope trimers elicited potent neutralizing antibodies (nAbs) in 2/8 rabbits (PLoS Pathog 11(5): e1004932) by taking advantage of a naturally absent glycan at position 197 that borders the CD4 binding site (CD4bs). In new immunizations, we attempted to improve nAb responses by removing the N362 glycan t...

Eliciting broad tier 2 neutralizing antibodies (nAbs) is a major goal of HIV-1 vaccine research. Here we investigated the ability of native, membrane-expressed JR-FL Env trimers to elicit nAbs. Unusually potent nAb titers developed in 2 of 8 rabbits immunized with virus-like particles (VLPs) expressing trimers (trimer VLP sera) and in 1 of 20 rabbi...

Primary isolates of HIV-1 resist neutralization by most antibodies to the CD4 binding site (CD4bs) on gp120 due to occlusion of this site on the trimeric spike. We describe 1F7, a human CD4bs monoclonal antibody that was found to be exceptionally potent against the HIV-1 primary isolate JR-FL. However, 1F7 failed to neutralize a patient-matched pri...

MAb 1F7 does not bind to auto-antigens. Several mAbs were tested for reactivity against a panel of antigens (lipids, proteins, and dsDNA). MAb 4E10 served as positive control (open blue circles), 1F7 is depicted as red squares. Each assay was performed in duplicate. Data are representative of at least 3 repeats. (TIFF)

Neutralization activity of mAb 1F7 against a cross-clade panel of 157 pseudotyped viruses. Neutralization was performed in the Monogram Biosciences assay format. IC50 values for mAbs b12, 2G12, 2F5, 4E10, PG9, and PG16, which were obtained using the same assay, were taken from Walker and colleagues [35]. (TIFF)

Sequence alignment of 1F7-resistant and 1F7-sensitive gp120s. Only positions are shown that were considered relevant for b12 binding [51] as well as glycosylations at positions 156, 197, and 301. Color-coding: non-polar – yellow/brown; polar uncharged – pink/purple; polar negatively charged – light green/dark green; polar positively charged – light...

Development of a vaccine for HIV-1 requires a detailed understanding of the neutralizing antibody responses that can be experimentally elicited to difficult-to-neutralize primary isolates. Rabbits were immunized with the gp120 subunit of HIV-1 JR-CSF envelope (Env) using a DNA-prime protein-boost regimen. We analyzed five sera that showed potent au...

Prime-boost immunization using JR-CSF gp120 elicits a range of JR-CSF neutralizing activities. IC50 values (1/dilution) of 24 sera from rabbits immunized with a JR-CSF gp120 DNA vaccine followed by JR-CSF gp120 protein are shown. The sera are from three immunization studies (Study 32, Study 41, and Study 14). The detailed immunization regime for ea...

Regions of gp120 targeted by rabbit sera are distinct but show some overlap with mAbs. The results of this study are represented visually using a model of the crystal structure of JR-FL gp120 core [102], shown here in the absence of bound CD4 and X5 antibody Fab fragment (pdb: 2B4C). (A) Positions of the asparagine residues in the 13 PNGS targeted...

Amino acid sequences of JRCSF and ST-008 gp120 proteins. Sequence alignment by ClustalW of JRCSF gp120 (GenBank: AAB03749) and ST-008 excluding the tPA leader sequence and spacer. Identities = 439/488 (89%), Positives = 457/488 (93%), Gaps = 12/488 (2%). (TIFF)

Comparison of Day 98 sera induced by gp120 deletion constructs. (DOC)

Reduction of neutralization potency in Day 98 sera induced by gp120 deletion constructs. (DOC)

Comparison of potency of two Env immunogens after protein boost. (DOC)

Subtype B HIV-1 env genes used for in vitro DNA recombination. (DOC)

Comparison of kinetic constants for the interactions between mAbs and wild-type and recombined gp120 proteins. (DOC)

A prophylactic vaccine is needed to slow the spread of HIV-1 infection. Optimization of the wild-type envelope glycoproteins to create immunogens that can elicit effective neutralizing antibodies is a high priority. Starting with ten genes encoding subtype B HIV-1 gp120 envelope glycoproteins and using in vitro homologous DNA recombination, we crea...

