Rapid access clinic for unexplained lymphadenopathy and suspected malignancy: prospective analysis of 1000 patients.

Background:In patients presenting with peripheral lymphadenopathy, it is critical to effectively identify those with underlying cancer who require urgent specialist care. Methods:We analyzed a large dataset of 1000 consecutive patients with unexplained lymphadenopathy referred between 2001 and 2009 to the Royal Marsden Hospital (RMH) rapid access lymph node diagnostic clinic (LNDC). Results:Cancer was diagnosed in 14% of patients. Factors predictive for malignant disease were male sex, age, supraclavicular and multiple site involvement. Cancer-associated symptoms were present for a median of 8 weeks. The median time from referral to start of cancer therapy was 53 days. Fine needle aspiration (FNA) was performed in 83% of patients with malignancies. Sensitivity and specificity of FNA were limited (50 and 87%, respectively for any malignancy; 30 and 79%, respectively for lymphoma). The vast majority of cancer patients received diagnostic biopsies on the basis of suspicious clinical and ultrasound findings; the FNA result contributed to establishing the diagnosis in only 4 cases. Conclusions:In conclusion, we demonstrate that Oncologist-led rapid access clinics are successful concepts to assess patients with unexplained lymphadenopathy. Our data suggest that a routine use of FNA should be reconsidered in this setting

Tractable RNA–ligand interaction kinetics

Abstract Background The binding of small ligands to RNA elements can cause substantial changes in the RNA structure. This constitutes an important, fast-acting mechanism of ligand-controlled transcriptional and translational gene regulation implemented by a wide variety of riboswitches. The associated refolding processes often cannot be explained by thermodynamic effects alone. Instead, they are governed by the kinetics of RNA folding. While the computational analysis of RNA folding can make use of well-established models of the thermodynamics of RNA structures formation, RNA–RNA interaction, and RNA–ligand interaction, kinetic effects pose fundamentally more challenging problems due to the enormous size of the conformation space. The analysis of the combined process of ligand binding and structure formation even for small RNAs is plagued by intractably large state spaces. Moreover, the interaction is concentration-dependent and thus is intrinsically non-linear. This precludes the direct transfer of the strategies previously used for the analysis of RNA folding kinetics. Results In our novel, computationally tractable approach to RNA–ligand kinetics, we overcome the two main difficulties by applying a gradient-based coarse graining to RNA–ligand systems and solving the process in a pseudo-first order approximation. The latter is well-justified for the most common case of ligand excess in RNA–ligand systems. We present the approach rigorously and discuss the parametrization of the model based on empirical data. The method supports the kinetic study of RNA–ligand systems, in particular at different ligand concentrations. As an example, we apply our approach to analyze the concentration dependence of the ligand response of the rationally designed, artificial theophylline riboswitch RS3. Conclusion This work demonstrates the tractability of the computational analysis of RNA–ligand interaction. Naturally, the model will profit as more accurate measurements of folding and binding parameters become available. Due to this work, computational analysis is available to support tasks like the design of riboswitches; our analysis of RS3 suggests strong co-transcriptional effects for this riboswitch. The method used in this study is available online, cf. Section “Availability of data and materials”

Beyond plug and pray : context sensitivity and in silico design of artificial neomycin riboswitches

Gene regulation in prokaryotes often depends on RNA elements such as riboswitches or RNA thermometers located in the 5′ untranslated region of mRNA. Rearrangements of the RNA structure in response, e.g., to the binding of small molecules or ions control translational initiation or premature termination of transcription and thus mRNA expression. Such structural responses are amenable to computational modelling, making it possible to rationally design synthetic riboswitches for a given aptamer. Starting from an artificial aptamer, we construct the first synthetic transcriptional riboswitches that respond to the antibiotic neomycin. We show that the switching behaviour in vivo critically depends not only on the sequence of the riboswitch itself, but also on its sequence context. We therefore developed in silico methods to predict the impact of the context, making it possible to adapt the design and to rescue non-functional riboswitches. We furthermore analyse the influence of 5′ hairpins with varying stability on neomycin riboswitch activity. Our data highlight the limitations of a simple plug-and-play approach in the design of complex genetic circuits and demonstrate that detailed computational models significantly simplify, improve, and automate the design of transcriptional circuits. Our design software is available under a free licence on GitHub (https://github.com/xileF1337/riboswitch_design)