Trials of vaccines for pancreatic ductal adenocarcinoma: Is there any hope of an improved prognosis?

Pancreatic tumors are chemoresistant and malignant, and there are very few therapeutic options for pancreatic cancer, as the disease is normally diagnosed at an advanced stage. Although attempts have been made to develop vaccine therapies for pancreatic cancer for a couple of decades, none of the resultant protocols or regimens have succeeded in improving the clinical outcomes of patients. We herein review vaccines tested within the past few years, including peptide, biological and multiple vaccines, and describe the three sets of criteria used to evaluate the therapeutic activity of vaccines in solid tumors.

Whole-genome analysis reveals the complex evolutionary dynamics of Kenyan G2P[4] human rotavirus strains.

Although G2P[4] rotaviruses are common causes of acute childhood diarrhoea in Africa, to date there are no reports on whole genomic analysis of African G2P[4] strains. In this study, the nearly complete genome sequences of two Kenyan G2P[4] strains, AK26 and D205, detected in 1982 and 1989, respectively, were analysed. Strain D205 exhibited a DS-1-like genotype constellation, whilst strain AK26 appeared to be an intergenogroup reassortant with a Wa-like NSP2 genotype on the DS-1-like genotype constellation. The VP2-4, VP6-7, NSP1, NSP3 and NSP5 genes of strain AK26 and the VP2, VP4, VP7 and NSP1-5 genes of strain D205 were closely related to those of the prototype or other human G2P[4] strains. In contrast, their remaining genes were distantly related, and, except for NSP2 of AK26, appeared to originate from or share a common origin with rotavirus genes of artiodactyl (ruminant and camelid) origin. These observations highlight the complex evolutionary dynamics of African G2P[4] rotaviruses.

Whole-genome characterization of human group C rotaviruses: identification of two lineages in the VP3 gene.

Group C rotavirus (GCRV) is distributed worldwide as an enteric pathogen in humans and animals. However, to date, whole-genome sequences are available only for a human strain (Bristol) and a porcine strain (Cowden). To investigate the genetic diversity of human GCRVs, nearly full-length sequences of all 11 RNA segments were determined for human GCRVs detected recently in India (v508), Bangladesh (BS347), China (Wu82 and YNR001) and Japan (OH567 and BK0830) and analysed phylogenetically with sequence data for GCRVs published previously. All the RNA segments of human GCRV strains except for the VP3 gene showed high levels of conservation (>93 % nucleotide sequence identity, >92 % amino acid sequence identity), belonging to a single genetic cluster distinct from those of animal GCRVs. In contrast, the VP3 genes of human GCRVs could be discriminated into two clusters, designated M2 and M3, that were distinguished phylogenetically from those of porcine and bovine GCRVs (clusters M1 and M4, respectively). Between M2 and M3, amino acid sequence identity of the VP3 gene was 84.1-84.7 %, whereas high identities were observed within each cluster (92.3-97.6 % for M2, 98.2-99.3 % for M3). Sequence divergence among the four VP3 clusters was observed throughout the amino acid sequence except for conserved motifs, including those possibly related to enzyme functions of VP3. The presence of obvious genetic diversity only in the VP3 gene among human GCRVs suggested that either the M2 or M3 VP3 gene of human GCRVs might have been derived through reassortment from an animal GCRV or from an unidentified human GCRV strain belonging to a novel genogroup.

Phylogenetic analysis of rotaviruses with predominant G3 and emerging G9 genotypes from adults and children in Wuhan, China.

Prevalence and phylogenetic relatedness of rotaviruses causing diarrheal diseases in children and adults were analyzed in Wuhan, China. During a period between June 2006 and February 2008, group A rotavirus was identified in 24.9% (280/1126) and 7.6% (83/1088) of specimens taken from children and adults, respectively. G3P[8] was the most frequent genotype in both children (66.3%) and adults (62.7%), followed by G1P[8] (20.3% and 26.2%, respectively). G9 was detected in specimens from six children (2.0%) and seven adults (5.6%). The VP7 genes of G3P[8] rotaviruses from children and adults showed extremely high sequence identities to each other (98.9-100%) and also to those of G3 viruses isolated in Wuhan in 2003-2004. In the phylogenetic analysis of the VP7 gene, the G3P[8] rotaviruses in Wuhan were clustered into a single lineage with some G3 viruses, which had been referred to as "the new variant G3" rotaviruses, reported recently in East Asia and Southeast Asia. Similar to G3P[8] rotaviruses, extremely high sequence identities between children and adults were observed for VP7 genes of G1 and G9 rotaviruses. The G9 viruses were clustered in the lineage of globally spreading strains, while G1 viruses were genetically close to those reported previously in China and Japan. These findings indicated the persistence of the variant G3 rotaviruses and spread of G9 rotaviruses derived from the global G9 lineage in Wuhan, and suggested that the rotaviruses were circulating among children and adults, irrelevant to the G types.

