The aquatic microbiome is composed of a multi-phylotype community of microbes, ranging from the numerically dominant viruses to the phylogenetically diverse unicellular phytoplankton. They influence ...key biogeochemical processes and form the base of marine food webs, becoming food for secondary consumers. Due to recent advances in next-generation sequencing, this previously overlooked component of our hydrosphere is starting to reveal its true diversity and biological complexity. We report here that 250 mL of seawater is sufficient to provide a comprehensive description of the microbial diversity in an oceanic environment. We found that there was a dominance of the order
(59%), with the family
being the most prevalent. The families
and
made up the remainder of pelagic double-stranded DNA (dsDNA) virome. Consistent with this analysis, the Cyanobacteria dominate (52%) the prokaryotic diversity. While the dinoflagellates and their endosymbionts, the superphylum Alveolata dominates (92%) the microbial eukaryotic diversity. A total of 834 prokaryotic, 346 eukaryotic and 254 unique virus phylotypes were recorded in this relatively small sample of water. We also provide evidence, through a metagenomic-barcoding comparative analysis, that viruses are the likely source of microbial environmental DNA (meDNA). This study opens the door to a more integrated approach to oceanographic sampling and data analysis.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
We present draft genome sequences for three strains of Xanthomonas species, each of which was associated with banana plants (Musa species) but is not closely related to the previously sequenced ...banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had been deposited as Xanthomonas campestris pathovar musacearum but in fact falls within the species Xanthomonas sacchari. Strain NCPPB1132 is more distantly related to Xanthomonas sacchari whilst strain NCPPB 1131 grouped in a distinct species-level clade related to X. sacchari, along with strains from ginger, rice, cotton and sugarcane. These three newly sequenced strains share many genomic features with the previously sequenced Xanthomonas albilineans, for example possessing an unsual metE allele and lacking the Hrp type III secretion system. However, they are distinct from Xanthomonas albilineans in many respects, for example showing little evidence of genome reduction. They also lack the SPI-1 type III secretion system found in Xanthomonas albilineans. Unlike X. albilineans, all three strains possess a gum gene cluster. The data reported here provide the first genome-wide survey of non-Hrp Xanthomonas species other than Xanthomonas albilineans, which is an atypical member of this group. We hope that the availability of complete sequence data for this group of organisms is the first step towards understanding their interactions with plants and identifying potential virulence factors.
Highly virulent bacterial pathogens cause acute infections which are exceptionally difficult to treat with conventional antibiotic therapies alone. Understanding the chain of events that are ...triggered during an infection of a host has the potential to lead to new therapeutic strategies. For the first time, the transcriptomic responses within the lungs of Balb/C mice have been compared during an acute infection with the intracellular pathogens
,
and
. Temporal changes were determined using RNAseq and a bioinformatics pipeline; expression of protein was also studied from the same sample. Collectively it was found that early transcriptomic responses within the infected host were associated with the (a) slowing down of critical cellular functions, (b) production of circulatory system components, (c) lung tissue integrity, and (d) intracellular regulatory processes. One common molecule was identified, Errfi1 (ErbB receptor feedback inhibitor 1); upregulated in response to all three pathogens and a potential novel marker of acute infection. Based upon the pro-inflammatory responses observed, we sought to synchronise each infection and report that 24 h p.i. of
infection closely aligned with 48 h p.i. of infection with
and
. Post-transcriptional modulation of RANTES expression occurred across all pathogens, suggesting that these infections directly or indirectly modulate cell trafficking through chemokine expression/detection. Collectively, this unbiased NGS approach has provided an in-depth characterisation of the host transcriptome following infection with these highly virulent pathogens ultimately aiding in the development of host-directed therapies as adjuncts or alternatives to antibiotic treatment.
