The intratumor mycobiome promotes lung cancer progression via myeloid-derived suppressor cells.

Although polymorphic microbiomes have emerged as hallmarks of cancer, far less is known about the role of the intratumor mycobiome as living microorganisms in cancer progression. Here, using fungi-enriched DNA extraction and deep shotgun metagenomic sequencing, we have identified enriched tumor-resident Aspergillus sydowii in patients with lung adenocarcinoma (LUAD). By three different syngeneic lung cancer mice models, we find that A. sydowii promotes lung tumor progression via IL-1ß-mediated expansion and activation of MDSCs, resulting in suppressed activity of cytotoxic T lymphocyte cells and accumulation of PD-1+ CD8+ T cells. This is mediated by IL-1ß secretion via ß-glucan/Dectin-1/CARD9 pathway. Analysis of human samples confirms that enriched A. sydowii is associated with immunosuppression and poor patient outcome. Our findings suggest that intratumor mycobiome, albeit at low biomass, promotes lung cancer progression and could be targeted at the strain level to improve patients with LUAD outcome.

Genetic and codon usage bias analyses of major capsid protein gene in Ranavirus.

The Ranavirus (one genus of Iridovidae family) is an emerging pathogen that infects fish, amphibian, and reptiles, and causes great economical loss and ecological threat to farmed and wild animals globally. The major capsid protein (MCP) has been used as genetic typing marker and as target to design vaccines. Herein, the codon usage pattern of 73 MCP genes of Ranavirus and Lymphocystivirus are studied by calculating effective number of codons (ENC), relative synonymous codon usage (RSCU), codon adaptation index (CAI), and relative codon deoptimization index (RCDI), and similarity index (SiD). The Ranavirus are confirmed to be classified into five groups by using phylogenetic analysis, and varied nucleotide compositions and hierarchical cluster analysis based on RSCU. The results revealed different codon usage patterns among Lymphocystivirus and five groups of Ranavirus. Ranavirus had six over-represented codons ended with G/C nucleotide, while Lymphocystivirus had six over-represented codons ended with A/T nucleotide. A comparative analysis of parameters that define virus and host relatedness in terms of codon usage were analyzed indicated that Amphibian-like ranaviruses (ALRVs) seem to possess lower ENC values and higher CAIs in contrast to other ranaviruses isolated from fishes, and two groups (FV3-like and CMTV-like group) of them had received higher selection pressure from their hosts as having higher relative codon deoptimization index (RCDI) and similarity index (SiD). The correspondence analysis (COA) and Spearman's rank correlation analyses revealed that nucleotide compositions, relative dinucleotide frequency, mutation pressure, and natural translational selection shape the codon usage pattern in MCP genes and the ENC-GC3S and neutrality plots indicated that the natural selection is the predominant factor. These results contribute to understanding the evolution of Ranavirus and their adaptions to their hosts.

Tlr22 structure and expression characteristic of barbel chub, Squaliobarbus curriculus provides insights into antiviral immunity against infection with grass carp reovirus.

Grass carp reovirus (GCRV) is the most virulent agent to Grass carp, Ctenopharyngodon idella, and causes a severe infectious disease called hemorrhagic disease of grass carp. Generally, barbel chub, Squaliobarbus curriculus, a genetically closely related species to grass carp, exhibits significant resistance against GCRV infection compared to grass carp. To investigate whether the Toll-like receptor 22 (tlr22) has got a vital role against the GCRV infection, the full cDNA sequence of tlr22 from barbel chub (Sctlr22) was cloned by RACE-PCR, and the structure and expression feature were studied. The complete cDNA sequence of Sctlr22 has a size of 3504 bp, encoding for 960 amino acid residues. Sctlr22 possesses typical structural features of the tlrs family, including 19 leucine rich repeats (LRRs), a transmembrane (TM) and a Toll/interleukin-1 receptor (TIR) domain. Phylogenetic analysis revealed that barbel chub Tlr22 was clustered together with the Tlr22 of grass carp (Citlr22). Structurally, barbel chub Tlr22 have two different structure in LRRs domain and TIR domain with grass carp (Susceptible to GCRV), but was similar to that of Danio rerio and Cyprinus carpio (Resistance to GCRV). Quantitative RT-PCR analysis has shown that Sctlr22 is prominently expressed in immune relevant tissues such as head kidney and spleen. After GCRV infection, Sctlr22 expression level was up-regulated in four tested tissues and the highest expression of Sctlr22 appeared fast and higher than Citlr22. The interferon-ß (ifn-ß) expression level in CIK cells over-expressing fused cDNA encoding the LRR domain of Sctlr22 to the transmembrane and TIR domain of Citlr22 was significantly higher than that cells overexpressing Citlr22 after GCRV infection. The virus titer was significantly reduced compared to Citlr22 over-expressing cells. These results suggested that Sctlr22 seems to play a vital role in the immune response against GCRV.

