Bacteriophage Infection of the Marine Bacterium Shewanella glacialimarina Induces Dynamic Changes in tRNA Modifications

Viruses are obligate intracellular parasites that, throughout evolution, have adapted numerous strategies to control the translation machinery, including the modulation of post-transcriptional modifications (PTMs) on transfer RNA (tRNA). PTMs are critical translation regulators used to further host immune responses as well as the expression of viral proteins. Yet, we lack critical insight into the temporal dynamics of infection-induced changes to the tRNA modification landscape (i.e., 'modificome'). In this study, we provide the first comprehensive quantitative characterization of the tRNA modificome in the marine bacterium Shewanella glacialimarina during Shewanella phage 1/4 infection. Specifically, we show that PTMs can be grouped into distinct categories based on modification level changes at various infection stages. Furthermore, we observe a preference for the UAC codon in viral transcripts expressed at the late stage of infection, which coincides with an increase in queuosine modification. Queuosine appears exclusively on tRNAs with GUN anticodons, suggesting a correlation between phage codon usage and PTM modification. Importantly, this work provides the basis for further studies into RNA-based regulatory mechanisms employed by bacteriophages to control the prokaryotic translation machinery.

POS1154 OUTCOMES AND RESOURCE UTILIZATION AFTER TOTAL HIP ARTHROPLASTY IN PATIENTS WITH CALCIUM PYROPHOSPHATE DEPOSITION DISEASE

Background

Total hip arthroplasty (THA) is a safe and effective treatment option in patients with advanced degenerative joint disease who have failed conservative management. Calcium pyrophosphate deposition disease (CPPD) is a common crystal-induced arthritis in older adults characterized by the deposition of calcium pyrophosphate crystals in the articular and periarticular tissues1. CPPD might manifested with acute and chronic arthritis that can lead to joint damage and the need for joint replacement. To our knowledge, no previous studies investigated the outcomes of CPPD patients who underwent THA.

Objectives

We aim to examine the mortality, in-hospital complications, and resource utilization following THA in patients with and without CPPD.

Methods

We queried the US National Inpatient Sample (NIS) database to identify patients who underwent THA between 2006 and 2014. The ICD-9 code 81.51 was used to identify the patients who underwent THA and of those, we classified 2 groups of patients: (i) those with ICD-9 codes defining CPPD (275.49 and 712.1–712.39) and (ii) those without any CPPD code. Data collection included patient demographics and comorbidities. Outcomes post-THA were in-hospital mortality, hospital length of stay, hospital charges, and discharge disposition. Associations between CPPD and specific morbidity were evaluated with chi-square tests. T tests were used for continuous variables.

Results

Among the 4,111,808 (adjusted for sampling weight) patients who underwent THA between 2006 and 2014, 6198 (0.15%) had CPPD, with a mean age of 77 years and 65.2% were females (Table 1). CPPD patients were more likely to be older (mean age 77 vs 72.7; p<0.001) than non-CPPD patients. Comorbidities more frequently observed among CPPD patients included chronic kidney disease, osteoarthritis, rheumatoid arthritis, gout, hyperparathyroidism and hypomagnesemia. Further, Charlson Comorbidity Index scores ≥ 2 was more frequent seen in CPPD (96.1% vs 89.1%, p <0.001). The in-hospital mortality post-THA was lower in the CPPD patients (0.76% vs 1.72%, p <0.001). THA in CPPD patients was associated with a longer mean length of stay than those without CPPD (6 vs 5.1 days; p <0.001) while mean total charges were not statistically different between the 2 groups (p=0.344). CPPD patients were more likely to be discharged to rehabilitation or other nursing facilities (p<0.001).

Table 1.

Demographics, clinical characteristics, outcomes and resource utilization of patients with and without CPPD who underwent hip arthroplasty between 2006-2014.

