Advanced exploitation of unmerged reflection data during processing and refinement with autoPROC and BUSTER

The validation of structural models obtained by macromolecular X-ray crystallography against experimental diffraction data, whether before deposition into the PDB or after, is typically carried out exclusively against the merged data that are eventually archived along with the atomic coordinates. It is shown here that the availability of unmerged reflection data enables valuable additional analyses to be performed that yield improvements in the final models, and tools are presented to implement them, together with examples of the results to which they give access. The first example is the automatic identification and removal of image ranges affected by loss of crystal centering or by excessive decay of the diffraction pattern as a result of radiation damage. The second example is the `reflection-auditing' process, whereby individual merged data items showing especially poor agreement with model predictions during refinement are investigated thanks to the specific metadata (such as image number and detector position) that are available for the corresponding unmerged data, potentially revealing previously undiagnosed instrumental, experimental or processing problems. The third example is the calculation of so-called F(early) - F(late) maps from carefully selected subsets of unmerged amplitude data, which can not only highlight the location and extent of radiation damage but can also provide guidance towards suitable fine-grained parametrizations to model the localized effects of such damage.

Swiss Survey on current practices and opinions on clinical constellations triggering the search for PNH clones

This national survey investigated the current practice in Switzerland by collecting participants' opinions on paroxysmal nocturnal hemoglobinuria (PNH) clone assessment and clinical practice.

Aim

This study aimed to investigate clinical indications prompting PNH clones' assessment and physician's accessibility of a flow cytometry facility, and also to understand clinical attitudes on the follow-up (FU) of patients with PNH clones.

Methods

The survey includes 16 multiple-choice questions related to PNH and targets physicians with a definite level of experience in the topic using two screener questions. Opinion on clinical management was collected using hypothetical clinical situations. Each participant had the option of being contacted to further discuss the survey results. This was an online survey, and 264 physicians were contacted through email once a week for 5 weeks from September 2020.

Results

In total, 64 physicians (24.2%) from 23 institutions participated (81.3% hematologists and 67.2% from university hospitals). All had access to flow cytometry for PNH clone testing, with 76.6% having access within their own institution. The main reasons to assess for PNH clones were unexplained thrombosis and/or hemolysis, and/or aplastic anemia (AA). Patients in FU for PNH clones were more likely to be aplastic anemia (AA) and symptomatic PNH. In total, 61% of the participants investigated PNH clones repetitively during FU in AA/myelodysplastic syndromes patients, even when there was no PNH clone found at diagnosis, and 75% of the participants tested at least once a year during FU. Opinions related to clinical management were scattered.

Conclusion

The need to adhere to guidelines for the assessment, interpretation, and reporting of PNH clones emerges as the most important finding, as well as consensus for the management of less well-defined clinical situations. Even though there are several international guidelines, clear information addressing specific topics such as the type of anticoagulant to use and its duration, as well as the indication for treatment with complement inhibitors in some borderline situations are needed. The analysis and the discussion of this survey provide the basis for understanding the unmet needs of PNH clone assessment and clinical practice in Switzerland.

Fever of Unknown Origin, a Vascular Event, and Immunosuppression in Tick-Endemic Areas: Think About Neoehrlichiosis

Three patients were referred to our hospital because of fever of unknown origin (FUO) and thrombosis or thrombophlebitis. All of them had been under immunosuppression (IS) with rituximab. Intensive diagnostics for FUO and blood cultures remained negative. Finally, the association of fever, immunosuppression, and a vascular event led to the suspicion of Candidatus Neoehrlichia mikurensis (CNM) infection. The diagnosis was confirmed by species-specific polymerase chain reaction (PCR) in the peripheral blood. Therapy with doxycycline or rifampicin led to the resolution of the disease. A liver biopsy was performed in one patient due to hepatomegaly and elevated liver enzymes demonstrating hemophagocytosis. To our knowledge, this is the first histopathological study of liver tissue in CNM infection. The evidence of hemophagocytosis raises the question of whether symptomatic CNM infection might be in part related to host inflammatory and immune responses.

Translational Studies Using the MALT1 Inhibitor (S)-Mepazine to Induce Treg Fragility and Potentiate Immune Checkpoint Therapy in Cancer

Introduction

Regulatory T cells (Tregs) play a critical role in the maintenance of immune homeostasis but also protect tumors from immune-mediated growth control or rejection and pose a significant barrier to effective immunotherapy. Inhibition of MALT1 paracaspase activity can selectively reprogram immune-suppressive Tregs in the tumor microenvironment to adopt a proinflammatory fragile state, which offers an opportunity to impede tumor growth and enhance the efficacy of immune checkpoint therapy (ICT).

Methods

We performed preclinical studies with the orally available allosteric MALT1 inhibitor (S)-mepazine as a single-agent and in combination with anti-programmed cell death protein 1 (PD-1) ICT to investigate its pharmacokinetic properties and antitumor effects in several murine tumor models as well as patient-derived organotypic tumor spheroids (PDOTS).

Results

(S)-mepazine demonstrated significant antitumor effects and was synergistic with anti-PD-1 therapy in vivo and ex vivo but did not affect circulating Treg frequencies in healthy rats at effective doses. Pharmacokinetic profiling revealed favorable drug accumulation in tumors to concentrations that effectively blocked MALT1 activity, potentially explaining preferential effects on tumor-infiltrating over systemic Tregs.

Conclusions

The MALT1 inhibitor (S)-mepazine showed single-agent anticancer activity and presents a promising opportunity for combination with PD-1 pathway-targeted ICT. Activity in syngeneic tumor models and human PDOTS was likely mediated by induction of tumor-associated Treg fragility. This translational study supports ongoing clinical investigations (ClinicalTrials.gov Identifier: NCT04859777) of MPT-0118, (S)-mepazine succinate, in patients with advanced or metastatic treatment-refractory solid tumors.