De novo annotation of the immune-enriched transcriptome provides insights into immune system genes of Chinese sturgeon (Acipenser sinensis).

Chinese sturgeon (Acipenser sinensis), one of the oldest extant actinopterygian fishes with very high evolutionary, economical and conservation interest, is considered to be one of the critically endangered aquatic animals in China. Up to date, the immune system of this species remains largely undetermined with little sequence information publicly available. Herein, the first comprehensive transcriptome of immune tissues for Chinese sturgeon was characterized using Illumina deep sequencing. Over 67 million high-quality reads were generated and de novo assembled into the final set of 91,739 unique sequences. The annotation pipeline revealed that 25,871 unigenes were successfully annotated in the public databases, of which only 2002 had significant match to the existing sequences for the genus Acipenser. Overall 22,827 unigenes were categorized into 52 GO terms, 12,742 were classified into 26 KOG categories, and 4968 were assigned to 339 KEGG pathways. A more detailed annotation search showed the presence of a notable representation of immune-related genes, which suggests that this non-teleost actinopterygian fish harbors the same intermediates as in the well known immune pathways from mammals and teleosts, such as pattern recognition receptor (PRR) signaling pathway, JAK-STAT signaling pathway, complement and coagulation pathway, T-cell receptor (TCR) and B-cell receptor (BCR) signaling pathways. Additional genetic marker discovery led to the retrieval of 20,056 simple sequence repeats (SSRs) and 327,140 single nucleotide polymorphisms (SNPs). This immune-enriched transcriptome of Chinese sturgeon represents a rich resource that adds to the currently nascent field of chondrostean fish immunogenetics and furthers the conservation and management of this valuable fish.

Comparative subproteome analysis of three representative Leptospira interrogans vaccine strains reveals cross-reactive antigens and novel virulence determinants.

Pathogenic Leptospira spp. causes leptospirosis in China and throughout the world. Here, we have sequenced two L. interrogans moderately virulent vaccine strains JDL03 (serovar Canicola) and JDL10 (serovar Hebdomadis) used in China. We selected a subproteomic approach to identify surface-exposed proteins including OMPs and extracellular proteins of these two strains plus a highly virulent vaccine strain 56601 (serovar Lai). Comparative surface-exposed proteome among the three strains indicated 81 cores, 61 dispensable and 122 unique surface-exposed proteins. Finally, the 10 highly conserved surface-exposed or subsurface proteins included two known cross-reactive antigens (LipL32 and LA_3469) and another two novel antigens (LA_0136 and LA_0505) displaying conserved immunoreactivity among 15 Chinese epidemic serovars. Furthermore, many potential virulence factors were detected in these identified surface-exposed proteins, such as Loa22, LipL32, LenC, LenF and OmpL37. Interestingly, LipL45, ClpA and ClpB, exhibiting obvious amino acid mutations among str.56601, str.JDL03 and JDL10, might contribute to virulence differences observed among these strains. Additionally, specific surface-exposed proteins in virulent str.56601 were considered to be key virulence determinants, such as Zn-dependent protease, cholesterol oxidase precursor, and so on. In all, we had relatively complete surface-exposed subproteomes of L. interrogans, which will enhance our understanding of leptospiral pathogenesis and key virulence determinants. BIOLOGICAL SIGNIFICANCE: The present work demonstrates the use of genomic sequencing and subproteomic studies for the identification of potential vaccine and diagnostic antigen candidates against leptospirosis. The data show the conserved surface-exposed proteins to be novel potentially vaccine/diagnostic candidates. Furthermore, the data also show that LipL45, ClpA, ClpB and a lipoprotein from these three strains plus another highly virulent strain Fiocruz L1-130 contain specific amino acid mutations in strains JDL03 and JDL10. The surface-exposed subproteome of pathogenic L. interrogans could provide valuable information to gain a more complete understanding of leptospiral pathogenesis and virulence determinants.

