High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis

Simonyan, Vahan; Chumakov, Konstantin; Dingerdissen, Hayley; Faison, William J.; Goldweber, Scott; Golikov, Anton; Gulzar, Naila; Karagiannis, Konstantinos; Lam, Phuc Vinh Nguyen; Maudru, Thomas; Muravitskaja, Olesja; Osipova, Ekaterina; Pan, Yang; Pschenichnov, Alexey; Rostovtsev, Alexandre; Santana‐Quintero, Luis V.; Smith, Krista; Thompson, Elaine E.; Tkachenko, Valery; Torcivia-Rodriguez, John; Voskanian, Alin; Wan, Qing; Wang, Jing; Wu, Tsung-Jung; Wilson, Carolyn A.; Mazumder, Raja

doi:10.1093/database/baw022

Cited by 63 publications

(52 citation statements)

References 26 publications

(28 reference statements)

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“…Besides naturally occurring variants, several mutations have been observed in the VISTA gene in a range of cancer types, albeit at very low frequencies. The most commonly observed mutation (six samples in TCGA and ICGC combined) is an R (arginine)/C (cysteine) substitution at position 86, which is located in the Ig‐like V‐type domain and probably results in loss of function . Interestingly, the next most frequent mutation (five samples in TCGA and ICGC combined) that may result in loss of function occurs at the next position, position 87, where R is substituted for W (tryptophan).…”

Section: Vista Function In Non‐hematopoietic Cells In Cancermentioning

confidence: 99%

VISTA: Coming of age as a multi-lineage immune checkpoint

ElTanbouly

Schaafsma

Noelle

et al. 2020

Clinical and Experimental Immunology

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The immune response is governed by a highly complex set of interactions among cells and mediators. T cells may be rendered dysfunctional by the presence of high levels of antigen in the absence of co-stimulation while myeloid cells may be programmed towards an immunosuppressive state that promotes cancer growth and metastasis while deterring tumor immunity. In addition, inhibitory programs driven by immune checkpoint regulators dampen anti-tumor immunity. The ideal cancer immunotherapy treatment will improve both cross-priming in the tumor microenvironment and relieve suppression by the inhibitory checkpoints. Recently, blockade of programmed cell death 1 (PD-1) and cytotoxic T lymphocyte antigen 4 (CTLA-4) has elicited impressive results, but not in all patients, so additional targets are under investigation. V-set immunoglobulin domain suppressor of T cell activation (VISTA) is a novel immunoregulatory receptor that is broadly expressed on cells of the myeloid and lymphoid lineages, and is frequently implicated as a poor prognostic indicator in multiple cancers. Importantly, antibody targeting of VISTA uniquely engages both innate and adaptive immunity. This, combined with the expression of VISTA and its non-redundant activities compared to other immune checkpoint regulators, qualifies VISTA to be a promising target for improving cancer immunotherapy.

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Section: Vista Function In Non‐hematopoietic Cells In Cancermentioning

confidence: 99%

VISTA: Coming of age as a multi-lineage immune checkpoint

ElTanbouly

Schaafsma

Noelle

et al. 2020

Clinical and Experimental Immunology

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“…Deep sequencing was performed using a MiSeq instrument (Illumina) using MiSeq Reagent Kit v2, 500-cycles (Illumina). Bioinformatic analysis was performed using inhouse SWARM and HIVE software 51 . The pipeline included quality controls to remove sequence information with phred scores below 30 and removal of adapter and index sequences, followed by alignment of sequence reads to the reference viral sequence, and computation of the profile of sequence heterogeneities 52,53 .…”