The HIV-1 envelope glycoprotein (Env) spike is challenging to study at the molecular level, due in part to its genetic variability, structural heterogeneity and lability. However, the extent of lability in Env function, particularly for primary isolates across clades, has not been explored. Here, we probe stability of function for variant Envs of a...

Methods to improve plasmid-mediated transgene expression are needed for gene medicine and gene vaccination applications. To maintain a low risk of insertional mutagenesis-mediated gene activation, expression-augmenting sequences would ideally function to improve transgene expression from transiently transfected intact plasmid, but not from spurious...

The external domains of the HIV-1 envelope glycoprotein (gp120 and the gp41 ectodomain, collectively known as gp140) contain all known viral neutralization epitopes. Various strategies have been used to create soluble trimers of the envelope to mimic the structure of the native viral protein, including mutation of the gp120-gp41 cleavage site, intr...

We employed directed molecular evolution to improve the cross-reactivity and immunogenicity of the Venezuelan equine encephalitis virus (VEEV) envelope glycoproteins. The DNA encoding the E1 and E2 proteins from VEEV subtypes IA/B and IE, Mucambo virus (MUCV), and eastern and western equine encephalitis viruses (EEEV and WEEV) were recombined in vi...

Specific proteolytic cleavage of the gp120 subunit of the HIV-1 envelope (Env) glycoprotein in the third variable domain (V3) has previously been reported to occur in several cell lines, including Chinese hamster ovary cells that have been used for production of Env-based HIV vaccine candidates. Here we report that this proteolytic activity on JRCS...

Immunogens that induce neutralizing antibodies to HIV-1 are essential components of a preventative vaccine. The HIV-1 Envelope (Env) contains conserved neutralizing epitopes, defined by monoclonal antibodies derived from infected individuals. We hypothesize that directed molecular evolution can create novel Env variants that render these neutralizi...

The efficacy of vaccines can be improved by increasing their immunogenicity, broadening their crossprotective range, as well as by developing immunomodulators that can be coadministered with the vaccine antigen. One technology that can be applied to each of these aspects of vaccine development is MolecularBreeding directed molecular evolution. Esse...

Vaccines that stimulate broadly neutralizing antibodies to HIV-1 will have a major impact on reducing transmission. However this remains an elusive goal because the antibodies induced by the envelope glycoprotein (Env) do not effectively neutralize primary isolates or viral strains that are important in transmission. Using DNA shuffling and screeni...

Viral, bacterial and parasitic pathogens have evolved multiple strategies to evade the immune response, facilitate transmission and establish chronic infections. One of the underlying strategies that pathogens have evolved is antigenic variation of immune response targets that reduce the affinity of antigen binding to antibodies and major histocomp...

DNA shuffling and screening technologies recombine and evolve genes in vitro to rapidly obtain molecules with improved biological activity and fitness. In this way, genes from related strains are bred like plants or livestock and their successive progeny are selected. These technologies have also been called molecular breeding-directed molecular ev...

The weakly immunogenic murine P1A Ag is a useful experimental model for the development of new vaccination strategies that could potentially be used against human tumors. An i.m. DNA-based immunization procedure, consisting of three inoculations with the P1A-coding pBKCMV-P1A plasmid at 10-day intervals, resulted in CTL generation in all treated BA...

DNA vaccination results in remarkably strong, broad-based immune responses to the encoded proteins and it is a simple and effective method of inducing cytotoxic T-lymphocyte (CTL) responses. Bone marrow-derived cells can take up and present exogenous antigenic protein liberated by transfected fibroblasts or myoblasts after the injection of such cel...

DNA vaccination is a simple and efficient method for the induction of cytotoxic T lymphocytes (CTLs). In the present study, we have examined the effect of the mutations of each of the 12 amino acids of the HBsAg Ld-restricted CTL epitope on the ability of the modified proteins to induce CTLs after DNA-based immunization. Replacement of glutamine or...