A new generation of sequencing technologies is revolutionizing molecular biology. Illumina's Solexa and Applied Biosystems' SOLiD generate gigabases of nucleotide sequence per week. However, a ...perceived limitation of these ultra-high-throughput technologies is their short read-lengths. De novo assembly of sequence reads generated by classical Sanger capillary sequencing is a mature field of research. Unfortunately, the existing sequence assembly programs were not effective for short sequence reads generated by Illumina and SOLiD platforms. Early studies suggested that, in principle, sequence reads as short as 20-30 nucleotides could be used to generate useful assemblies of both prokaryotic and eukaryotic genome sequences, albeit containing many gaps. The early feasibility studies and proofs of principle inspired several bioinformatics research groups to implement new algorithms as freely available software tools specifically aimed at assembling reads of 30-50 nucleotides in length. This has led to the generation of several draft genome sequences based exclusively on short sequence Illumina sequence reads, recently culminating in the assembly of the 2.25-Gb genome of the giant panda from Illumina sequence reads with an average length of just 52 nucleotides. As well as reviewing recent developments in the field, we discuss some practical aspects such as data filtering and submission of assembly data to public repositories.
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We present a draft genome sequence for enset (Ensete ventricosum) available via the Sequence Read Archive (accession number SRX202265) and GenBank (accession number AMZH01. Enset feeds 15 million ...people in Ethiopia, but is arguably the least studied African crop. Our sequence data suggest a genome size of approximately 547 megabases, similar to the 523-megabase genome of the closely related banana (Musa acuminata). At least 1.8% of the annotated M. acuminata genes are not conserved in E. ventricosum. Furthermore, enset contains genes not present in banana, including reverse transcriptases and virus-like sequences as well as a homolog of the RPP8-like resistance gene. We hope that availability of genome-wide sequence data will stimulate and accelerate research on this important but neglected crop.
Pseudomonas aeruginosa PUPa3 is a rhizosphere-colonizing and plant growth-promoting strain isolated from the rhizosphere of rice. This strain has, however, been shown to be pathogenic in two ...nonmammalian infection models. Here we report the draft genome sequence of P. aeruginosa PUPa3.
Abstract
Existing immunotherapies for multiple myelomas (MM), including bispecific antibodies, antibody-drug conjugates and chimeric antigen receptor-based strategies, have targeted the B-cell ...maturation antigen (BCMA) that is expressed at the surface of malignant plasma cells (PCs). Although promising, clinical outcomes are hampered by resistance mechanisms that include BCMA extracellular domain shedding and cell-surface downregulation. In addition, BCMA expression is known to be variable among MM patients. Transmembrane activator and CAML interactor (TACI), another member of the tumor necrosis factor receptor (TNFR) super family, represents another viable drug target. TACI expression largely overlaps with BCMA and expression is also increased in PCs of MM patients. Interestingly, TACI may have a role in maintaining an immunosuppressive tumor microenvironment as its expression was observed to be upregulated in Tregs in MM patient's tumor load. Activation of TACI in Tregs triggers their proliferation and survival further supporting a pro-tumoral role for this receptor. Altogether, the dual targeting of both BCMA and TACI should be beneficial to the efficient removal of malignant PCs. Despite low sequence homology, BCMA and TACI share a similar 3D structure, which is likely the reason that APRIL (A proliferation-Inducing ligand) binds to both receptors. We applied our proprietary Rational Antibody Discovery platform to successfully direct the generation of mouse IgG clones able to bind a conserved epitope on BCMA and TACI with sub-nanomolar affinities. In addition, these antibodies were able to inhibit the binding of BCMA to APRIL - an interaction known to favor MM tumor growth and survival. Two IgG clones were successfully humanized and retained their capacity to bind to both BCMA and TACI when heterologously expressed on HEK293, or endogenously expressed in MM cancer cell lines such as H929. No cross-reactivity to other TNFR family members was observed. In antibody-dependent cell-mediated cytotoxicity (ADCC) assays, these clones were able to induce efficient cell killing by binding either BCMA or TACI. Moreover, our lead dual-specific anti-BCMA/anti-TACI antibody (HMBD-009) showed better tumor control compared to other anti-BCMA only antibodies in pre-clinical tumor models of MM. Dual-specific antibodies able to efficiently target both BCMA and TACI represent a promising new avenue to improve the elimination of malignant PCs from MM patients.
Citation Format: Fabien M. Decaillot, Dipti Thakkar, Siyu Guan, Konrad Paszkiewicz, Piers J. Ingram, Jerome D. Boyd-Kikurp. Dual-specific antibodies that bind to BCMA and TACI (HMBD-009) enable better targeting of multiple myeloma in pre-clinical models abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1889.