No CPDD, n (%) (N=4105610)CPPD, n (%) (N=6198)P-value*Age in years at admission, median (mean ± SD)75 (72.7 ± 31.5)80 (77.0 ± 24.2)<0.001†Female2507971 (61.1)3979 (64.2)<0.001Chronic kidney disease516688 (12.5)1154 (18.6)<0.001Osteoarthritis684171 (16.6)1280(20.6)< 0.001Gout139648 (3.4)330 (5.3)<0.001Rheumatoid arthritis199175 (4.8)478(7.7)<0.001Hyperparathyroidism7959 (0.1)24(0.3)<0.001Hypomagnesemia100390 (2.45)239 (3.86)<0.001Charlson Comorbidity Index score ≥ 23659906 (89.1)5961(96.1)<0.001Outcomes/Resource utilizationLength of stay, (mean ± SD)5.15 ± 11.726.04 ± 13.91<0.001†Total hospital charges, (mean ± SD)$ 41284 ± 108238($ 42757 ± 124894)0.344†Death during hospitalization70706 (1.7)47 (0.7)<0.001†Discharge DispositionHome (including home health care)2653860 (64.7)3558 (57.4)<0.001All others§1447312 (35.3)2635 (42.5)<0.001

*Chi-square P except †t-test

§All others include transfer to nursing or rehabilitation facility.

Conclusion

CPPD patients who underwent THA were more likely to be older, with a higher comorbidity burden, longer length of stay, and discharged to a non-home setting, than non-CPPD patients.

References

[1]Rosenthal AK, Ryan LM. Calcium Pyrophosphate Deposition Disease. N Engl J Med. 2016;d 374(26):2575-84.

Disclosure of Interests

None declared

AB1508 A NOVEL PATHOGENIC VARIANT IN ZNF462 GENE ASSOCIATED WITH WEISS-KRUSZKA SYNDROME AND SLE

Background

Weiss-Kruszka syndrome (WSKA) is an autosomal dominant congenital anomaly syndrome due to mutations in the ZNF462 gene and manifests with developmental delay and multiple craniofacial abnormalities with variable expressivity1. It is also characterized by cognitive impairment, whilst about a third of the affected individuals belong to the autism spectrum. Although the disease is inherited with the autosomal dominant manner, most of the described subjects (95%) had de novo variants with no affected family members1. WSKA has been recently described and only 26 (including our patient) affected individuals have been classified to date2. Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by the presence of autoantibodies and multi-organ inflammation. Genetic factors might play an important role in disease pathogenesis in patients with childhood-onset SLE.

Objectives

To describe the case of a SLE patient who was found to have WSKA related to a novel pathogenic autosomal dominant (AD) variant in the ZNF462 gene, and inform clinicians of a possible association between the 2 conditions.

Methods

A 25-year-old Caucasian female with a history of SLE, diagnosed at the age of 14, manifested with malar rash, Raynaud’s phenomenon, arthritis, thrombocytopenia, positive ANA, ds-DNA antibody and hypocomplementemia. At the age of 17, she developed renal dysfunction due to lupus nephritis class IV, and she was treated with glucocorticoids (GCs), cyclophosphamide and hydroxychloroquine. In Oct 2020, she was admitted to the hospital for thrombotic thrombocytopenic purpura due to lupus exacerbation. She was successfully treated with GCs, plasma exchange and rituximab. During her hospitalization, the presence of various clinical features raised the suspicion of a genetic syndrome. First, the patient exhibited dysmorphic features such as hypertelorism, prognathism, arched eyebrows, flattened nasal bridge, small upper lip, mild intellectual disability, and a history of childhood-onset SLE. Whole exome sequencing (WES) by NGS was used for the genetic investigation of the patient.

Figure 1.

Results

The patient underwent genetic evaluation with WES and the novel heterozygous AD pathogenic variant c.4142delT (p.lle1381ThrfsTer16) in ZNF462 gene was identified. Confirmation of the identified variant was also verified by sanger sequencing. Pathogenic variants in the ZNF462 gene were previously described in patients with the recently reported WSKA of which several characteristics are compatible with our patient’s features. The ZFN462 encodes a zinc-finger transcription factor that plays a role in embryonic development, transcriptional regulation, and chromatin remodelling. Given that chromatin remodelling has been implicated in the pathogenesis of SLE, the association of this novel ZNF462 variant in the development of SLE, needs to be determined3.