Clinical Aureobasidium Isolates Are More Fungicide Sensitive than Many Agricultural Isolates

Fungicide applications in agriculture and medicine can promote the evolution of resistant, pathogenic fungi, which is a growing problem for disease management in both settings. Nonpathogenic mycobiota are also exposed to fungicides, may become tolerant, and could turn into agricultural or medical problems, for example, due to climate change or in immunocompromised individuals. However, quantitative data about fungicide sensitivity of environmental fungi is mostly lacking. Aureobasidium species are widely distributed and frequently isolated yeast-like fungi. One species, A. pullulans, is used as a biocontrol agent, but is also encountered in clinical samples, regularly. Here, we compared 16 clinical and 30 agricultural Aureobasidium isolates based on whole-genome data and by sensitivity testing with the 3 fungicides captan, cyprodinil, and difenoconazole. Our phylogenetic analyses determined that 7 of the 16 clinical isolates did not belong to the species A. pullulans. These isolates clustered with other Aureobasidium species, including A. melanogenum, a recently separated species that expresses virulence traits that are mostly lacking in A. pullulans. Interestingly, the clinical Aureobasidium isolates were significantly more fungicide sensitive than many isolates from agricultural samples, which implies selection for fungicide tolerance of non-target fungi in agricultural ecosystems. IMPORTANCE Environmental microbiota are regularly found in clinical samples and can cause disease, in particular, in immunocompromised individuals. Organisms of the genus Aureobasidium belonging to this group are highly abundant, and some species are even described as pathogens. Many A. pullulans isolates from agricultural samples are tolerant to different fungicides, and it seems inevitable that such strains will eventually appear in the clinics. Selection for fungicide tolerance would be particularly worrisome for species A. melanogenum, which is also found in the environment and exhibits virulence traits. Based on our observation and the strains tested here, clinical Aureobasidium isolates are still fungicide sensitive. We, therefore, suggest monitoring fungicide sensitivity in species, such as A. pullulans and A. melanogenum, and to consider the development of fungicide tolerance in the evaluation process of fungicides.

Commissioning of the novel Continuous Angle Multi-energy Analysis spectrometer at the Paul Scherrer Institut

We report on the commissioning results of the cold neutron multiplexing secondary spectrometer CAMEA (Continuous Angle Multi-Energy Analysis) at the Swiss Spallation Neutron Source at the Paul Scherrer Institut, Switzerland. CAMEA is optimized for efficient data acquisition of scattered neutrons in the horizontal scattering plane, allowing for detailed and rapid mapping of low-energy excitations under extreme sample environment conditions.

EXTH-07. AN ANTISENSE OLIGONUCLEOTIDE AGAINST TUMOR MICROTUBES IN GLIOBLASTOMA AS A NEW THERAPEUTIC OPTION TO IMPROVE TUMOR SPECIFIC THERAPY

Glioblastomas are known to be highly therapy resistant tumors. The description of tumor microtubes (TMs) as long cellular protrusions that connect glioblastoma cells to a network resistant against all standard therapies advanced the basic biological understanding of the disease and offers a new therapeutic target. An antisense oligonucleotide (ASO) against the production of a protein involved in formation and function of TMs was developed and tested in a xenograft mouse model of human glioblastoma cells. After the implantation of fluorescent tumor cells under a chronic cranial window and the establishment of the tumor, the ASO treatment was started with a continuous micropump application directly into the central nervous system (CNS) and treatment effects were observed in a two-photon microscope. Furthermore, co-treatment with irradiation was tested and tumor size as well as protein expression evaluated in and ex vivo. This led to the conclusion that the setup of combined continuous pump application and two photon microscopy is technically feasible and tolerable. It offers the possibility of applying compounds directly into the CNS under live and longitudinal readouts. The fluorescently tagged ASO was traced in the brain parenchyma over weeks proving a high stability of the compound. In combination with radiotherapy, animals treated with the active ASO against the protein of formation and function of TMs showed a smaller tumor size than animals treated with radiotherapy and the non-targeting ASO. The targeted protein was expressed less in the treated animals then the animals receiving the control ASO and the extend of protein expression correlated with tumor size. Hence, after successful therapies with ASOs in other neurologic diseases and the need for better therapeutic options for glioblastoma patients, the development of an ASO against a protein involved in the TM formation and function offers a new therapeutic option with high translational potential.

Neighborhood Characteristics Associated with Running in Metro Vancouver: A Preliminary Analysis

Running can improve physical health and psychological wellbeing. However, the characteristics of conducive running environments are relatively unknown. This study determines neighborhood factors that attract running and explores how age and gender mediate built environment preferences. Spatial patterns of runners in Metro Vancouver were identified using crowdsourced fitness data from Strava, a popular application for tracking physical activities. The influence of socio-economic status (SES), green and/or blue space, and urbanicity on route popularity was assessed using a Generalized Linear Model (GLM). The influence of these neighborhood variables was also calculated for runners by age and gender. The results show high neighborhood SES, the presence of green and/or blue space, and high population density are associated with increased running activities in all age and gender groups. This study contributes a novel approach to understanding conducive running environments by demonstrating the utility of crowdsourced data in combination with data about urban environments. The patterns of this large group of runners can be used to inform planning for cities that promote running, as well as seek to encourage equal participation among different ages and genders.

Bond-specific fragmentation of oligopeptides via electronic stopping of swift heavy ions in molecular films

Highly bond-specific fragmentation of oligopeptides induced by swift heavy ion (SHI) irradiation was investigated by means of mass spectrometry. In pronounced contrast to measurements of samples irradiated with keV ions, oligopeptides which were exposed to 946 MeV Au ions show a high abundance of specific fragments. The highly bond-specific nature of SHI-induced fragmentation is attributed to electronic stopping as the most relevant energy loss mechanism for SHI in the oligopeptide samples in combination with the subsequent coupling between the excited electronic and the atomic subsystem. Fragmentation induced by SHI is observed to be further influenced by the structure of the oligopeptides, suggesting that electronic excitation and/or the electronic-vibrational coupling depend on the details of the molecular structure.

