International clinical practice guidelines for the treatment and prophylaxis of venous thromboembolism in patients with cancer

BACKGROUND

 Guidelines addressing the management of venous thromboembolism (VTE) in cancer patients are heterogeneous and their implementation has been suboptimal worldwide.

OBJECTIVES

To establish a common international consensus addressing practical, clinically relevant questions in this setting.

METHODS

An international consensus working group of experts was set up to develop guidelines according to an evidence-based medicine approach, using the GRADE system.

RESULTS

For the initial treatment of established VTE: low-molecular-weight heparin (LMWH) is recommended [1B]; fondaparinux and unfractionated heparin (UFH) can be also used [2D]; thrombolysis may only be considered on a case-by-case basis [Best clinical practice (Guidance)]; vena cava filters (VCF) may be considered if contraindication to anticoagulation or pulmonary embolism recurrence under optimal anticoagulation; periodic reassessment of contraindications to anticoagulation is recommended and anticoagulation should be resumed when safe; VCF are not recommended for primary VTE prophylaxis in cancer patients [Guidance]. For the early maintenance (10 days to 3 months) and long-term (beyond 3 months) treatment of established VTE, LMWH for a minimum of 3 months is preferred over vitamin K antagonists (VKA) [1A]; idraparinux is not recommended [2C]; after 3-6 months, LMWH or VKA continuation should be based on individual evaluation of the benefit-risk ratio, tolerability, patient preference and cancer activity [Guidance]. For the treatment of VTE recurrence in cancer patients under anticoagulation, three options can be considered: (i) switch from VKA to LMWH when treated with VKA; (ii) increase in LMWH dose when treated with LMWH, and (iii) VCF insertion [Guidance]. For the prophylaxis of postoperative VTE in surgical cancer patients, use of LMWH o.d. or low dose of UFH t.i.d. is recommended; pharmacological prophylaxis should be started 12-2 h preoperatively and continued for at least 7-10 days; there are no data allowing conclusion that one type of LMWH is superior to another [1A]; there is no evidence to support fondaparinux as an alternative to LMWH [2C]; use of the highest prophylactic dose of LMWH is recommended [1A]; extended prophylaxis (4 weeks) after major laparotomy may be indicated in cancer patients with a high risk of VTE and low risk of bleeding [2B]; the use of LMWH for VTE prevention in cancer patients undergoing laparoscopic surgery may be recommended as for laparotomy [Guidance]; mechanical methods are not recommended as monotherapy except when pharmacological methods are contraindicated [2C]. For the prophylaxis of VTE in hospitalized medical patients with cancer and reduced mobility, we recommend prophylaxis with LMWH, UFH or fondaparinux [1B]; for children and adults with acute lymphocytic leukemia treated with l-asparaginase, depending on local policy and patient characteristics, prophylaxis may be considered in some patients [Guidance]; in patients receiving chemotherapy, prophylaxis is not recommended routinely [1B]; primary pharmacological prophylaxis of VTE may be indicated in patients with locally advanced or metastatic pancreatic [1B] or lung [2B] cancer treated with chemotherapy and having a low risk of bleeding; in patients treated with thalidomide or lenalidomide combined with steroids and/or chemotherapy, VTE prophylaxis is recommended; in this setting, VKA at low or therapeutic doses, LMWH at prophylactic doses and low-dose aspirin have shown similar effects; however, the efficacy of these regimens remains unclear [2C]. Special situations include brain tumors, severe renal failure (CrCl<30 mL min(-1) ), thrombocytopenia and pregnancy. Guidances are provided in these contexts.

CONCLUSIONS

Dissemination and implementation of good clinical practice for the management of VTE, the second cause of death in cancer patients, is a major public health priority.

International clinical practice guidelines for the treatment and prophylaxis of thrombosis associated with central venous catheters in patients with cancer

BACKGROUND

Although long-term indwelling central venous catheters (CVCs) may lead to pulmonary embolism (PE) and loss of the CVC, there is lack of consensus on management of CVC-related thrombosis (CRT) in cancer patients and heterogeneity in clinical practices worldwide.