Conclusion

This is the first report of a patient with coexisting SLE and WSKA due to a novel variant. It illustrates the need for further research in order to elucidate any possible pathophysiologic link among the 2 conditions.

References

[1]Weiss K, Wigby K, Fannemel M, Henderson LB, Beck N, Ghali N, Study DDD, Anderlid BM, Lundin J, Hamosh A, Jones MC, Ghedia S, Muenke M, Kruszka P. Haploinsufficiency of ZNF462 is associated with craniofacial anomalies, corpus callosum dysgenesis, ptosis, and developmental delay. Eur J Hum Genet. 2017 Aug;25(8):946-951. doi: 10.1038/ejhg.2017.86. Epub 2017 May 17. PMID: 28513610; PMCID: PMC5567153.

[2]Park J, Ha DJ, Seo GH, Maeng S, Kang SM, Kim S, Lee JE. Empty Sella Syndrome Associated with Growth Hormone Deficiency: the First Case Report of Weiss-Kruszka Syndrome. J Korean Med Sci. 2021 May 10;36(18):e133. doi: 10.3346/jkms.2021.36.e133. PMID: 33975400; PMCID: PMC8111047.

[3]Surace AEA, Hedrich CM. The Role of Epigenetics in Autoimmune/Inflammatory Disease. Front Immunol. 2019 Jul 4;10:1525. doi: 10.3389/fimmu.2019.01525. PMID: 31333659; PMCID: PMC6620790.

Disclosure of Interests

None declared

Native RNA Purification Method for Small RNA Molecules Based on Asymmetrical Flow Field-Flow Fractionation

RNA molecules provide promising new possibilities for the prevention and treatment of viral infections and diseases. The rapid development of RNA biology and medicine requires advanced methods for the purification of RNA molecules, which allow fast and efficient RNA processing, preferably under non-denaturing conditions. Asymmetrical flow field-flow fractionation (AF4) enables gentle separation and purification of macromolecules based on their diffusion coefficients. The aim of the study was to develop an AF4 method for efficient purification of enzymatically produced antiviral small interfering (si)RNA molecules and to evaluate the overall potential of AF4 in the separation of short single-stranded (ss) and double-stranded (ds) RNA molecules. We show that AF4 separates monomeric ssRNA from dsRNA molecules of the same size and monomeric ssRNA from multimeric forms of the same ssRNA. The developed AF4 method enabled the separation of enzymatically produced 27-nt siRNAs from partially digested substrate dsRNA, which is potentially toxic for mammalian cells. The recovery of AF4-purified enzymatically produced siRNA molecules was about 70%, which is about 20% higher than obtained using anion-exchange chromatography. The AF4-purified siRNAs were not toxic for mammalian cells and fully retained their biological activity as confirmed by efficient inhibition of herpes simplex virus 1 replication in cell culture. Our work is the first to develop AF4 methods for the separation of short RNA molecules.

Cold-Active Shewanella glacialimarina TZS-4T nov. Features a Temperature-Dependent Fatty Acid Profile and Putative Sialic Acid Metabolism