One challenge of biotechnology is to find ways to optimize enzymes, cytokines, vaccines or transgenes in new contexts that are typically not found in nature. The approach of DNA shuffling is a test-tube process that takes advantage of recombination to generate libraries of chimeric genes, which can then be screened to identify the encoded proteins...

To improve the immunogenicity of epitopes from the envelope protein of HIV-1, we have developed gene gun-delivered subunit DNA vaccines by inserting the sequences encoding the V3 region into the hepatitis B virus (HBV) envelope gene, often called the surface antigen (HBsAg). We have examined the possibility of modifying the immune response to V3 by...

Some patients with small cell lung cancer (SCLC) or neuroblastoma develop an immune response against HuD, a human homologue of the Drosophila protein, elav, which is expressed in the nucleus and to a lesser degree the cytoplasm of neurons and tumor cells. This immune response is characterized by antibodies (anti-Hu) that at high titers are associat...

The murine adult IIB myosin heavy chain (IIB MyHC) gene is expressed only in certain skeletal muscle fibers. Within the proximal promoter are two A + T-rich motifs, mAT1 and mAT2, which greatly enhance muscle-specific transcription; myogenic cells contain proteins that bind to these sequences. MEF-2 binds to both mAT1 and mAT2; a mutation abolishin...

DNA vaccination involves the direct injection of a suitable designed plasmid DNA molecule into a tissue such that the antigenic proteins encoded by the plasmid are expressed in the cells of the treated host. This extraordinarily simple approach has been translated into practice for many antigens from infectious agents, for putative tumor antigens,...

In the present study, we have investigated the T cell response to the HBsAg, normally secreted as multivalent particles, and to beta-galactosidase, a cytoplasmic antigen, delivered as plasmid DNAs. We found that cytokines characteristic of a Th1 phenotype are produced in mice immunized by these plasmid DNAs. Using repeated injections of low doses o...

Hepatitis B virus (HBV) remains a serious worldwide health problem and the possibility to control it will depend on the availability of safe, effective and affordable vaccines. Recombinant protein or plasma-derived vaccines containing HBV surface antigen (HBsAg) are safe and generally efficacious, however, they are too expensive for widespread use...

To determine whether DNA based immunization could protect newborn chimpanzees against a challenge infection with hepatitis B virus, two chimpanzees were immunized on the day of birth with a plasmid coding for hepatitis B surface antigen, and boosted at 6 and 24 weeks. Both animals produced transient antibody to the hepatitis B surface antigen. Foll...

We have previously characterized the proximal promoter of the mouse IIB myosin heavy chain (MyHC) gene, which is expressed only in fast-contracting glycolytic skeletal muscle fibers. We show here that the substitution into this promoter of a non-canonical TATA sequence from the IgH gene results in inactivity in muscle cells, even though TATA-bindin...

Transgenic mice expressing the sequences coding for the envelope proteins of the hepatitis B virus (HBV) in the liver have been used as a model of the HBV chronic carrier state. We evaluated the possibility of inducing a specific immune response to the viral envelope antigens and thus potentially controlling chronic HBV infection. Using HBV-specifi...

A novel and powerful method for vaccine research, colloquially known as DNA vaccines, involves the deliberate introduction into tissues of a DNA plasmid carrying an antigen-coding gene that transfects cells in vivo and results in an immune response. DNA vaccines have several distinct advantages, which include ease of manipulation, use of a generic...

Plasmid DNA is widely used for direct gene transfer in animals to study gene therapy, gene regulation, drug delivery and genetic immunization. Here we compare cesium chloride and anion-exchange purified plasmid DNA for direct gene transfer in mouse muscle and show no differences in efficiency of transfection with reporter genes or in humoral respon...

Intramuscular (i.m.) injection of mice with plasmid DNA expression vectors containing all or part of the hepatitis B virus (HBV) gene encoding the envelope proteins induces a strong humoral response to the HBV surface antigen (HBsAg) which is sustained for up to 74 weeks without boost. After a single i.m. injection of 100 micrograms DNA, antibodies...