OBJECTIVES

To establish common international Good Clinical Practices Guidelines (GCPG) for the management of CRT in cancer patients.

METHODS

An international working group of experts was set up to develop GCPG according to an evidence-based medicine approach, using the GRADE system.

RESULTS

For the treatment of established CRT in cancer patients, we found no prospective randomized studies, two non-randomized prospective studies and one retrospective study examining the efficacy and safety of low-molecular-weight heparin (LMWH) plus vitamin K antagonists (VKAs). One retrospective study evaluated the benefit of CVC removal and two small retrospective studies were on thrombolytic drugs. For the treatment of symptomatic CRT, anticoagulant treatment (AC) is recommended for a minimum of 3 months; in this setting, LMWHs are suggested. VKAs can also be used, in the absence of direct comparisons of these two types of anticoagulants in this setting [Guidance]. The CVC can be kept in place if it is functional, well-positioned and non-infected and there is good resolution under close surveillance; whether the CVC is kept or removed, no standard approach in terms of AC duration has been established [Guidance]. For the prophylaxis of CRT in cancer patients, we found six randomized studies investigating the efficacy and safety of VKA vs. placebo or no treatment, one on the efficacy and safety of unfractionnated heparin, six on the value of LMWH, one double-blind randomized and one non randomized study on thrombolytic drugs and six meta-analyses of AC and CVC thromboprophylaxis. Type of catheter (open-ended like the Hickman(®) catheter vs. closed-ended catheter with a valve like the Groshong(®) catheter), its position (above, below or at the junction of the superior vena cava and the right atrium) and method of placement may influence the onset of CRT on the basis of six retrospective trials, four prospective non-randomized trials, three randomized trials and one meta-analysis. In light of these data: use of AC for routine prophylaxis of CRT is not recommended [1A]; a CVC should be inserted on the right side, in the jugular vein, and distal extremity of the CVC should be located at the junction of the superior vena cava and the right atrium [1A].

CONCLUSION

Dissemination and implementation of these international GCPG for the prevention and treatment of CRT in cancer patients at each national level is a major public health priority, needing worldwide collaboration.

Active genes in junk DNA? Characterization of DUX genes embedded within 3.3 kb repeated elements

The human genome contains hundreds of repeats of the 3.3 kb family in regions associated with heterochromatin. We have previously isolated a 3.3 kb-like cDNA encoding a double homeodomain protein (DUX1). Demonstration that the protein was expressed in human rhabdomyosarcoma TE671 cells, and characterization of a homologous promoter suggested that functional DUX genes might be present in 3.3 kb elements. In the present study, we describe two nearly identical 3.3 kb/DUX genes derived from PAC 137F16 (DUX3), and TE671 genomic DNA (DUX5), both mapping to all the acrocentric chromosomes. Their promoters harbor a GC and a TATAA box, and the open reading frame of the intronless structural part encodes two DUX proteins differing by alternative translation initiation. The shorter protein of the DUX5 gene is identical to DUX1. Using a protein truncation test, we could show that these two proteins are encoded by total RNA, but not by poly (A)(+) RNA, from different human tissues and cell lines. Our results indicate that active genes of unusual structure are present in chromosome regions characterized by large amounts of heterochromatic repetitive DNA.