Isolation and characterization of two novel plasmids from pathogenic Leptospira interrogans serogroup Canicola Serovar Canicola strain Gui44.

BACKGROUND: Previous genomic analysis of pathogenic Leptospira has identified two circular chromosomes but no plasmid. This study aims to investigate potential extrachromosomal elements of L.interrogans serovar Canicola strain Gui44. METHODOLOGY: Two novel plasmids, pGui1 and pGui2, were isolated from the pathogenic strain Gui44, using a modified alkaline lysis method. Southern blotting was performed to determine the presence and size of them. Then, 454 and Hiseq sequencing were applied to obtain and analyze the complete sequences of the two plasmids. Furthermore, real-time quantitative PCR and next-generation sequencing were used to compare relative copy numbers of the two plasmids with that of the chromosomes. Finally, after serial passages in vitro for more than 2 years, the strain Gui44 was subsequently re-sequenced to estimate stability of the two plasmids. PRINCIPAL FINDINGS: The larger plasmid, pGui1, 74,981 base pairs (bp) in length with GC content of 34.63%, possesses 62 open reading frames (ORFs). The smaller plasmid, pGui2, is 66,851 bp in length with GC content of 33.33%, and contains 63 ORFs. The replication initiation proteins encoded by pGui1 and pGui2 demonstrate significant sequence similarity with LA1839 (86% and 88%), a well-known replication protein in another pathogenic L.interrogans serovar Lai strain Lai, suggesting the ability for autonomous plasmid replication. Quantitative PCR and next-generation sequencing confirms a single copy of both plasmids and their stable presence in the strain Gui44 with in vitro serial passages after more than 2 years. Interestingly, the two plasmids both contain a significant number of novel genes (35 in pGui1 and 52 in pGui2). CONCLUSIONS: This report confirms the presence of two separate circular plasmids in serovar Canicola strain Gui44 and provides a new understanding of genomic organization, adaptation, evolution and pathogenesis of Leptospira, which will aid in the development of in vivo genetic manipulation systems in pathogenic Leptospira species.

Construction of a recombinant eukaryotic vector for a grass carp reovirus VP6 gene and its expression in vitro and in vivo.

A recombinant plasmid expressing the VP6 inner capsid coding gene of grass carp reovirus (GCRV) was constructed and expressed in a Ctenopharyngodon idellus kidney (CIK) cell line and grass carps. The VP6 gene was amplified by RT-PCR, cloned into a pEGFP-N1 eukaryotic expression vector and transfected into CIK cells. Results from enhanced green fluorescent protein (EGFP) experiments and flow cytometry showed highest protein expression at 48 h. The immunoreactivity of fusion protein was confirmed using an indirect immunofluorescent assay. The specific binding between the fusion protein and polyclonal mouse GCRV VP6-specific antiserum indicated that the fusion protein was translated in vitro and had good immunogenicity. An antiviral activity assay showed that the virus titer was 100-fold lower in the GCRV VP6 expressed cells than in the pEGFP-N1 transfected cells. The expression levels of three immune genes in the head kidney of grass carps injected with the recombinant plasmid were used. Mx, TLR3 and IgM mRNA expression increased sharply at the 1st and 15th days post-injection (dpi). Specific antibodies were detected 30 days after vaccination. Neutralizing titers of the antibodies in vaccinated fish detected ranged from 160 to 320. Intramuscular injection of grass carps with 1 µg of pEGFP-N1-VP6 was found to provide strong protection against GCRV. These results suggested that the VP6 gene was a good candidate for the design of GCRV-DNA vaccines and to investigate the use of cytokines as co-stimulatory molecules.

Pathological and microbiological findings from mortality of the Chinese giant salamander (Andrias davidianus).