The expression of myosin isoforms was studied in regenerated rat soleus muscle during either normal or altered postural activity. Regeneration was induced following injury by venom from the Notechis scutatus scutatus snake. Immunohistochemical analysis showed that, in regenerating soleus muscle after 3 wk of hindlimb suspension, nearly all fibers r...

Occasionally, a major change in vaccine methodology comes along. Such would appear to be the case with the advent of DNA-mediated immunization, colloquially known as DNA vaccines. This represents a radical new way to deliver antigens; it involves the direct introduction of a plasmid DNA encoding an antigenic protein which is then expressed within c...

The particulate form of the major envelope or surface (S) protein of hepatitis B virus (HBV) can be taken up by antigen-presenting cells and processed for class I presentation as an exogenous protein. We have used several DNA plasmid vectors expressing the HBV envelope proteins to determine whether these sequences are able to induce cytotoxic T lym...

Direct gene transfer by intramuscular injection of plasmid DNA encoding an antigenic protein may be used for the purpose of immunization. Several factors influence the uptake and expression of plasmid DNA in skeletal muscle, which in turn influence the immune response to the expressed protein. Physical barriers and other factors may impede the diff...

The use of plasmid vectors expressing the HBsAg, along with improved protocols for transfection of muscle fibers (Refs. 3-6 and Davis et al., this volume), have provided the reagents and methods with which to investigate the characteristics of the strong immune response given by this antigen after DNA-mediated immunization. Analysis of the fine spe...

We investigated the myogenic properties of rabbit fast or slow muscle satellite cells during their differentiation in culture, with a particular attention to the expression of myosin heavy chain and myogenic regulatory factor genes. Satellite cells were isolated from Semimembranosus proprius (slow-twitch muscle; 100% type I fibres) and Semimembrano...

Vectors expressing the first 58 amino acids of the hepatitis C virus (HCV) nucleocapsid alone or as a fusion protein with the middle (pre-S2 and S) or major (S) surface antigens of hepatitis B virus (HBV) were constructed. Intramuscular immunization of BALB/c mice with the chimeric constructs in the form of naked DNA elicited humoral responses to a...

The mouse mutants ADR ("arrested development of righting") and the allelic CRP ("cramp") are characterized by a myotonic phenotype resulting from a dysfunction of the skeletal muscle chloride channel which leads to myotonic trains of action potentials in response to stimuli. Compared to normal mouse muscle, numerous biochemical modifications have b...

We have studied the effect of several myogenic regulatory factors on the activity of the promoter for a mouse gene encoding a skeletal myosin heavy chain (MyHC) expressed in adult (type IIB) muscle fibers. Co-transfection of myogenic factors is necessary for activity of the IIB promoter in mouse C2 myotubes in culture but not in quail myotubes in c...

Intramuscular injection of plasmid DNA expression vectors encoding the three envelope proteins of the hepatitis B virus (HBV) induced humoral responses in C57BL/6 mice specific to several antigenic determinants of the viral envelope. The first antibodies appeared within 1-2 weeks after injection of DNA and included antibodies of the IgM isotype. Ov...

A new and unusual approach for evoking an immune response has recently been introduced—that of DNA-based immunization. Purified plasmid DNA, containing protein coding sequences and the necessary regulatory elements to express them, can be introduced into tissues of the organism by means of a parenteral injection or by particle bombardment. The numb...

Nucleic acid-based immunization refers to the induction of an immune response to an antigen expressedin vivo subsequent to the introduction of coding sequences in the form of either DNA or RNA. To date, most examples of nucleic acid-based immunization have used DNA encoding a polypeptide sequence, thus the subsequent discussion will be restricted t...

DNA vaccines belong to the new technology of nucleic acid-based immunization, also known as genetic immunization. This describes the induction of an immune response to an antigenic protein expressed in vivo after introducing its encoding polynucleotide. In theory, the encoding sequences can be in the form of either DNA or mRNA. However, in practice...