Single-particle cryo-EM structures from iDPC-STEM at near-atomic resolution

In electron cryomicroscopy (cryo-EM), molecular images of vitrified biological samples are obtained by conventional transmission microscopy (CTEM) using large underfocuses and subsequently computationally combined into a high-resolution three-dimensional structure. Here, we apply scanning transmission electron microscopy (STEM) using the integrated differential phase contrast mode also known as iDPC-STEM to two cryo-EM test specimens, keyhole limpet hemocyanin (KLH) and tobacco mosaic virus (TMV). The micrographs show complete contrast transfer to high resolution and enable the cryo-EM structure determination for KLH at 6.5 Å resolution, as well as for TMV at 3.5 Å resolution using single-particle reconstruction methods, which share identical features with maps obtained by CTEM of a previously acquired same-sized TMV data set. These data show that STEM imaging in general, and in particular the iDPC-STEM approach, can be applied to vitrified single-particle specimens to determine near-atomic resolution cryo-EM structures of biological macromolecules.

Myeloid-derived suppressor cells in lymphoma: The good, the bad and the ugly

Lymphomas cause significant morbidity and mortality worldwide. A substantial number of patients ultimately relapse after standard treatment. However, the efficacy of these therapies can be counteracted by the patients' immune system, more specifically by myeloid-derived suppressor cells (MDSC). MDSC are a heterogeneous group of immature myeloid cells that suppress the innate and adaptive immune system via different mechanisms and accumulate under pathological conditions, such as cancer. MDSC play a role in the induction and progression of cancer and immune evasion. Increased numbers of MDSC have been reported in different lymphoma subtypes and are associated with a poor clinical outcome. This review aims to clarify the role of MDSC and their working mechanism in different lymphoma subtypes. Furthermore, the effect of MDSC on immunotherapies will be discussed.

Thresholding of cryo-EM density maps by false discovery rate control

Cryo-EM now commonly generates close-to-atomic resolution as well as intermediate resolution maps from macromolecules observed in isolation and in situ. Interpreting these maps remains a challenging task owing to poor signal in the highest resolution shells and the necessity to select a threshold for density analysis. In order to facilitate this process, a statistical framework for the generation of confidence maps by multiple hypothesis testing and false discovery rate (FDR) control has been developed. In this way, three-dimensional confidence maps contain signal separated from background noise in the form of local detection rates of EM density values. It is demonstrated that confidence maps and FDR-based thresholding can be used for the interpretation of near-atomic resolution single-particle structures as well as lower resolution maps determined by subtomogram averaging. Confidence maps represent a conservative way of interpreting molecular structures owing to minimized noise. At the same time they provide a detection error with respect to background noise, which is associated with the density and is particularly beneficial for the interpretation of weaker cryo-EM densities in cases of conformational flexibility and lower occupancy of bound molecules and ions in the structure.

Quantitative structural information from single-molecule FRET

Single-molecule studies can be used to study biological processes directly and in real-time. In particular, the fluorescence energy transfer between reporter dye molecules attached to specific sites on macromolecular complexes can be used to infer distance information. When several measurements are combined, the information can be used to determine the position and conformation of certain domains with respect to the complex. However, data analysis schemes that include all experimental uncertainties are highly complex, and the outcome depends on assumptions about the state of the dye molecules. Here, we present a new analysis algorithm using Bayesian parameter estimation based on Markov Chain Monte Carlo sampling and parallel tempering termed Fast-NPS that can analyse large smFRET networks in a relatively short time and yields the position of the dye molecules together with their respective uncertainties. Moreover, we show what effects different assumptions about the dye molecules have on the outcome. We discuss the possibilities and pitfalls in structure determination based on smFRET using experimental data for an archaeal transcription pre-initiation complex, whose architecture has recently been unravelled by smFRET measurements.

Elucidation of the viral disassembly switch of tobacco mosaic virus

Stable capsid structures of viruses protect viral RNA while they also require controlled disassembly for releasing the viral genome in the host cell. A detailed understanding of viral disassembly processes and the involved structural switches is still lacking. This process has been extensively studied using tobacco mosaic virus (TMV), and carboxylate interactions are assumed to play a critical part in this process. Here, we present two cryo‐EM structures of the helical TMV assembly at 2.0 and 1.9 Å resolution in conditions of high Ca²⁺ concentration at low pH and in water. Based on our atomic models, we identify the conformational details of the disassembly switch mechanism: In high Ca²⁺/acidic pH environment, the virion is stabilized between neighboring subunits through carboxyl groups E95 and E97 in close proximity to a Ca²⁺ binding site that is shared between two subunits. Upon increase in pH and lower Ca²⁺ levels, mutual repulsion of the E95/E97 pair and Ca²⁺ removal destabilize the network of interactions between adjacent subunits at lower radius and release the switch for viral disassembly.