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

Abstract P106: Reprogramming regulatory T cells (Treg) using a MALT1 inhibitor for cancer therapy

Background Despite transforming effects of immune checkpoint blockade (ICB) therapy, objective response rates are low for most solid tumors. In the tumor microenvironment (TME), regulatory T cells are functionally unstable, likely due to changes in Treg metabolism seen in the tumor milieu. Destabilized Treg are susceptible to reprogramming wherein they can be induced to lose their immunosuppressive function and to secrete interferon-gamma (IFN-g). Thus, Treg reprogramming offers a novel strategy to sensitize unresponsive tumors to ICB. Notably, blockade of MALT1 protease induces Treg reprogramming in the TME but without affecting Treg in healthy tissue. MPT-0118, an orally dosed MALT1 inhibitor, was developed to reprogram Treg in the TME and is currently being assessed in patients with advanced tumors. Approach Treatments included MPT-0118 and anti-PD-1. In vivo studies in mice assessed anti-tumor effects using D4M.3A, B16F10, and MC38 syngeneic tumors. Human and mouse tumor tissues were evaluated for Treg reprogramming by in situ hybridization or flow cytometry. Studies in rats and dogs assessed pharmacokinetics and safety. Results MPT-0118 demonstrated dose-dependent in vivo anti-tumor activity. Consistent with the hypothesis that Treg reprogramming supports anti-tumor immunity by initiating IFN-g-driven tumor inflammation, the effect was strongest in combination with anti-PD-1 and in models that are not responsive to ICB alone. MPT-0118-treated tumors showed an increase in IFN-g-secreting Treg, associated with decelerated tumor growth. Ex vivo, MPT-0118 induced Treg reprogramming in tumors resected from patients with colorectal and endometrial cancers. While MPT-0118 caused Treg to produce IFN-g, no changes in the frequencies of Treg circulating in blood were detected in rats. Modeling of the human effective dose and toxicology studies demonstrate a >2x therapeutic window in patients. Conclusions MPT-0118 Treg reprogramming represents a novel strategy with the potential to improve responses to ICB therapy in solid tumors. A Phase 1/1b dose-escalation and cohort-expansion clinical trial evaluating MPT-0018 is underway.

Citation Format: Peter Keller, Irina Mazo, Yun Gao, Vijayapal Reddy, Francisco Caballero, Sam Kazer, Dannah Miller, Roberto Gianani, James E. Marvin, Bret Stephens, Gregory L. Beatty, Ulrich H. von Andrian, Thorsten R. Mempel. Reprogramming regulatory T cells (Treg) using a MALT1 inhibitor for cancer therapy [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 P106.

861 Reprogramming regulatory T cells (Treg) using a MALT1 inhibitor for cancer therapy

Background

MALT1 protease is a promising target in aggressive lymphomas1, and two phase 1 clinical trials in hematological cancers are ongoing (NCT03900598, NCT04876092). More recently, MALT1 protease inhibition was also shown to reprogram regulatory T cells (Treg) in solid tumors, causing them to lose their immunosuppressive function and secrete interferon-gamma (IFN).2 Changes in Treg metabolism in the tumor microenvironment (TME) may account for their destabilization and selective susceptibility to reprogramming in tumor tissue.3 4 5 While strong MALT1 inhibition can cause Treg depletion in blood and induce autoimmune toxicity,6 a therapeutic window for a differentiated MALT1 inhibitor that reprograms destabilized Treg in the TME before affecting Treg in healthy tissue may exist.2 MPT-0118 is an orally dosed MALT1 inhibitor developed to reprogram destabilized Treg in the TME without causing autoimmune symptoms. A Phase 1/1b dose-escalation and cohort-expansion clinical trial evaluating MPT-0118 is underway (NCT04859777).

Methods

Human xenograft models of lymphoma were used to assess the direct activity of MPT-0118 on MALT1-dependent (but not not MALT1-independent) hematologic tumors. Effects of MPT-0118 on solid tumors were determined in syngeneic cancer models. Human and mouse tumor tissues were evaluated for Treg reprogramming by in situ hybridization or flow cytometry. Patient-derived organotypic tumor spheroids were assessed for immune-mediated cell killing. Studies in rodents and dogs assessed pharmacokinetics (PK) and safety.

Results

MPT-0118 was selective and effective in preventing growth of aggressive MALT1 protease-dependent lymphomas. Beyond direct activity on hematologic malignancies, MPT-0118 also increased anti-tumor immune responses as single-agent or in combination with anti-PD-1 in syngeneic tumor models that are otherwise unresponsive to immune checkpoint blockade (ICB). MPT-0118-treated syngeneic tumors showed an increase in IFN-secreting Treg, associated with decelerated tumor growth. PK studies reveal that MPT-0118 has a high volume of distribution, and effective inhibitor concentrations are reached in the murine tumors upon oral dosing. The drug candidate caused tumor-associated Treg to produce IFN without changing the frequency of Treg circulating in the blood. Ex vivo, MPT-0118 induced Treg reprogramming in tumors resected from patients with colorectal and endometrial cancers and cell killing in spheroids derived from patients with colorectal cancer.

Conclusions

The MALT1 inhibitor MPT-0118 is a clinical candidate for treating MALT1-expressing lymphomas and Treg-infiltrated solid tumors. MPT-0118 exploits the therapeutic opportunity presented by destabilized Treg in the TME. Treg reprogramming represents a novel strategy with the potential to improve responses to ICB therapy in a broad range of solid tumors.

References

Nagel D, Spranger S, Vincendeau M, Grau M, Raffegerst S, Kloo B, Hlahla D, Neuenschwander M, Peter von Kries J, Hadian K, Dörken B, Lenz P, Lenz G, Schendel DJ, Krappmann D. Pharmacologic inhibition of MALT1 protease by phenothiazines as a therapeutic approach for the treatment of aggressive ABC-DLBCL. Cancer Cell 2012 December 11;22(6):825–37.