The Chinese giant salamander, Andrias davidianus, is a nationally protected and cultured species in China. Recently, a severe epizootic occurred in cultured Chinese giant salamanders in Hubei, Hunan, Sichuan, Shaanxi, and Zhejiang provinces of China, causing substantial economic losses. The typical clinical signs of diseased larval animals were jaw and abdominal swelling and subcutaneous hemorrhaging. Diseased adult animals exhibited skin hemorrhages, ulceration of the hind limbs, and multiple hemorrhagic spots in the visceral organs. Histopathological observation indicated tissue necrosis and cytoplasmic inclusions in the spleen, liver and kidney, suggestive of viral disease. A viral agent was isolated from affected tissues in cell culture. The virus was determined to be pathogenic after experimental infection. Electron microscopy revealed iridovirus-like virions with a size of 140-180 nm in diameter inside the kidney of naturally infected animals and in cell culture. The major capsid protein (MCP) of the virus exhibited 98-99 % sequence identity to ranaviruses. Additionally, phylogenetic analysis indicated that the virus belonged to the genus Ranavirus. Comparative analysis of the MCP gene sequence with those of other viruses previously isolated from Chinese giant salamanders revealed that these isolates were highly similar, although a few variations were observed. The virus was preliminarily named Chinese giant salamander iridovirus (GSIV).

IFN-γ in turtle: conservation in sequence and signalling and role in inhibiting iridovirus replication in Chinese soft-shelled turtle Pelodiscus sinensis.

The IFN-γ gene was identified in a turtle, the Chinese soft-shelled turtle, Pelodiscus sinensis, with its genome consisting of 4 exons and 3 introns. The deduced amino acid sequence of this gene contains a signal peptide, an IFN-γ family signature motif (130)IQRKAVNELFPT, an NLS motif (155)KRKR and three potential N-glycosylation sites. As revealed by real-time quantitative PCR, the gene was constitutively expressed in all tested organs/tissues, with higher level observed in blood, intestine and thymus. An induced expression of IFN-γ at mRNA level was observed in peripheral blood leucocytes (PBLs) in response to in vitro stimulation of LPS and PolyI:C. The overexpression of IFN-γ in the Chinese soft-shelled turtle artery (STA) cell line resulted in the increase in the expression of transcriptional regulators, such as IRF1, IRF7 and STAT1, and antiviral genes, such as Mx, PKR, implying possibly the existence of a conserved signalling network and role for IFN-γ in the turtle. Furthermore, the infection of soft-shelled turtle iridovirus (STIV) in the cell line transfected with IFN-γ may cause the cell death as demonstrated with the elevated lactate dehydrogenase (LDH) level and cell mortality. However, the mechanism involved in the antiviral activity may require further investigation.

Analysis of variable genomic loci in white spot syndrome virus to predict its origins in Procambarus clarkii crayfish farmed in China.

Variable genomic loci were examined in 4 white spot syndrome virus (WSSV) isolates (08HB, 09HB, 08JS and 09JS) from Procambarus clarkii crayfish collected from Jiangsu and Hubei Provinces in China in 2008 and 2009. In ORF75, sequence variation detected in the 4 isolates, as well as in isolates sequenced previously, suggested that WSSV might have segregated into 2 lineages since first emerging as a serious pathogen of farmed shrimp in East Asia in the early-mid 1990s, with one lineage remaining in East Asia and the other separating to South Asia. In ORF23/24, deletions of 9.31, 10.97, or 11.09 kb were evident compared to a reference isolate from Taiwan (WSSV-TW), and, in ORF14/15, deletions of 5.14 or 5.95 kb were evident compared to a reference isolate from Thailand with the largest genome size (TH-96-II). With respect to these genome characteristics, the crayfish isolates 08HB, 09HB and 08JS were similar to WSSV-TW and the isolate 09JS was similar to a reference isolate from China (WSSV-CN). In addition to these loci, sequence variation was evident in ORF94 and ORF125 that might be useful for differentiating isolates and in epidemiological tracing of WSSV spread in crayfish farmed in China. However, as all 4 crayfish isolates possessed a Homologous Region 9 sequence identical to isolate WSSV-TW and another Thailand isolate (WSSV-TH), and as their transposase sequence was identical to isolates WSSV-CN and WSSV-TH, these 2 loci were not useful in predicting their origins.

[Highly efficient inhibition on replication of grass carp reovirus mediated by chemically synthesized small interfering RNAs].