Abstract
HER3 activation, through NRG1 ligand-dependent and independent heterodimerization with HER2 or EGFR, can drive tumor growth and survival via potent PI3K pathway signaling. HER3 activation ...has emerged as an important mechanism for both tumor progression and acquired resistance to standard of care therapies in multiple indications. With an effective biomarker strategy to select for patients with HER3 driven cancer, potent inhibition of HER3-driven heterodimerization has the potential to confer profound clinical impact. HER3 targeting approaches to date have not shown expected clinical efficacy. Suboptimal HER3 inhibition is one possible explanation; to prevent downstream PI3K signalling, it is critical to fully block both ligand-dependent and independent HER3 activation. Further, despite the clinical evaluation of several anti-HER3 antibodies, only limited progress has been made to establish predictive biomarkers of response to HER3 inhibition. The most thoroughly studied biomarkers predicting response have been increased expression and genomic rearrangements of the HER3 ligand, NRG1. For example, oncogenic NRG1-fusions have been identified as tumor drivers in up to 0.2% of all solid cancers. Few biomarkers predicting lack of response have been reported to date. HMBD-001, is an unique anti-HER3 antibody rationally developed to bind the dimerization interface of HER3 in order to block all HER3 heterodimerization. In contrast to other anti-HER3 antibodies that predominantly bind to the NRG1 binding domain, we observed potent and superior in vitro and in vivo tumor growth inhibition for HMBD-001 in multiple cancer models, including NRG1-fusion driven models. We show that HMBD-001 binds to HER3 with high affinity even in the presence of high concentrations of NRG1, in contrast to other antibodies in which NRG1 competes for the HER3 ligand binding site, thereby decreasing affinity and likely potency. Notably, HMBD-001 treatment of an NRG1-fusion ovarian PDX model showed superior tumor growth inhibition compared with anti-HER3 and anti-HER2/HER3 bispecific antibodies targeting the NRG1 binding domain of HER3. To develop a robust biomarker signature for patient selection beyond NRG1-fusions, we interrogated the genomic and transcriptomic data of all preclinical models for which HMBD-001 efficacy data was available, including in vitro and in vivo models representing multiple HER3 associated cancer sub-types. We identified a novel gene signature that was robustly predictive of HMBD-001 response across a wide range of cancers, including loss of function and gain of function mutations in specific downstream mediators of the MAPK and PI3K signaling pathways. In conclusion, the superior potency of HMBD-001 in preclinical models predicts more complete inhibition of HER3 and better responses in HER3 driven cancers that can be identified using a novel gene signature biomarker. Clinical trials of HMBD-001 in HER3 driven cancers, including those with NRG1-fusions, are expected to commence in 2021.
Citation Format: Dipti Thakkar, Shalini Paliwal, Shreya Kar, Namita Gandhi, Konrad Paszkiewicz, Piers Ingram, Jerome Boyd-Kirkup. An anti-HER3 antibody, HMBD-001, that uniquely binds to and blocks the HER3 heterodimerization interface, shows superior tumor growth inhibition in biomarker-defined preclinical cancer models including NRG1-fusion driven cancers abstract. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P197.
Motivation: In recent years graph-theoretic descriptions have been applied to aid the analysis of a number of complex biological systems. However, such an approach has only just begun to be applied ...to examine protein structures and the network of interactions between residues with promising results. Here we examine whether a graph measure known as closeness is capable of predicting regions where a protein can be split to form a viable circular permutant. Circular permutants are a powerful experimental tool to probe folding mechanisms and more recently have been used to design split enzyme reporter proteins. Results: We test our method on an extensive set of experiments carried out on dihydrofolate reductase in which circular permutants were constructed for every amino acid position in the sequence, together with partial data from studies on other proteins. Results show that closeness is capable of correctly identifying significantly more residues which are suitable for circular permutation than solvent accessibility. This has potential implications for the design of successful split enzymes having particular importance for the development of protein–protein interaction screening methods and offers new perspectives on protein folding. More generally, the method illustrates the success with which graph-theoretic measures encapsulate the variety of long and short range interactions between residues during the folding process. Contact:konrad.paszkiewicz@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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