Di Pilato M, Kim EY, Cadilha BL, Prüßmann JN, Nasrallah MN, Seruggia D, Usmani SM, Misale S, Zappulli V, Carrizosa E, Mani V, Ligorio M, Warner RD, Medoff BD, Marangoni F, Villani AC, Mempel TR. Targeting the CBM complex causes Treg cells to prime tumours for immune checkpoint therapy. Nature 2019 June;570(7759):112–116.

Lim SA, Wei J, Nguyen TM, Shi H, Su W, Palacios G, Dhungana Y, Chapman NM, Long L, Saravia J, Vogel P, Chi H. Lipid signalling enforces functional specialization of Treg cells in tumours. Nature 2021 March;591(7849):306–311.

Zappasodi R, Serganova I, Cohen IJ, Maeda M, Shindo M, Senbabaoglu Y, Watson MJ, Leftin A, Maniyar R, Verma S, Lubin M, Ko M, Mane MM, Zhong H, Liu C, Ghosh A, Abu-Akeel M, Ackerstaff E, Koutcher JA, Ho PC, Delgoffe GM, Blasberg R, Wolchok JD, Merghoub T. CTLA-4 blockade drives loss of Treg stability in glycolysis-low tumours. Nature 2021 March;591(7851):652–658.

Overacre-Delgoffe AE, Chikina M, Dadey RE, Yano H, Brunazzi EA, Shayan G, Horne W, Moskovitz JM, Kolls JK, Sander C, Shuai Y, Normolle DP, Kirkwood JM, Ferris RL, Delgoffe GM, Bruno TC, Workman CJ, Vignali DAA. Interferon-γ drives Treg fragility to promote anti-tumor immunity. Cell 2017 June 1;169(6):1130–1141.e11.

Martin K, Junker U, Tritto E, Sutter E, Rubic-Schneider T, Morgan H, Niwa S, Li J, Schlapbach A, Walker D, Bigaud M, Beerli C, Littlewood-Evans A, Rudolph B, Laisney M, Ledieu D, Beltz K, Quancard J, Bornancin F, Zamurovic Ribrioux N, Calzascia T. Pharmacological inhibition of MALT1 protease leads to a progressive IPEX-Like pathology. Front Immunol 2020 April 30;11:745.

P10.02 Combined methods of a micropump system and a chronic cranial window allows tumor observation with multi photon laser scanning microscopy under continuous treatment

BACKGROUND

Glioblastomas are notoriously therapy resistant tumors. As opposed to other tumor entities, no major advances in therapeutic success have been made in the past decades. This has been calling for a deeper biological understanding of the tumor, its growth and resistance patterns. We have been using a xenograft glioma model, where human glioblastoma cells are implanted under chronic cranial windows and studied longitudinally over many weeks and months using multi photon laser scanning microscopy (MPLSM). To test the effect of (new) drugs, a stable and direct delivery system avoiding the blood-brain-barrier has come into our interest.

MATERIAL AND METHODS

We implanted cranial windows and fluorescently labeled human glioblastoma stem-like cells into NMRI nude mice to follow up on the tumor development in our MPLSM model. After tumor establishment, an Alzet® micropump was implanted to directly deliver agents via a catheter system continuously over 28 days directly under the cranial window onto the brain surface. Using the MPLSM technique, the continuous delivery and infusion of drugs onto the brain and into the tumor was measured over many weeks in detail using MPLSM.

RESULTS

The establishment of the combined methods allowed reliable concurrent drug delivery over 28 days bypassing the blood-brain-barrier. Individual regions and tumor cells could be measured and followed up before, and after the beginning of the treatment, as well as after the end of the pump activity. Fluorescently labelled drugs were detectable in the MPLSM and its distribution into the brain parenchyma could be quantified. After the end of the micropump activity, further MPLSM measurements offer the possibility to observe long term effects of the applied drug on the tumor.

CONCLUSION

The combination of tumor observation in the MPSLM and concurrent continuous drug delivery is a feasible and reliable method for the investigation of (novel) anti-tumor agents, especially drugs that are not blood-brain-barrier penetrant. Morphological or even functional changes of individual tumor cells can be measured under and after treatment. These techniques can be used to test new drugs targeting the tumor, its tumor microtubes and tumor cells networks, and measure the effects longitudinally.

PDBeCIF: an open-source mmCIF/CIF parsing and processing package

Background

Biomacromolecular structural data outgrew the legacy Protein Data Bank (PDB) format which the scientific community relied on for decades, yet the use of its successor PDBx/Macromolecular Crystallographic Information File format (PDBx/mmCIF) is still not widespread. Perhaps one of the reasons is the availability of easy to use tools that only support the legacy format, but also the inherent difficulties of processing mmCIF files correctly, given the number of edge cases that make efficient parsing problematic. Nevertheless, to fully exploit macromolecular structure data and their associated annotations such as multiscale structures from integrative/hybrid methods or large macromolecular complexes determined using traditional methods, it is necessary to fully adopt the new format as soon as possible.

Results

To this end, we developed PDBeCIF, an open-source Python project for manipulating mmCIF and CIF files. It is part of the official list of mmCIF parsers recorded by the wwPDB and is heavily employed in the processes of the Protein Data Bank in Europe. The package is freely available both from the PyPI repository (http://pypi.org/project/pdbecif) and from GitHub (https://github.com/pdbeurope/pdbecif) along with rich documentation and many ready-to-use examples.

Conclusions

PDBeCIF is an efficient and lightweight Python 2.6+/3+ package with no external dependencies. It can be readily integrated with 3rd party libraries as well as adopted for broad scientific analyses.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-021-04271-9.

Horse owners' attitudes towards and motivators for using complementary and alternative veterinary medicine

BACKGROUND

Complementary and alternative veterinary medicine (CAVM) is becoming increasingly popular in horses.