Ptychographic coherent x-ray diffractive imaging in the water window

Coherent x-ray diffractive microscopy enables full reconstruction of the complex transmission function of an isolated object to diffraction-limited resolution without relying on any optical elements between the sample and detector. In combination with ptychography, also specimens of unlimited lateral extension can be imaged. Here we report on an application of ptychographic coherent diffractive imaging (PCDI) in the soft x-ray regime, more precisely in the so-called water window of photon energies where the high scattering contrast between carbon and oxygen is well-suited to image biological samples. In particular, we have reconstructed the complex sample transmission function of a fossil diatom at a photon energy of 517 eV. In imaging a lithographically fabricated test sample a resolution on the order of 50 nm (half-period length) has been achieved. Along with this proof-of-principle for PCDI at soft x-ray wavelengths, we discuss the experimental and technical challenges which can occur especially for soft x-ray PCDI.

Reproducibility of fetal renal pelvis volume measurement using three-dimensional ultrasound

OBJECTIVE

To assess the reproducibility of fetal renal pelvis volume measurement in hydronephrotic kidneys using transabdominal three-dimensional (3D) ultrasound.

METHODS

The fetal renal pelvis volume was measured using 3D ultrasound in one kidney in each of 15 fetuses with hydronephrosis in the second or third trimester of pregnancy. Hydronephrosis was diagnosed when the fetus had an anteroposterior renal pelvis diameter > or = 5 mm. After volume acquisition by one of the observers, the repeatability of volume calculation with manual delineation of the fetal renal pelvis was assessed by six different observers using the Virtual Organ Computer-aided AnaLysis (VOCAL(trade mark)) imaging program. The intraclass correlation coefficients (ICC), coefficient of variation (CV) and within- and between-observer repeatability coefficient (r) were calculated and Bland-Altman plots were constructed.

RESULTS

Both intra- and interobserver reliability of the fetal renal pelvis volume measurements were considered to be very good. For intraobserver reliability, the ICC was 0.996 and the CV was 10.8%. For the overall interobserver reliability, the ICC was 0.998 and the CV was 15.7%; the interobserver reliability between pairs of observers had ICCs between 0.994 and 0.999, and CVs between 19.5% and 7.6% for inexperienced and experienced observers, respectively.

CONCLUSION

With 3D ultrasound using the VOCAL imaging program, it is technically feasible to reproduce fetal renal pelvis volume measurements. Further research to establish the clinical applications of this technology is warranted.

Studies with the optically active isomers of the new diuretic drug ozolinone. II. Inhibition by d-ozolinone of furosemide-induced diuresis

The effect of the non-diuretic dextrorotatory isomer of ozolinone on furosemide-induced diuresis was studied by means of clearance and micropuncture techniques in rats. After intravenous injection, d-ozolinone antagonized the furosemide-induced increase in renal fluid and electrolyte excretion in a dose-related manner. Microperfusion experiments of Henle's loop in vivo revealed that d-ozolinone did not interfere with the action of furosemide at this tubular site. However, d-ozolinone markedly decreased the furosemide to inulin clearance ratio, presumably as a consequence of inhibition of furosemide secretion into the proximal tubules. It is assumed that, in consequence of a high affinity for the proximal organic acid transport system, d-ozolinone depresses proximal tubular furosemide secretion and prevents transfer of this diuretic to the tubular fluid. Thus, under the influence of d-ozolinone, furosemide cannot reach the loop of Henle in sufficient amounts and its diuretic effect is blocked.