Two short interfering RNAs (siRNA-RdRp1286, siRNA-RdRp1441) and one short interfering RNA (siRNA-OCP117), targeted to the RNA dependent RNA polymerase (RdRp) gene and outer capsid protein (OCP) gene of Grass carp reovirus (GCRV) respectively, were chemically synthesized and transfected into the CIK cells by lipofectamine 2000. 6 hours after transfection, the transfected CIK cells were challenged with GCRV. The culture media were collected at 48h post challenge and the virus was titrated in microculture system to evaluate the inhibition effect on GCRV replication mediated by siRNAs. Referring to the mRNA level of housekeeping gene beta-actin, RT-PCR was applied to detect the level of GCRV mRNA in transfected and challenged CIK cells. The results showed that the viral titer (lgTCID50/0. 1mL) in siRNA-RdRp1286, siRNA-RdRp1441 and siRNA-OCP117 transfected CIK cells were 4.41 +/- 0.16, 3.83 +/- 0.44 and 1.94 +/- 0.42 respectively, which were significantly lower than that in virus infection positive control (7.92 +/- 0.52) (P < 0.01). No significant change in viral titer was observed in the group transfected with siRNA negative control after challenged with GCRV (7.50 +/- 0.17, P > 0.05). Compared with the mRNA transcriptional level of beta-actin gene in virus infection positive control, the mRNA levels of GCRV in siRNA-RdRpl 286, siRNA-RdRp1 441 and siRNA-OCP117 transfected CIK cells were reduced significantly and the inhibition rate reached to (82.08 +/- 2.15)%, (89.19 +/- 1.14).% and (92.62 +/- 0.17)%, respectively. The mRNA level of GCRV in the siRNA negative control group had no noticeable change (P > 0 05).

[Isolation and identification of channel catfish (Ictalurus punctatus) hemorrhage reovirus].

By using cell culture and virus infection methods, a new reovirus had been isolated from channel catfish (Ictalurus punctatus) suffered with severe hemorrhage and had been identified as channel catfish reovirus (CCRV) after artificial infection in fish, electron microscopy observation, physical-chemical tests, genomic SDS-PAGE analysis and sequencing. In artificial infection test, the typical symptoms of channel catfish hemorrhage as naturally occurred could be reproduced. The isolated virus could cause typical cytopathic effect in CCO and CCK cell lines. Electron microscopy observation of ultra-thin section samples of CCRV infected CCO and CCK cells revealed that the virus replicated in cytoplasm, arrayed in crystalline, and had a non-enveloped double capsid with a diameter of 60-70 nm. Frozen-thawed, 56 degrees C 1 h, chloroform and ether had no significant effects on CCRV titer, 65 degrees C 1 h could significantly inactivated the viral infectivity. The CCRV genome SDS-PAGE analysis and nuclease sensitivity test showed that the virus genome was the same as that of viruses in Aquareovirudae and consisted of 11 segments of dsRNA assigned into three classes L1, L2, L3; M1, M2, M3 and S1, S2, S3, S4, S5 with a range of size from 0.9 to 4.4 kb. The Cloning and sequencing of the CCRV S4 segment indicated the nucleic acid number of CCRV S4 was 909 bp in length, which was exactly the same as that of GCRV S4 (AF403396) and GSRV S4 (AF403407) segments. The BLAST of CCRV S4 sequence in NCBI GenBank showed that it had a 99% and 90% similarity in sequence to the GCRV S4 and GSRV S4 segments, respectively.

[High-titer preparation of HIV-1-based defective lentivector and it mediated efficient gene transfer].

Lentivectors have drawn considerable attention recently and become important delivery vehicles for gene transfer manipulation. By Transiently co-transfecting 293T packaging cells with three DNA plasmids system encoding lentivector constituents, a protocol for bulky preparation of human immunodeficiency virus type-1 ( HIV-1)-based defective lentivector with high titer has been established. Transient co-transfection of 293T packaging cells resulted in production of high-titer vector (1.1 x 10 IU/ml), which can be further concentrated over 100-fold through a single step centrifugation. The vector was capable of efficiently transducing a variety of cells from both primate and non-primate sources, including of human T-lymphoblastoid cell line. Long-term culture of vector transduced cells showed a stable expression of foreign gene over 18 months detected by RT-PCR. Assessment of potential generation of replication-competent virus revealed no detection of p24 antigen protein or infectious particles in vector-transduced cells.