METHODS

Online, cross-sectional survey in 1532 horse owners. Attitude towards CAVM, subjective norms, perceived behavioural control and intention for future CAVM use were measured based on the theory of planned behaviour. Structural equation modelling was performed to characterize factors influencing intention to use CAVM.

RESULTS

Past use of CAVM, predominantly manual therapies and herbal supplements, was reported by 72.5% of all participants. Frequently reported indications were improving horse's well-being, illness which did not resolve after conventional treatment and chronic illness. The attitude towards CAVM was positive with a median (interquartile range) score of 6 of 7 (4.75-7.00). Predictors for past CAVM use were higher owner age, alternative medicine self-use and higher education (non-university). The strongest predictor of future CAVM usage was perceived behavioural control and perceived CAVM efficacy, as well as positive attitude towards and perceived knowledge about CAVM. The veterinarian was reported as a source of information about CAVM by 86.4% of all participants.

CONCLUSIONS

Horse owners showed a high intention to use CAVM with the owners' perceived behavioural control and perceived CAVM efficacy as the strongest predictor. Veterinarian-client communication is important to inform horse owners correctly.

The rare hemoglobin variant Hb Mizuho: report of a Swiss family and literature review

Hb Mizuho is a very rare unstable hemoglobin; here, we describe the clinical history of three Swiss family members with Hb Mizuho together with a systematic review of the previously six published cases. The clinical history of the adult woman we report here is unique since this is the first Hb Mizuho presenting with Moyamoya complications and the first case reported with long-term erythrocyte exchange. The literature review showed that Hb Mizuho was mainly reported as a de novo mutation, with the exception of children descended from known cases. All published patients with this unstable hemoglobin showed severe hemolytic anemia with the exception of one; all were regularly transfused. Patients with higher HbF levels might require fewer transfusions. All patients underwent splenectomy at a median age of 4 years and had variable clinical improvement; some achieved complete resolution of transfusion dependency after splenectomy. Iron overload in Hb Mizuho patients seems to be mainly attributed to transfusions and has less to do with ineffective erythropoiesis. Diagnosis might be challenging; a normal hemoglobin electrophoresis should not rule out the diagnosis of unstable hemoglobin in patients with otherwise unexplained hemolytic anemia. This series shows the enormous utility of using molecular techniques for diagnosis.

The effects of intravenous iron supplementation on fatigue and general health in non-anemic blood donors with iron deficiency: a randomized placebo-controlled superiority trial

We investigated whether intravenous iron supplementation improves fatigue and general health in non-anemic repeat adult blood donors with iron deficiency (ferritin ≤ 50 µg/L). Of 1,487 potentially eligible participants, 203 were randomly assigned to a single intravenous dose of 800 mg iron-carboxymaltose and 202 to placebo; 393 participants completed the trial. At 6 to 8 weeks after intervention, self-rated mean fatigue scores (numeric rating scale from 1-10, primary outcome) were 3.9 ± 1.8 in the iron supplementation group and 4.0 ± 2.2 in the placebo group, showing no group difference (p = 0.819). Pre-specified subgroup analyses of gender, ferritin < 25 µg/L and fatigue ≥ 4 points, as well as exploratory analyses of lower ferritin cut-offs did not reveal any between-group differences. In terms of secondary outcomes, the mean differences were 114.2 µg/L for ferritin (95% CI 103.1-125.3) and 5.7 g/L for hemoglobin (95% CI 4.3-7.2) with significantly higher values in the iron supplementation group. No group differences were observed for different measures of general well-being and other clinical and safety outcomes. Intravenous iron supplementation compared with placebo resulted in increase of ferritin and hemoglobin levels in repeat blood donors with low iron stores, yet had no effect on fatigue and general well-being.

Next-Generation Sequencing for the Diagnosis of Challenging Culture-Negative Endocarditis

Diagnosis of culture-negative infective endocarditis usually implies indirect pathogen identification by serologic or molecular techniques. Clinical metagenomics, relying on next-generation sequencing (NGS) is an emerging approach that allows pathogen identification in challenging situations, as evidenced by a clinical case. We sequenced the DNA extracted from the surgically-removed frozen valve tissue from a patient with suspected infective endocarditis with negative blood and valve cultures. Mapping of the sequence reads against reference genomic sequences, a 16S rRNA gene database and clade-specific marker genes suggested an infection caused by Cardiobacterium hominis.

The sympathomimetic agonist mirabegron did not lower JAK2-V617F allele burden, but restored nestin-positive cells and reduced reticulin fibrosis in patients with myeloproliferative neoplasms: results of phase II study SAKK 33/14

The β-3 sympathomimetic agonist BRL37344 restored nestin-positive cells within the stem cell niche, and thereby normalized blood counts and improved myelofibrosis in a mouse model of JAK2-V617F-positive myeloproliferative neoplasms. We therefore tested the effectiveness of mirabegron, a β-3 sympathomimetic agonist, in a phase II trial including 39 JAK2-V617F-positive patients with myeloproliferative neoplasms and a mutant allele burden more than 20%. Treatment consisted of mirabegron 50 mg daily for 24 weeks. The primary end point was reduction of JAK2-V617F allele burden of 50% or over, but this was not reached in any of the patients. One patient achieved a 25% reduction in JAK2-V617F allele burden by 24 weeks. A small subgroup of patients showed hematologic improvement. As a side study, bone marrow biopsies were evaluated in 20 patients. We found an increase in the nestin+ cells from a median of 1.09 (interquartile range 0.38-3.27)/mm2 to 3.95 (interquartile range 1.98-8.79)/mm2 (P<0.0001) and a slight decrease of reticulin fibrosis from a median grade of 1.0 (interquartile range 0-3) to 0.5 (interquartile range 0-2) (P=0.01) between start and end of mirabegron treatment. Despite the fact that the primary end point of reducing JAK2-V617F allele burden was not reached, the observed effects on nestin+ mesenchymal stem cells and reticulin fibrosis is encouraging, and shows that mirabegron can modify the microenvironment where the JAK2-mutant stem cells are maintained. (Registered at clinicaltrials.gov identifier: 02311569).