Species of genus Shewanella are among the most frequently identified psychrotrophic bacteria. Here, we have studied the cellular properties, growth dynamics, and stress conditions of cold-active Shewanella strain #4, which was previously isolated from Baltic Sea ice. The cells are rod-shaped of ~2μm in length and 0.5μm in diameter, and they grow between 0 and 25°C, with an optimum at 15°C. The bacterium grows at a wide range of conditions, including 0.5–5.5% w/v NaCl (optimum 0.5–2% w/v NaCl), pH 5.5–10 (optimum pH 7.0), and up to 1mM hydrogen peroxide. In keeping with its adaptation to cold habitats, some polyunsaturated fatty acids, such as stearidonic acid (18:4n-3), eicosatetraenoic acid (20:4n-3), and eicosapentaenoic acid (20:5n-3), are produced at a higher level at low temperature. The genome is 4,456kb in size and has a GC content of 41.12%. Uniquely, strain #4 possesses genes for sialic acid metabolism and utilizes N-acetyl neuraminic acid as a carbon source. Interestingly, it also encodes for cytochrome c3 genes, which are known to facilitate environmental adaptation, including elevated temperatures and exposure to UV radiation. Phylogenetic analysis based on a consensus sequence of the seven 16S rRNA genes indicated that strain #4 belongs to genus Shewanella, closely associated with Shewanella aestuarii with a ~97% similarity, but with a low DNA–DNA hybridization (DDH) level of ~21%. However, average nucleotide identity (ANI) analysis defines strain #4 as a separate Shewanella species (ANI score=76). Further phylogenetic analysis based on the 92 most conserved genes places Shewanella strain #4 into a distinct phylogenetic clade with other cold-active marine Shewanella species. Considering the phylogenetic, phenotypic, and molecular characterization, we conclude that Shewanella strain #4 is a novel species and name it Shewanella glacialimarina sp. nov. TZS-4_T, where glacialimarina means sea ice. Consequently, S. glacialimarina TZS-4_T constitutes a promising model for studying transcriptional and translational regulation of cold-active metabolism.

Asymmetrical flow field-flow fractionation in purification of an enveloped bacteriophage ϕ6

Basic and applied virus research requires specimens that are purified to high homogeneity. Thus, there is much interest in the efficient production and purification of viruses and their subassemblies. Advances in the production steps have shifted the bottle neck of the process to the purification. Nonetheless, the development of purification techniques for different viruses is challenging due to the complex biological nature of the infected cell cultures as well as the biophysical and -chemical differences in the virus particles. We used bacteriophage ϕ6 as a model virus in our attempts to provide a new purification method for enveloped viruses. We compared asymmetrical flow field-flow fractionation (AF4)-based virus purification method to the well-established ultracentrifugation-based purification of ϕ6. In addition, binding of ϕ6 virions to monolithic anion exchange columns was tested to evaluate their applicability in concentrating the AF4 purified specimens. Our results show that AF4 enables one-hour purification of infectious enveloped viruses with specific infectivity of ~1 × 10¹³ PFU/mg of protein and ~65-95% yields. Obtained purity was comparable with that obtained using ultracentrifugation, but the yields from AF4 purification were 2-3-fold higher. Importantly, high quality virus preparations could be obtained directly from crude cell lysates. Furthermore, when used in combination with in-line light scattering detectors, AF4 purification could be coupled to simultaneous quality control of obtained virus specimen.

Halophilic viruses with varying biochemical and biophysical properties are amenable to purification with asymmetrical flow field-flow fractionation

Viruses come in various shapes and sizes, and a number of viruses originate from extremities, e.g. high salinity or elevated temperature. One challenge for studying extreme viruses is to find efficient purification conditions where viruses maintain their infectivity. Asymmetrical flow field-flow fractionation (AF4) is a gentle native chromatography-like technique for size-based separation. It does not have solid stationary phase and the mobile phase composition is readily adjustable according to the sample needs. Due to the high separation power of specimens up to 50 µm, AF4 is suitable for virus purification. Here, we applied AF4 for extremophilic viruses representing four morphotypes: lemon-shaped, tailed and tailless icosahedral, as well as pleomorphic enveloped. AF4 was applied to input samples of different purity: crude supernatants of infected cultures, polyethylene glycol-precipitated viruses and viruses purified by ultracentrifugation. All four virus morphotypes were successfully purified by AF4. AF4 purification of culture supernatants or polyethylene glycol-precipitated viruses yielded high recoveries, and the purities were comparable to those obtained by the multistep ultracentrifugation purification methods. In addition, we also demonstrate that AF4 is a rapid monitoring tool for virus production in slowly growing host cells living in extreme conditions.