Direct gene transfer by intramuscular injection of plasmid DNA encoding an antigenic protein may be used for the purpose of immunization. DNA-based immunization may be of value for basic immunological research and vaccine development. Several factors influence the uptake and expression of plasmid DNA in skeletal muscle, which in turn influence the...

If the field of gene therapy of human diseases is in its infancy, attempts to modulate the expression of transferred genes is an endeavor which is still in gestation. The midwives to the birth of this area are those molecular biologists who are actively involved in the study of the control of gene expression. In particular, the tremendous surge of...

The possibility of inducing an immune response to a protein expressed directly from an introduced gene represents an alternative to classic vaccination. We evaluated the ability of plasmid-based eukaryotic expression vectors to produce the Hepatitis B surface antigen (HBsAg) after injection of pure DNA into mouse tibialis anterior muscles. DNA was...

Direct gene transfer into skeletal muscle offers several therapeutic possibilities. We assessed direct intramuscular injection of recombinant plasmids, adenovirus, or retrovirus in normal or regenerating muscles of mice. The incorporation and expression of reporter genes introduced by any of these three vectors is greater in regenerating than in ma...

Adult fast myosin heavy chain (MHC) isoforms are accumulated in fibers of rat hindlimb skeletal muscle which initially contain neonatal MHC at birth. The specific factors controlling these transitions are not known, but in rat and mouse muscle tissue the transition between the neonatal and adult fast MHC proteins does not appear to require continuo...

Myosin heavy chain (MyHC) isoforms are encoded by a multigene family in vertebrates. We used genomic DNA mapping by pulse field gel electrophoresis to demonstrate that, in humans, the embryonic, fetal, fast IIB and IIX MyHC genes and a gene coding for a non-identified striated muscle MyHC fast-type isoform (NI), are contained within a 320 kb SalI g...

Striated muscle is the only tissue found to be capable of taking up and expressing reporter genes that are transferred in the form of plasmid DNA. Thus, direct gene transfer is a potential method of gene therapy for the primary inherited myopathies. However, results to date have had insufficient and too variable expression to consider using direct...

During striated muscle development, the glycolytic enzyme enolase (EC 4.2.1.11) undergoes an isozymic transition, from the embryonic αα form towards the muscle-specific forms αβ and ββ. The regulation of this transition was analyzed in mouse hindlimb muscles from embryonic day 15 (E15) to the adult stage. The quantitative modulations of the levels...

The mouse gene encoding a myosin heavy chain (MHC) protein expressed in type IIB fibers of adult skeletal muscle has been cloned and its promoter isolated. A number of DNA sequence motifs are found within the first 2.5 kilobases of the promoter which are similar to motifs present in the promoters of other muscle-specific genes. One sequence located...

While it recently has been demonstrated that it is possible to modify the phenotypic expression of murine dystrophy (dy/dy) (i.e., prevent myofiber loss) by subjecting the extensor digitorum longus (EDL) muscle of 14-day-old dy/dy mice to transient neonatal denervation (Moschella and Ontell, 1987), the mechanism responsible for this phenomenon has...

We have isolated the mouse gene for the MHC isoform expressed in adult type IIB (fast-contracting, glycolytic) skeletal muscle fibers, and determined the DNA sequence of the promoter region. This sequence represents the first example of a promoter for a gene encoding an adult-specific isoform of a mammalian skeletal MHC. The proximal 200 bp of the...

This chapter describes the advantages and limits of the one-tube amplification protocol versus the two-step method. In some experimental conditions, the one-tube amplification method is as efficient as the two-step method but much less time consuming. It is a method particularly suitable for routine amplification of a large number of RNA samples. T...

The effect of perinatal undernutrition on the postnatal elimination of immature myosin isoforms in rat diaphragm muscle was examined using electrophoretic and immunocytochemical techniques. Electrophoresis of native myosin showed that neonatal bands were present in diaphragm muscles of both control and undernourished rats on day 4. By day 21, the n...