Fulminant Essential Thrombocythemia Associated with Acquired Von Willebrand Syndrome and Bleeding Episodes in a 14-year-old Girl

BACKGROUND

 Essential thrombocythemia is a chronic myeloproliferative neoplasm. It is extremely rare in children below 15 years of age with an estimated annual incidence of only 0.09 per million. Usually, clinical symptoms associated with essential thrombocythemia are mild or absent.

CASE

 Here, we present the case of a 14-year-old female patient fulminantly presenting with acute symptoms comprising visual impairment, palmar and plantar stabbing pain. Blood count revealed massive thrombocytosis of 2373 × 10⁹/L. Bone marrow morphology showed elevated numbers of mature megakaryocytes. Von Willebrand factor activity/antigen ratio was significantly reduced compatible with an acquired Von Willebrand syndrome associated with high platelet counts. Molecular analyses for driver mutations of myeloproliferative neoplasms including JAK2V617F, CALR and MPL were negative. Acute therapy comprising hyperhydration and oxygen supply complemented by acetylsalicylic acid led to amelioration of symptoms. Medication with hydroxycarbamide maintained a significant reduction of platelet counts but had to be reduced or withheld several times due to neutropenia. Repeated bleeding episodes observed in the course were clearly associated with increases in platelet counts above 1200 × 10⁹/L explained by acquired von Willebrand syndrome. Sixteen months after diagnosis, therapy was switched to pegylated interferon and platelet counts could be stabilized without significant side effects.

MXCuBE2: the dawn of MXCuBE Collaboration

MXCuBE2 is the second-generation evolution of the MXCuBE beamline control software, initially developed and used at ESRF - the European Synchrotron. MXCuBE2 extends, in an intuitive graphical user interface (GUI), the functionalities and data collection methods available to users while keeping all previously available features and allowing for the straightforward incorporation of ongoing and future developments. MXCuBE2 introduces an extended abstraction layer that allows easy interfacing of any kind of macromolecular crystallography (MX) hardware component, whether this is a diffractometer, sample changer, detector or optical element. MXCuBE2 also works in strong synergy with the ISPyB Laboratory Information Management System, accessing the list of samples available for a particular experimental session and associating, either from instructions contained in ISPyB or from user input via the MXCuBE2 GUI, different data collection types to them. The development of MXCuBE2 forms the core of a fruitful collaboration which brings together several European synchrotrons and a software development factory and, as such, defines a new paradigm for the development of beamline control platforms for the European MX user community.

Low-grade infections as a possible cause of arthrofibrosis after total knee arthroplasty

Purpose

Arthrofibrosis after total knee arthroplasty represents a considerable burden for the patient and a therapeutic challenge for the practitioner. One possible cause discussed in the literature is a low-grade infection. This hypothesis should be examined within the scope of this retrospective study.

Patients and methods

Nineteen patients with clinical symptoms of arthrofibrosis after primary total knee arthroplasty were examined between January, 1999 and January, 2012. Incorrect positioning was radiologically ruled out. All patients were examined clinically (score of Freeman as well as Blauth and Jäger), radiologically (component and leg alignment, patella height according to Insall and Salvati), microbiologically (culture-based procedures), molecular biologically (PCR) and histologically in the course of an open revision of the prosthesis.

Results

According to the score of Freeman et al. (1977), a highly significant improvement in pain (p = 0.007) and in the overall score (p = 0.003) was shown. The knee joint mobility did not change significantly (p = 0.795). PCR was negative in 17 patients. One patient showed a PCR-positive result of the synovial membrane for Corynebacterium spp., while Staphylococcus warneri was detected in the culture. Another patient had a positive result of synovia PCR for Enterococcus cecorum as well as Corynebacterium spp. However, this culture was sterile. In 16 patient samples, no bacterial growth was detectable. Two samples were not evaluable. The main histopathological findings were synovialitis and fibrosis.

Conclusion

The hypothesis of low-grade-infection-induced arthrofibrosis after total knee arthroplasty could not be confirmed in this study. However, based on this small study population the conclusion needs to be confirmed by new and larger studies, ideally prospectively designed including a control group.

Adverse outcome of AML with aberrant CD16 and CD56 NK cell marker expression

Natural killer cells mediate antibody-dependent cell-mediated cytotoxicity, and CD16 exerts key functions to induce antibody-dependent cell-mediated cytotoxicity response. Because the prognostic relevance of aberrant CD16 expression in AML patients at diagnosis is unknown, we analyzed 325 AML patients undergoing intensive chemotherapy for aberrant CD16+ and CD56+ natural killer-cell marker expression. CD56+ AML patients had inferior median event-free (EFS; P = 0.0699) and overall survival (OS; 10.9 versus 20.6 months; P = 0.0132). Patients expressing CD16 had worse median EFS (P = 0.0622) and OS (13.0 versus 45.9 months; P = 0.0277). EFS for CD16+/CD56+ patients was 5.7 months compared with 7.1 months for CD16-/CD56- (P = 0.3690), and OS was 10.6 months for CD16+/CD56+ patients compared with 52.2 months for CD16-/CD56- patients (P = 0.0311). Patients with CD16+/CD56+ expression had a lower probability to achieve complete remission after 2 induction cycles (52% versus 72%). Our data suggest that AML patients with aberrant CD16 and CD56 expression have adverse survival outcomes.

Botulinum neurotoxin injection for the treatment of epiphora in nasolacrimal duct obstruction

PURPOSE

Retrospective long-term study to evaluate the efficacy of botulinum neurotoxin A (BoNT/A) therapy for epiphora due to non-surgical nasolacrimal duct obstruction.

INTRODUCTION

BoNT/A has been used successfully since 2000 in axillary hyperhidrosis to reduce secretory disorders. Some isolated cases of hyperlacrimation or crocodile tear syndrome have been treated on this basis. We used BoNT/A to decrease lacrimal secretion in cases of epiphora.