Phylogenetic analysis of rotaviruses with genotypes G1, G2, G9 and G12 in Bangladesh: evidence for a close relationship between rotaviruses from children and adults.

To clarify the phylogenetic relatedness of rotaviruses causing gastroenteritis in children and adults, an epidemiologic investigation was conducted in Mymensingh, Bangladesh, during the period between July 2004 and June 2006. A total of 2,540 stool specimens from diarrheal patients from three hospitals were analyzed. Overall, rotavirus-positive rates in children and adults were 26.4 and 10.1%, respectively. Among the 155 rotavirus specimens examined genetically from both children and adults, the most frequent G genotype was G2 (detection rate: 54.0 and 47.6%, respectively), followed by G1 (21.2 and 26.2%, respectively), and G9 (15.9 and 9.5%, respectively). G12 was also detected in five specimens (3.2% in total; four children and one adult). Sequence identities of VP7 genes of G2 rotaviruses from children and adults were higher than 97.8%, while these Bangladeshi G2 viruses showed generally lower identities to G2 rotaviruses reported elsewhere in the world, except for some strains reported in African countries. Similarly, extremely high sequence identities between children and adults were observed for VP7 genes of G1, G9 and G12 rotaviruses, and also for the VP4 genes of P[4], P[6], and P[8] viruses. Rotaviruses from children and adults detected in this study were included in a single cluster in phylogenetic dendrograms of VP7 or VP4 genes of individual G/P types. Rotaviruses with two emerging types, G9 and G12, had VP7 genes that were phylogenetically close to those of individual G-types recently reported in Bangladesh and India and were included in the globally spreading lineages of these G-types. These findings suggested that genetically identical rotaviruses, including those with the emerging types G9 and G12, were circulating among children and adults in city and rural areas of Bangladesh.

Whole genomic characterization of a human rotavirus strain B219 belonging to a novel group of the genus Rotavirus.

Novel rotavirus strains B219 and ADRV-N derived from adult diarrheal cases in Bangladesh and China, respectively, are considered to belong to a novel rotavirus group (species) distinct from groups A, B, and C, by genetic analysis of five viral genes encoding VP6, VP7, NSP1, NSP2, and NSP3. In this study, the nucleotide sequences of the remaining six B219 gene segments encoding VP1, VP2, VP3, VP4, NSP4, and NSP5 were determined. The nucleotide sequences of the group B human rotavirus VP1 and VP3 genes were also determined in order to compare the whole genome of B219 with those of group A, B, and C rotavirus genomes. The nucleotide and deduced amino acid sequences of all B219 gene segments showed considerable identity to the ADRV-N (strain J19) sequences (87.7-94.3% and 88.7-98.7%, respectively). In contrast, sequence identity to groups A-C rotavirus genes was less than 61%. However, functionally important domains and structural characteristics in VP1-VP4, NSP4, and NSP5, which are conserved in group A, B, or C rotaviruses, were also found in the deduced amino acid sequences of the B219 proteins. Hence, the basic structures of all B219 viral proteins are considered to be similar to those of the known rotavirus groups.

Diversity of staphylocoagulase and identification of novel variants of staphylocoagulase gene in Staphylococcus aureus.

Staphylocoagulase (SC) is a major phenotypic determinant of Staphylococcus aureus. Serotype of SC (coagulase type) is used as an epidemiological marker and 10 types (I-X) have been discriminated so far. To clarify genetic diversity of SC within a single and among different serotype(s), we determined approximately 1500 bp-nucleotide sequences of SC gene encoding D1, D2, and central regions (N-terminal half and central regions of SC; SC(NC)) for a total of 33 S. aureus strains comprising two to three strains from individual coagulase types (I-VIII, X) and 10 strains which were not determined as previously known SC serotypes (ND-strains). Amino acid sequence identities of SC(NC) among strains with a single coagulase type of II, III, IV, V, VI and X were extremely high (more than 99%), whereas lower identity (56-87%) was observed among different types. In contrast, within a single coagulase type of I, VII, or VIII, sequence divergence was found (lowest identity; 82%). SC(NC) sequences from the ND-strains were discriminated into two genetic groups with an identity of 71% to each other (tentatively assigned to genotypes [XI] and [XII]), and exhibited less than 86% sequence identities to those of most known coagulase types. All the types [XI] and [XII] strains were methicillin susceptible and belonged to different sequence types from those of coagulase types I-X strains reported so far by multilocus sequence typing. These findings indicated genetic heterogeneity of SC in coagulase types I, VII, and VIII strains, and the presence of two novel SC genotypes related to antigenicity of SC serotypes.