Section: Deep Sequencing Of Poliovirus Genomic Materialsmentioning

confidence: 99%

Development of a new oral poliovirus vaccine for the eradication end game using codon deoptimization

et al. 2020

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Enormous progress has been made in global efforts to eradicate poliovirus, using live-attenuated Sabin oral poliovirus vaccine (OPV). However, as the incidence of disease due to wild poliovirus has declined, vaccine-derived poliovirus (VDPV) has emerged in areas of low-vaccine coverage. Coordinated global cessation of routine, type 2 Sabin OPV (OPV2) use has not resulted in fewer VDPV outbreaks, and continued OPV use in outbreak-response campaigns has seeded new emergences in low-coverage areas. The limitations of existing vaccines and current eradication challenges warranted development of more genetically stable OPV strains, most urgently for OPV2. Here, we report using codon deoptimization to further attenuate Sabin OPV2 by changing preferred codons across the capsid to non-preferred, synonymous codons. Additional modifications to the 5′ untranslated region stabilized known virulence determinants. Testing of this codon-deoptimized new OPV2 candidate (nOPV2-CD) in cell and animal models demonstrated that nOPV2-CD is highly attenuated, grows sufficiently for vaccine manufacture, is antigenically indistinguishable from Sabin OPV2, induces neutralizing antibodies as effectively as Sabin OPV2, and unlike Sabin OPV2 is genetically stable and maintains an attenuation phenotype. In-human clinical trials of nOPV2-CD are ongoing, with potential for nOPV strains to serve as critical vaccine tools for achieving and maintaining polio eradication.npj Vaccines (2020) 5:26 ; https://doi.

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“…Data availability. NGS data and raw sequencing reads, as analyzed with the HIVE software package (37), are deposited at https://hive.biochemistry.gwu.edu/review/NDV_LaSota_strain_PV.…”

Section: Discussionmentioning

confidence: 99%

Newcastle Disease Virus-Based Vectored Vaccine against Poliomyelitis

Viktorova

Khattar

Kouiavskaia

et al. 2018

J Virol

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The poliovirus eradication initiative has spawned global immunization infrastructure and dramatically decreased the prevalence of the disease, yet the original virus eradication goal has not been met. The suboptimal properties of the existing vaccines are among the major reasons why the program has repeatedly missed eradication deadlines. Oral live poliovirus vaccine (OPV), while affordable and effective, occasionally causes the disease in the primary recipients, and the attenuated viruses rapidly regain virulence and can cause poliomyelitis outbreaks. Inactivated poliovirus vaccine (IPV) is safe but expensive and does not induce the mucosal immunity necessary to interrupt virus transmission. While the need for a better vaccine is widely recognized, current efforts are focused largely on improvements to the OPV or IPV, which are still beset by the fundamental drawbacks of the original products. Here we demonstrate a different design of an antipoliovirus vaccine based on production of virus-like particles (VLPs). The poliovirus capsid protein precursor, together with a protease required for its processing, are expressed from a Newcastle disease virus (NDV) vector, a negative-strand RNA virus with mucosal tropism. In this system, poliovirus VLPs are produced in the cells of vaccine recipients and are presented to their immune systems in the context of active replication of NDV, which serves as a natural adjuvant. Intranasal administration of the vectored vaccine to guinea pigs induced strong neutralizing systemic and mucosal antibody responses. Thus, the vectored poliovirus vaccine combines the affordability and efficiency of a live vaccine with absolute safety, since no full-length poliovirus genome is present at any stage of the vaccine life cycle. A new, safe, and effective vaccine against poliovirus is urgently needed not only to complete the eradication of the virus but also to be used in the future to prevent possible virus reemergence in a postpolio world. Currently, new formulations of the oral vaccine, as well as improvements to the inactivated vaccine, are being explored. In this study, we designed a viral vector with mucosal tropism that expresses poliovirus capsid proteins. Thus, poliovirus VLPs are produced , in the cells of a vaccine recipient, and are presented to the immune system in the context of vector virus replication, stimulating the development of systemic and mucosal immune responses. Such an approach allows the development of an affordable and safe vaccine that does not rely on the full-length poliovirus genome at any stage.

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High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis

Cited by 63 publications

References 26 publications

VISTA: Coming of age as a multi-lineage immune checkpoint

VISTA: Coming of age as a multi-lineage immune checkpoint

Development of a new oral poliovirus vaccine for the eradication end game using codon deoptimization

Newcastle Disease Virus-Based Vectored Vaccine against Poliomyelitis

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