METHODS

We reviewed the qualitative and quantitative degree of improvement of epiphora after botulinum neurotoxin injections in the palpebral lobe of the lacrimal gland, carried out in an ophthalmic centre between 2009 and 2016. Epiphora was graded using a questionnaire, Munk scores and Schirmer tests before and after injections. Severity of side effects was recorded.

RESULTS

Twenty-seven palpebral lacrimal glands of twenty patients with epiphora, mean age 65±13, were treated with BoNT/A (Botox^® or Xeomin^®) from April 2009 to April 2016. The epiphora was induced by persistent nasolacrimal duct stenosis after surgical treatment. No conventional medical nor surgical treatment was effective at this time. The technique of injection, dilution and dosage were specific. We re-injected 14/27 cases on an as-needed basis, 7/27 cases three times, 3/27 cases four times, and 2/27 cases (same patient both glands) five times. The Schirmer test measured a decrease of lacrimal secretion in 24/27 (89%) lacrimal glands after neurotoxin injection. Side effects were ptosis in 4 cases and transient esotropia in 2 cases. The authors describe the injection techniques, the dosage, the volume and concentration of BoNT/A.

CONCLUSION

Patients with epiphora can be treated effectively with BoNT/A to reduce lacrimal secretion of the principal lacrimal gland in its palpebral portion. Ninety percent of the patients were very satisfied, with few side effects (ptosis or mild diplopia lasting from 3 days to 3 weeks). More studies are needed to delineate which types of epiphora can be treated with BoNT/A.

Standardization of 8-color flow cytometry across different flow cytometer instruments: A feasibility study in clinical laboratories in Switzerland

The EuroFlow Consortium developed a fully standardized flow cytometric approach from instrument settings, through antibody panel, reagents and sample preparation protocols, to data acquisition and analysis. The Swiss Cytometry Society (SCS) promoted a study to evaluate the feasibility of using such standardized measurements of 8-color data across two different flow cytometry platforms - Becton Dickinson (BD) FACSCanto II and Beckman Coulter (BC) Navios, aiming at increasing reproducibility and inter-laboratory comparability of immunophenotypic data in clinical laboratories in Switzerland. The study was performed in two phases, i.e. a learning phase (round 1) and an analytical phase (rounds 2 and 3) consisting of a total of three rounds. Overall, 10 laboratories using BD FACSCanto II (n=6) or BC Navios (n=4) flow cytometers participated. Each laboratory measured peripheral blood samples from healthy donors stained with a uniform antibody panel of reagents - EuroFlow Lymphoid Screening Tube (LST) - applying the EuroFlow standardized protocols for instrument setup and sample preparation (www.EuroFlow.org). All data files were analyzed centrally and median fluorescence intensity (MedFI) values for individual markers on defined lymphocyte subsets were recorded; variability from reference MedFI values was assessed using performance scores. Data troubleshooting and discussion of the results with the participants followed after each round at SCS meetings. The results of the learning phase demonstrated that standardized instrument setup and data acquisition are feasible in routine clinical laboratories without previous experience with EuroFlow. During the analytical phase, highly comparable data were obtained at the different laboratories using either BD FACSCanto II or BC Navios. The coefficient of variation of MedFI for 7 of 11 markers performed repeatedly below 30%. In the last study round, 89% of participants scored over 90% MedFI values within the acceptance criteria (P-score), in line with the results of the EuroFlow quality assessment rounds performed by the EuroFlow expert laboratories(Kalina et al., 2015). Central analysis of data allowed identification of deviations from the standardized procedures and technical issues (e.g. failure to perform correct instrument setup and improper compensation). In summary, here we show that inter-laboratory cross-platform standardization of 8-color flow cytometric measurements in clinical laboratories is feasible and allows for fully comparable MedFI results across BD FACSCanto II and BC Navios instruments. However, adherence to standardized protocols is crucial. Thus, training of the laboratory personnel in the EuroFlow standardized procedures is highly recommended to prevent errors in instrument setup and sample preparation.

Development of a Novel Lead that Targets M. tuberculosis Polyketide Synthase 13

Widespread resistance to first-line TB drugs is a major problem that will likely only be resolved through the development of new drugs with novel mechanisms of action. We have used structure-guided methods to develop a lead molecule that targets the thioesterase activity of polyketide synthase Pks13, an essential enzyme that forms mycolic acids, required for the cell wall of Mycobacterium tuberculosis. Our lead, TAM16, is a benzofuran class inhibitor of Pks13 with highly potent in vitro bactericidal activity against drug-susceptible and drug-resistant clinical isolates of M. tuberculosis. In multiple mouse models of TB infection, TAM16 showed in vivo efficacy equal to the first-line TB drug isoniazid, both as a monotherapy and in combination therapy with rifampicin. TAM16 has excellent pharmacological and safety profiles, and the frequency of resistance for TAM16 is ∼100-fold lower than INH, suggesting that it can be developed as a new antitubercular aimed at the acute infection. PAPERCLIP.

False low holotranscobalamin levels in a patient with a novel TCN2 mutation

BACKGROUND

Measurement of holotranscobalamin (holoTC) is increasingly used as a screening test for cobalamin (Cbl) deficiency. A level well below the reference interval strongly supports a deficient state. We examined a 21-year-old woman diagnosed as Cbl deficient because of an extremely low holoTC level as measured by the Abbott Architect Assay.

METHODS

The patient was evaluated for Cbl deficiency employing an in-house holoTC method as well as other routine markers of Cbl status. Further analyses included exploration of the Cbl binding proteins employing gel filtration of a serum sample saturated with 57 Co-labeled Cbl and Sanger sequencing of exons 1-9 and the intron-exon boundaries of the TCN2 gene, the gene coding for transcobalamin (TC).