The microtubule-binding protein Hook3 interacts with a cytoplasmic domain of scavenger receptor A.

The class A scavenger receptor (SR-A) is a multifunctional transmembrane glycoprotein that is implicated in atherogenesis, innate immunity, and cell adhesion. Despite extensive structure-function studies of the receptor, intracellular molecules that directly interact with SR-A and regulate the receptor trafficking have not been determined. In the current study, we have identified a microtubule-binding protein, Hook3, as a novel interacting partner of SR-A. The association between a rat Hook3 isoform and SR-A was suggested by yeast two-hybrid screening and mass spectrometry analysis of SR-A-cytoplasmic domain-bound proteins in rat alveolar macrophages. The binding of overexpressed and endogenous human Hook3 to SR-A was demonstrated by pull-down assay and co-immunoprecipitations. Furthermore, endogenous murine SR-A and HK3 co-sedimented from cell lysates isolated from Raw264.7 murine macrophage cells. The interaction of Hook3 with SR-A was significantly stimulated after SR-A had recognized the extracellular ligand. Studies using truncations demonstrated that the positively charged C-terminal Val614-Ala717 region of human Hook3 was required for the interaction with the negatively charged residues, Glu12, Asp13, and Asp15 in the human SR-A cytoplasmic domain. By transfecting small interfering RNA targeting Hook3, total and surface expression, receptor-mediated ligand uptake and protein stability of SR-A were significantly promoted, whereas the protein synthesis and maturation were not altered. We propose for the first time that Hook3 may participate in the turnover of the endocytosed scavenger receptor.

Genetic analysis of mec A homologues in Staphylococcus sciuri strains derived from mastitis in dairy cattle.

Methicillin-resistant Staphylococcus aureus (MRSA) is defined by the presence of the mec A gene, which is considered to have been transferred horizontally from unknown bacterial species to S. aureus. As a candidate of evolutionary precursor of the mec A, the mec A-like gene (mec A homologue), which is ubiquitously present in Staphylococcus sciuri has been proposed. In this study, sequences of the mec A homologue in four S. sciuri strains (SCBM 1-SCBM 4) derived from dairy cows were determined to analyze their genetic characteristics and relatedness to mec A and the mec A homologue reported so far. The mec A-like gene sequences of the four S. sciuri strains were identical with each other and were considered to encode a product comprising 665 amino acids that is one amino acid smaller in size than products of mec A-like gene reported previously for S. sciuri strains K1, K1 1, and K3 (mec A1). The mec A homologue of a representative strain SCBM 1 showed 79.3--79.8% sequence identity to MRSA mec A and 93.4--94.4% identity to mec A homologues reported for the three S. sciuri strains. Between S. sciuri strain SCBM 1 and strains K1, K1 1, or K3, amino acid sequence identities in transpeptidase domain of the mec A-like gene product (98.2--98.5%) were higher than those in the transglycosylase domain (92.1--94.3%). In addition, SCBM 1 showed extremely high sequence identities of hsp 60, sodA, and rpoB genes (more than 98.7%) to S. sciuri strains, while showing 70.3--94.2% identity of these genes to other staphylococcal species. These findings indicated that mec A homologues in S. sciuri may be genetically more divergent than mec A in MRSA and methicillin-resistant coagulase-negative staphylococci.

Detection of a novel aph(2") allele (aph[2"]-Ie) conferring high-level gentamicin resistance and a spectinomycin resistance gene ant(9)-Ia (aad 9) in clinical isolates of enterococci.