[Graft-versus-Host Disease (GvHD) - an update : Part 1: Pathophysiology, clinical features and classification of GvHD]

GvHD remains associated with significant morbidity and mortality despite new techniques for allogeneic stem cell transplantation (SCT), such as optimized conditioning regimens. Within the past ten years, the incidence of acute GvHD has remained unchanged and the incidence of chronic GvHD has even increased. The traditional classification of GvHD according to the time of clinical manifestation is now out-dated. Acute GvHD symptoms may even occur after 100 days; vice versa, primary chronic GvHD may already be observed one month after stem cell transplantation. The current classification introduced by the National Institutes of Health includes classic acute GvHD (up to 100 days), late-onset acute GvHD (after 100 days), as well as an overlap syndrome showing features of acute and chronic GvHD and classic chronic GvHD without any time limit. Diagnosis of GvHD of the skin remains difficult because of histological similarities to drug eruptions and viral exanthems. In this first part of the article the pathophysiology, classification, skin manifestations of acute and chronic GvHD and the histopathology will be presented. In a second part the prognosis, prophylaxis and therapy of GvHD will be discussed.

25 Years of Small-Molecule Optimization at Novartis: A Retrospective Analysis of Chemical Series Evolution

In the drug development process, optimization of properties and biological activities of small molecules is an important task to obtain drug candidates with optimal efficacy when first applied in subsequent clinical studies. However, despite its importance, large-scale investigations of the optimization process in early drug discovery are lacking, likely due to the absence of historical records of different chemical series used in past projects. Here, we report a retrospective reconstruction of ∼3000 chemical series from the Novartis compound database, which allows us to characterize the general properties of chemical series as well as the time evolution of structural properties, ADMET properties, and target activities. Our data-driven approach allows us to substantiate common MedChem knowledge. We find that size, fraction of sp³-hybridized carbon atoms (F_sp³), and the density of stereocenters tend to increase during optimization, while the aromaticity of the compounds decreases. On the ADMET side, solubility tends to increase and permeability decreases, while safety-related properties tend to improve. Importantly, while ligand efficiency decreases due to molecular growth over time, target activities and lipophilic efficiency tend to improve. This emphasizes the heavy-atom count and log D as important parameters to monitor, especially as we further show that the decrease in permeability can be explained with the increase in molecular size. We highlight overlaps, shortcomings, and differences of the computationally reconstructed chemical series compared to the series used in recent internal drug discovery projects and investigate the relation to historical projects.

Atomic force microscopy of chromatin arrays reveal non-monotonic salt dependence of array compaction in solution

Compaction of DNA in chromatin is a hallmark of the eukaryotic cell and unravelling its structure is required for an understanding of DNA involving processes. Despite strong experimental efforts, many questions concerning the DNA packing are open. In particular, it is heavily debated whether an ordered structure referred to as the “30 nm fibre” exist in vivo. Scanning probe microscopy has become a cutting edge technology for the high-resolution imaging of DNA- protein complexes. Here, we perform high-resolution atomic force microscopy of non-cross-linked chromatin arrays in liquid, under different salt conditions. A statistical analysis of the data reveals that array compaction is salt dependent in a non-monotonic fashion. A simple physical model can qualitatively explain the observed findings due to the opposing effects of salt dependent stiffening of DNA, nucleosome stability and histone-histone interactions. While for different salt concentrations different compaction states are observed, our data do not provide support for the existence of regular chromatin fibres. Our studies add new insights into chromatin structure, and with that contribute to a further understanding of the DNA condensation.