RESULTS

The patient had normal hematological variables throughout. Despite initial treatment with Cbl, holoTC as measured by the Abbott assay remained low, while holoTC measured with the in-house assay was normal, and behaved as TC upon gel-filtration. By Sanger sequencing, we detected a homozygous single point mutation c.855T>A in exon 6 of TCN2, corresponding to a asparagine (Asn) to lysine (Lys) substitution in position 267 of the mature protein.

CONCLUSIONS

We describe a novel point mutation of the TCN2 gene. The mutation does not seem to interfere with the function of TC, but the mutation may well explain the low level of holoTC detected by the Abbott assay. Our results underscores that mutations of TCN2 have to be considered when implausible holoTC results are obtained.

Epidemiology of invasive aspergillosis and azole resistance in patients with acute leukaemia: the SEPIA Study

Invasive aspergillosis (IA) is a serious hazard to high-risk haematological patients. There are increasing reports of azole-resistant Aspergillus spp. This study assessed the epidemiology of IA and azole-resistant Aspergillus spp. in patients with acute leukaemia in Germany. A prospective multicentre cohort study was performed in German haematology/oncology centres. The incidence of probable and proven aspergillosis according to the revised EORTC/MSG criteria was assessed for all patients with acute leukaemia [acute myeloid leukaemia (AML) and acute lymphoblastic leukaemia (ALL)]. Cases were documented into a web-based case report form, and centres provided data on standards regarding prophylactic and diagnostic measures. Clinical isolates were screened centrally for azole resistance and, if applicable, underlying resistance mechanisms were analysed. Between September 2011 and December 2013, 179 cases of IA [6 proven (3.4%) and 173 probable (96.6%)] were diagnosed in 3067 patients with acute leukaemia. The incidence of IA was 6.4% among 2440 AML patients and 3.8% among 627 ALL patients. Mortality at Day 84 was 33.8% (49/145) and attributable mortality was 26.9% (39/145). At Day 84, 53 patients (29.6%) showed a complete response, 25 (14.0%) a partial response and 17 (9.5%) a deterioration or failure. A total of 77 clinical Aspergillus fumigatus isolates were collected during the study period. Two episodes of azole-resistant IA (1.1%) were caused by a TR/L98H mutation in the cyp51A gene. With only two cases of IA due to azole-resistant A. fumigatus, a change of antifungal treatment practices in Germany does not appear warranted currently.

Polyelectrolyte Multilayer Film Coating and Stability at the Surfaces of Oral Prosthesis Base Polymers: an in vitro and in vivo Study

A new type of coating involving a layer-by-layer technique has been recently reported. This coating is composed of a polyelectrolyte multilayer film that confers specific properties on surfaces to which it is applied. Here, we studied the applicability of such a technique to the coating of oral prostheses, by first testing the construction of polyelectrolyte multilayer films on several polymers used in oral prosthesis bases, and, subsequently, by studying the stability of these coatings in vitro, in human saliva, and in vivo in a rat model. We demonstrated that the multilayered films are able to coat the surfaces of all tested polymers completely, thus increasing their wettability. We also showed that saliva does not degrade the film after 7 days in vitro and after 4 days in vivo. Taken together, our results establish that the layer-by-layer technique is suitable for the coating of oral devices.

EPID-based dosimetry to verify IMRT planar dose distribution for the aS1200 EPID and FFF beams

We proposed to perform a basic dosimetry commissioning on a new imager system, the Varian aS1200 electronic portal imaging device (EPID) and TrueBeam 2.0 linear accelerator for flattened (FF) and flattening filter‐free (FFF) beams, then to develop an image‐based quality assurance (QA) model for verification of the system delivery accuracy for intensity‐modulated radiation therapy (IMRT) treatments. For dosimetry testing, linearity of dose response with MU, imager lag, and effectiveness of backscatter shielding were investigated. Then, an image‐based model was developed to convert images to planar dose onto a virtual water phantom. The model parameters were identified using energy fluence of the Acuros treatment planning system (TPS) and, reference dose profiles and output factors measured at depths of 5, 10, 15, and 20 cm in water phantom for square fields. To validate the model, its calculated dose was compared to measured dose from MapCHECK 2 diode arrays for 36 IMRT fields at 10 cm depth delivered with 6X, 6XFFF, 10X, and 10XFFF energies. An in‐house gamma function was used to compare planar doses pixel‐by‐pixel. Finally, the method was applied to the same IMRT fields to verify their pretreatment delivery dose compared with Eclipse TPS dose. For the EPID commissioning, dose linearity was within 0.4% above 5 MU and ∼1% above 2 MU, measured lag was smaller than the previous EPIDs, and profile symmetry was improved. The model was validated with mean gamma pass rates (standard deviation) of 99.0% (0.4%), 99.5% (0.6%), 99.3% (0.4%), and 98.0% (0.8%) at 3%/3 mm for respectively 6X, 6XFFF, 10X, and 10XFFF beams. Using the same comparison criteria, the beam deliveries were verified with mean pass rates of 100% (0.0%), 99.6% (0.3%), 99.9% (0.1%), and 98.7% (1.4%). Improvements were observed in dosimetric response of the aS1200 imager compared to previous EPID models, and the model was successfully developed for the new system and delivery energies of 6 and 10 MV, FF, and FFF modes.

PACS number(s): 87.53.Oq, 87.53.Xd

Phenylephrine-induced epistaxis in a six-year-old Quarter horse with nephrosplenic entrapment

Left dorsal displacement of the large colon is a common cause of colic in horses. Treatment consists of surgery, rolling the horse under general anesthesia or intravenous administration of phenylephrine. Treatment with phenylephrine, an α1-adrenergic drug, is often associated with sweating and trembling. Especially in horses of more than 15 years old, fatal hemorrhage may occur due to hemothorax or hemoperitoneum. Therefore, phenylephrine treatment is generally not given in horses over 15 years of age. In this report, severe epistaxis in a six-year-old Quarter horse is described after intravenous administration of 22.5 μg/kg BW phenylephrine, and it is highlighted that hemorrhage may also occur in younger horses.