Aminoglycoside-modifying enzymes (AMEs) are major factors that confer aminoglycoside resistance to enterococci. In an epidemiologic study on distribution of 12 AME genes in 534 recent clinical strains isolated from a Japanese hospital, two uncommon AME genes, ant(9)-Ia and a novel aph(2") allele, aph(2")-Ie, were detected. ant(9)-Ia had been reported only in Staphylococcus aureus and encodes spectinomycin adenylyltransferase ANT(9)-I, which confers resistance to spectinomycin. The ant(9)-Ia gene was detected in three strains, a single strain each of Enterococcus faecalis, E. faecium, and E. avium. Nucleotide sequences of ant(9)-Ia from these three enterococcal species were identical to that reported for S. aureus and considered to be located on Tn 554. The new aph(2") allele, designated aph(2")-Ie, was identified in three E. faecium strains. The aph(2")-Ie allele was genetically close to aph(2")-Id reported in E. casseliflavus (93.7% amino acid sequence identity; 96.3% similarity), while distant from aph(2")-Ia, aph(2")-Ib, or aph(2")-Ic (26.3-29.5% amino acid sequence identity). Sequence divergence between APH(2")-Id and APH(2")-Ie was mostly located in amino-terminal half. In contrast, sequences corresponding to the three motifs required for aminoglycoside phosphotransferase were conserved except for a single amino acid. Three E. faecium strains having aph(2")-Ie showed high-level resistance to gentamicin and streptomycin, but not to kanamycin, dibekacin, and tobramycin, unlike enzyme specificity described for aph(2")-Id in E. casseliflavus. Such a difference in resistance phenotype was suggested to be related to amino acid sequence divergence between APH(2")-Id and APH(2")-Ie.

Adenovirus E4orf6 targets pp32/LANP to control the fate of ARE-containing mRNAs by perturbing the CRM1-dependent mechanism.

E4orf6 plays an important role in the transportation of cellular and viral mRNAs and is known as an oncogene product of adenovirus. Here, we show that E4orf6 interacts with pp32/leucine-rich acidic nuclear protein (LANP). E4orf6 exports pp32/LANP from the nucleus to the cytoplasm with its binding partner, HuR, which binds to an AU-rich element (ARE) present within many protooncogene and cytokine mRNAs. We found that ARE-mRNAs, such as c-fos, c-myc, and cyclooxygenase-2, were also exported to and stabilized in the cytoplasm of E4orf6-expressing cells. The oncodomain of E4orf6 was necessary for both binding to pp32/LANP and effect for ARE-mRNA. C-fos mRNA was exported together with E4orf6, E1B-55kD, pp32/LANP, and HuR proteins. Moreover, inhibition of the CRM1-dependent export pathway failed to block the export of ARE-mRNAs mediated by E4orf6. Thus, E4orf6 interacts with pp32/LANP to modulate the fate of ARE-mRNAs by altering the CRM1-dependent export pathway.

Analysis of the prevalence of tetracycline resistance genes in clinical isolates of Enterococcus faecalis and Enterococcus faecium in a Japanese hospital.

Prevalence of seven tetracycline resistance (TC(R)) genes--tet(L), tet(M), tet(K), tet(O), tet(S), tet(T), and tet(U)--which are known to be distributed to gram-positive cocci was analyzed for 224 Enterococcus faecalis and 46 Enterococcus faecium clinical isolates obtained in a Japanese hospital. Any of the TC(R) genes was detected in 75.9% of all the enterococcal strains. The tet(M) was detected at highest rates in both E. faecalis (75.0%) and E. faecium (69.6%), followed by tet(L), which was harbored in 6.7% of E. faecalis isolates and 30.4% of E. faecium isolates. The tet(O), tet(S), and tet(T) were detected in E. faecalis at low frequencies mostly associated with tet(M), while tet(K) and tet(U) were not detected. Nucleotide sequences of tet(S) from E. faecalis strains were identical to that reported in Listeria monocytogenes. Sequences of tet(O) from two E. faecalis strains were almost identical to each other and also to those from Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus mutans, Campylobacter jejuni, and Campylobacter coli, although minor sequence divergence was observed. The tet(T), which had been reported only in Streptococcus pyogenes, was found in five E. faecalis strains. Sequence of the enterococcal tet(T) differed from that of S. pyogenes by only four nucleotides (four amino acids) and showed high sequence identity (99.8%, amino acid level). Enterococcal strains with any one TC(R) gene or those with two TC(R) genes showed generally similar MICs of tetracyclines, and no evident difference in resistance level was observed.

Phylogenetic analysis of a human group B rotavirus WH-1 detected in China in 2002.