Structural interpretation of cryo-EM image reconstructions

The productivity of single-particle cryo-EM as a structure determination method has rapidly increased as many novel biological structures are being elucidated. The ultimate result of the cryo-EM experiment is an atomic model that should faithfully represent the computed image reconstruction. Although the principal approach of atomic model building and refinement from maps resembles that of the X-ray crystallographic methods, there are important differences due to the unique properties resulting from the 3D image reconstructions. In this review, we discuss the practiced work-flow from the cryo-EM image reconstruction to the atomic model. We give an overview of (i) resolution determination methods in cryo-EM including local and directional resolution variation, (ii) cryo-EM map contrast optimization including complementary map types that can help in identifying ambiguous density features, (iii) atomic model building and (iv) refinement in various resolution regimes including (v) their validation and (vi) discuss differences between X-ray and cryo-EM maps. Based on the methods originally developed for X-ray crystallography, the path from 3D image reconstruction to atomic coordinates has become an integral and important part of the cryo-EM structure determination work-flow that routinely delivers atomic models.

[Graft-versus-host disease (GvHD) - an update. Part 2: prognosis and therapy of GvHD]

Graft-versus-host disease (GvHD) remains one of the major complications after allogeneic stem cell transplantation (SCT) and is responsible for morbidity, mortality and decrease in quality of life of patients after SCT. The most important preventive approach is the selection of a donor with best possible HLA compatibility between donor and recipient. Basic prophylaxis of acute GvHD begins already prior to transplantation and usually consists of cyclosporine with or without methotrexate. In the past few years, many new therapies have been introduced for the treatment of acute and chronic GvHD. Extracorporeal photopheresis (ECP), for example, represents a promising treatment option for acute and chronic GvHD with very few side effects. For chronic GvHD mTOR inhibitors (sirolimus, everolimus) may replace calcineurin-inhibitors with the advantage of not inducing malignant skin tumors. Guidelines are available ort he management of acute and chronic GvHD. While pathophysiology, classification and skin manifestations of GvHD have been already presented in the first part of this article, this second part covers the prognosis, prevention and treatment of GvHD.

Prediction of Small-Molecule Developability Using Large-Scale In Silico ADMET Models

Early in silico assessment of the potential of a series of compounds to deliver a drug is one of the major challenges in computer-assisted drug design. The goal is to identify the right chemical series of compounds out of a large chemical space to then subsequently prioritize the molecules with the highest potential to become a drug. Although multiple approaches to assess compounds have been developed over decades, the quality of these predictors is often not good enough and compounds that agree with the respective estimates are not necessarily druglike. Here, we report a novel deep learning approach that leverages large-scale predictions of ∼100 ADMET assays to assess the potential of a compound to become a relevant drug candidate. The resulting score, which we termed bPK score, substantially outperforms previous approaches and showed strong discriminative performance on data sets where previous approaches did not.

Single pulse coherence measurements in the water window at the free-electron laser FLASH

The spatial coherence of free-electron laser radiation in the water window spectral range was studied, using the third harmonic (λ<(3rd) = 2.66 nm) of DESY's Free-electron LASer in Hamburg (FLASH). Coherent single pulse diffraction patterns of 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) multilamellar lipid stacks have been recorded. The intensity histogram of the speckle pattern around the first lamellar Bragg peak, corresponding to the d = 5 nm periodicity of the stack, reveals an average number of transverse modes of M¯ = 3.0 of the 3rd harmonic. Using the lipid stack as a 'monochromator', pulse-to-pulse fluctuations in the third harmonic λ(3rd) have been determined to be 0.033 nm.

Confidence maps: statistical inference of cryo-EM maps

Confidence maps provide complementary information for interpreting cryo-EM densities as they indicate statistical significance with respect to background noise. They can be thresholded by specifying the expected false-discovery rate (FDR), and the displayed volume shows the parts of the map that have the corresponding level of significance. Here, the basic statistical concepts of confidence maps are reviewed and practical guidance is provided for their interpretation and usage inside the CCP-EM suite. Limitations of the approach are discussed and extensions towards other error criteria such as the family-wise error rate are presented. The observed map features can be rendered at a common isosurface threshold, which is particularly beneficial for the interpretation of weak and noisy densities. In the current article, a practical guide is provided to the recommended usage of confidence maps.