Immunohistochemical analysis of myosin heavy chain (MHC) isoform expression in perinatal and adult rat diaphragm muscles was performed with antibodies which permitted the identification of all known MHC isoforms found in typical rat muscles. Isoform switching, leading to the emergence of the adult phenotype, was more complex than had been previousl...

Myosin isozymes and their fiber distribution were studied during regeneration of the soleus muscle of young adult (4–6 week old) rats. Muscle degeneration and regeneration were induced by a single subcutaneous injection of a snake toxin, notexin. If reinnervation of the regenerating muscle was allowed to occur (functional innervation nearly complet...

The postnatal elimination of embryonic and neonatal myosin isoforms in the rat extensor digitorum longus, diaphragm, and soleus muscles was compared using electrophoresis and immunohistochemical techniques. Electrophoresis of native myosin showed that neonatal bands were present in all three muscles on day 4 but were absent from the day 21 extensor...

The formation of human myotubes in culture is accompanied by the induction of developmentally regulated, muscle-specific genes. We have studied the expression of human myosin light chain proteins and mRNAs during myogenesis in culture, in particular the skeletal embryonic myosin light chain 1 (MC1emb), which is indistinguishable from MLC1 of adult...

It is known that a deficiency in thyroid hormone delays the post-natal maturation of several mammalian tissues. In striated muscle tissue, hypothyroidism delays or inhibits some of the isoform transitions of myosin heavy chains which would occur during normal development. In this paper, using the mouse mutant dwarf, we demonstrate an influence of t...

The developmental pattern of slow myosin expression has been studied in mouse embryos from the somitic stage to the period of secondary fiber formation and in myogenic cells, cultured from the same developmental stages. The results obtained, using a combination of different polyclonal and monoclonal antibodies, indicate that slow myosin is coexpres...

Nous présentons une application des techniques d'apprentissage symbolique. Cette application permet l'extraction automatique et la formalisation d'expertise biologique. Elle a pour support une méthode d'analyse de protéines- Ê: l'électrophorèse bidimensionnelle. Cette dernière produit des gels plans dont on extrait les paramètres numériques par tra...

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The appearance of the mRNA for the adult fast IIB myosin heavy chain (MHC) was examined during postnatal development of rats using an S1 nuclease assay. In normal rats, a large increase in the adult MHC mRNA began at 6-7 days after birth, whereas daily injections of newborn rats with 3 micrograms of triiodothyronine (T3) resulted in a precocious in...

The dwarf mutant is an autosomal recessive mutation of the mouse which causes a defective development of those anterior pituitary cells responsible for the production of thyroid-stimulating hormone, growth hormone, and prolactin. These mice are thus genetically hypothyroid and provide a model system in which one can investigate the influence of thy...

The intermediate filament (IF) composition of muscle cells of various sources is still a controversial issue. In the present study, the IF composition of bovine Purkinje fibres (PFs), atrial and ventricular myocardium, and gastric smooth muscle (SM) has been compared using biochemical and immunocytochemical methods. The Mr of the major IF subunit p...

To investigate possible alterations of myocardial performance in young rats, cardiac hypertrophy was induced by stenosis of the ascending aorta (AS) in three groups of 25-day-old rats that were compared with three groups of sham-operated controls (C). The cardiac overload duration was 8-10 days, 1 mo, and 2 mo in groups 1, 2, and 3, respectively. M...

When adult mouse muscle fibers are co-cultured with embryonic mouse spinal cord, the muscle regenerates to form myotubes that develop cross-striations and contractions. We have investigated the myosin heavy chain (MHC) isoforms present in these cultures using polyclonal antibodies to the neonatal, adult fast, and slow MHC isoforms of rat (all of wh...

Two myosin heavy chains (MHCs), alpha and beta, which exhibit different levels of ATPase activity related to the different velocities of muscle shortening, are differentially expressed in rat cardiac ventricles, depending on the developmental stage and the thyroid status of the animals. In contrast, no changes have been reported concerning the expr...