A human group B rotavirus strain WH-1 was detected in an adult sporadic case of diarrhea in Wuhan, China in 2002. In this study, the gene sequences of WH-1 were determined in order to examine the phylogenetic relatedness to other human group B rotaviruses found previously in China (ADRV, in 1982), India (CAL-1, in 1998), and Bangladesh (Bang373, in 2000), as well as animal viruses, and to estimate the mutation rate of group B rotavirus. VP7 (major outer capsid protein) gene of WH-1 showed extremely high sequence identity (98.6%) to ADRV and showed relatively high sequence identities to CAL-1 (92.5%) and Bang373 (92.4%). In contrast, identities to animal (bovine and murine) group B rotaviruses were considerably lower (61-64%). Other gene segments of WH-1 encoding VP2, VP4, VP6, NSP1-NSP3, and NSP5 also showed high sequence identities to ADRV genes (98-99%), which were generally higher than those to CAL-1 genes and Bang373 genes (90-95%). However, amino acid sequence identities between WH-1 and ADRV were almost the same (VP2, VP6, and NSP3), or lower (NSP2) than those between WH-1 and CAL-1 (or Bang373). Since rates of synonymous substitution and transition between WH-1 and ADRV were similar for all the segments analyzed, genetic evolution was considered to have occurred neutrally and at a similar speed in most of the RNA segments. Based on the sequence divergence between WH-1 and ADRV, the mutation rate in natural condition of human group B rotavirus was estimated as 7.9 x 10(-4) substitution/site per year. The frequency of synonymous substitution between ADRV and Bang373 was 5.7 times higher than that between ADRV and WH-1, suggesting that the group B rotaviruses of Indian-Bangladeshi lineage diverged from that of Chinese lineage several decades ago.

Genetic analysis of group B human rotaviruses detected in Bangladesh in 2000 and 2001.

Group B rotaviruses detected in Bangladesh in 2000 and 2001 were analyzed genetically to clarify relatedness to human group B rotaviruses reported previously in China and India, and to animal group B rotaviruses. VP7 gene sequences of the Bangladeshi group B rotaviruses (Bang373, Bang544, Bang334, and Bang402) were almost identical to each other and also showed high sequence identity to the Indian strain CAL-1 (98%) and Chinese strain adult diarrhea rotavirus (ADRV) (92%), while identities to bovine and murine viruses were considerably low (60-63%). Other genes of Bang373 and Bang544 encoding VP2, VP4, VP6, and NSP1 through NSP5 also showed much higher sequence identities to those of CAL-1 (97.7-99.4%) than to those of ADRV (89.9-93.9%). Characterization of nucleotide substitutions among Bang373, CAL-1, and ADRV suggested that all the gene segments might have evolved neutrally at similar mutation rates, while some of the gene segments (e.g., VP2 gene) were suggested to be more conserved than others. In conclusion, group B rotaviruses detected in Bangladesh represented by Bang373 and the Indian virus CAL-1 were considered as virtually identical viruses which are distinct genetically from ADRV, and it was suggested that Bang373 (CAL-1)-like group B rotavirus (Bengali strains) might be distributed primarily in an area around the Bay of Bengal.

Analysis of genomic diversity and evolution of the low-level antiseptic resistance gene smr in Staphylococcus aureus.

A multidrug efflux pump specified by the smr gene mediates low-level antiseptic resistance in staphylococci. We analyzed the genomic diversity of smr and its gene cassette, a structural unit containing smr and terminal direct repeats (DRs), in 22 clinical strains of Staphylococcus aureus isolated over 9 years in a Japanese hospital. Although open reading frames (ORFs) of all the smr genes examined were identical to those reported previously (e.g., qacD in pSK41), smr gene cassettes were classified into three groups (types 1, 2, and 3). The type 1 cassette had an identical genetic organization to that found in the plasmid pSK41, a putative prototype of the smr gene cassette, which contains DRs flanking smr. In the type 2 cassette, the rep gene and a putative replication nick site were found upstream of smr, between a SSOA (single-strand origin) sequence and DR1c, which are components of the type 1 cassette DR. In the type 3 cassette detected in a single strain, IS431 was located between the 3' end of smr and DR. It was suggested by genomic comparison that type 2 and type 3 cassettes might have been derived from the type 1 cassette via insertion of foreign DNA sequence, and that the type 2 cassette might be a precursor form of some previously reported smr cassettes, such as those in pSK108 and pNVH99. Although MICs of antiseptics and ethidium bromide were generally the same among strains having type 1, 2, or 3 smr gene cassette, the type 1 cassette was detected most frequently. Moreover, the copy number of the smr gene in the type 2 cassette was found to be much higher than that in the type 1 or type 3 cassette.