Widespread Shortening of 3’ Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection

The contribution of pre-mRNA processing mechanisms to the regulation of immune responses remains poorly studied despite emerging examples of their role as regulators of immune defenses. We sought to investigate the role of mRNA processing in the cellular responses of human macrophages to live bacterial infections. Here, we used mRNA sequencing to quantify gene expression and isoform abundances in primary macrophages from 60 individuals, before and after infection with Listeria monocytogenes and Salmonella typhimurium. In response to both bacteria we identified thousands of genes that significantly change isoform usage in response to infection, characterized by an overall increase in isoform diversity after infection. In response to both bacteria, we found global shifts towards (i) the inclusion of cassette exons and (ii) shorter 3’ UTRs, with near-universal shifts towards usage of more upstream polyadenylation sites. Using complementary data collected in non-human primates, we show that these features are evolutionarily conserved among primates. Following infection, we identify candidate RNA processing factors whose expression is associated with individual-specific variation in isoform abundance. Finally, by profiling microRNA levels, we show that 3’ UTRs with reduced abundance after infection are significantly enriched for target sites for particular miRNAs. These results suggest that the pervasive usage of shorter 3’ UTRs is a mechanism for particular genes to evade repression by immune-activated miRNAs. Collectively, our results suggest that dynamic changes in RNA processing may play key roles in the regulation of innate immune responses.     

Marginal zone lymphoma-derived interfollicular diffuse large B-cell lymphoma harboring 20q12 chromosomal deletion and missense mutation of <Emphasis Type="Italic">BIRC3</Emphasis> gene: a case report

Background

Diffuse large B-cell lymphoma (DLBCL) typically leads to effacement of the nodal architecture by an infiltrate of malignant cells. Rarely (<1%), DLBCL can present with an interfollicular pattern (DLBCL-IF) preserving the lymphoid follicles. It has been postulated that DLBCL-IF is derived from marginal zone B cells and may represent a large-cell transformation of marginal zone lymphoma (MZL), however no direct evidence has been provided to date. Here we describe a rare case of a diagnostically challenging DLBCL-IF involving a lymph node in a patient with a prior history of lymphadenopathy for several years and MZL involving skin.

Case presentation

A 53-year old man presented to our Dermatology Clinic due to a 1-year history of generalized itching, fatigue of 2–3 month’s duration, nausea and mid back rash that was biopsied. PET (positron emission tomography)/CT (computed tomography) was performed and revealed inguinal, pelvic, retroperitoneal, axillary, and cervical lymphadenopathy. The patient was referred to surgery for excisional biopsy of a right inguinal lymph node.Diagnostic H&E stained slides and ancillary studies were reviewed for the lymph node and skin specimens. B-cell clonality by PCR and sequencing studies were performed on both specimens.We demonstrate that this patient’s MZL and DLBCL-IF are clonally related, strongly suggesting that transformation of MZL to DLBCL had occurred. Furthermore, we identified a novel deletion of the long arm of chromosome 20 (del(20q12)) and a missense mutation in BIRC3 (Baculoviral IAP repeat-containing protein 3) in this patient’s DLBCL that are absent from his MZL, suggesting that these genetic alterations contributed to the large cell transformation.

Conclusions

To our knowledge, this is the first report providing molecular evidence for a previously suspected link between MZL and DLBCL-IF. In addition, we describe for the first time del(20q12) and a missense mutation in BIRC3 in DLBCL. Our findings also raise awareness of DLBCL-IF and discuss the diagnostic pitfalls of this rare entity.

     

Development of a core outcome set for clinical trials in rosacea: study protocol for a systematic review of the literature and identification of a core outcome set using a Delphi survey

BackgroundRosacea is a chronic inflammatory disorder affecting millions of individuals worldwide. Diagnosis is based on signs and symptoms with management and treatment aimed to suppress inflammatory lesions, erythema, and telangiectasia. While many clinical trials of rosacea exist, the lack of consensus in outcome reporting across all trials poses a concern. Proper evaluation and comparison of treatment modalities is challenging. In order to address the inconsistencies present, this project aims to determine a core set of outcomes which should be evaluated in all clinical trials of rosacea.Methods/designThis project will utilize a methodology similar to previous core outcome set research. A long list of outcomes will be extracted over four phases: (1) systematic literature review, (2) patient interviews, (3) other published sources, and (4) stakeholder involvement. Potential outcomes will be examined by the Steering Committee to provide further insight. The Delphi process will then be performed to prioritize and condense the list of outcomes generated. Two homogenous groups of physicians and patients will participate in two consecutive rounds of Delphi surveys. A consensus meeting, composed of physicians, patients, and stakeholders, will be conducted after the Delphi exercise to further select outcomes, taking into account participant scores. By the end of the meeting, members will vote and decide on a final recommended set of core outcomes. For the duration of the study, we will be in collaboration with both the Core Outcome Measures in Effectiveness Trials (COMET) and Cochrane Skin Group - Core Outcome Set Initiative (CSG-COUSIN).DiscussionThis study aims to develop a core outcome set to guide assessment in clinical trials of rosacea. The end-goal is to improve the reliability and consistency of outcome reporting, thereby allowing sufficient evaluation of treatment effectiveness and patient satisfaction.

Electronic supplementary material

The online version of this article (doi:10.1186/s13063-016-1554-3) contains supplementary material, which is available to authorized users.     

Detecting the native ligand orientation by interfacial rigidity: SiteInterlock

Understanding the physical attributes of protein‐ligand interfaces, the source of most biological activity, is a fundamental problem in biophysics. Knowing the characteristic features of interfaces also enables the design of molecules with potent and selective interactions. Prediction of native protein‐ligand interactions has traditionally focused on the development of physics‐based potential energy functions, empirical scoring functions that are fit to binding data, and knowledge‐based potentials that assess the likelihood of pairwise interactions. Here we explore a new approach, testing the hypothesis that protein‐ligand binding results in computationally detectable rigidification of the protein‐ligand interface. Our SiteInterlock approach uses rigidity theory to efficiently measure the relative interfacial rigidity of a series of small‐molecule ligand orientations and conformations for a number of protein complexes. In the majority of cases, SiteInterlock detects a near‐native binding mode as being the most rigid, with particularly robust performance relative to other methods when the ligand‐free conformation of the protein is provided. The interfacial rigidification of both the protein and ligand prove to be important characteristics of the native binding mode. This measure of rigidity is also sensitive to the spatial coupling of interactions and bond‐rotational degrees of freedom in the interface. While the predictive performance of SiteInterlock is competitive with the best of the five other scoring functions tested, its measure of rigidity encompasses cooperative rather than just additive binding interactions, providing novel information for detecting native‐like complexes. SiteInterlock shows special strength in enhancing the prediction of native complexes by ruling out inaccurate poses. Proteins 2016; 84:1888–1901. © 2016 Wiley Periodicals, Inc.     

Spatial distribution of proteins in the quagga mussel adhesive apparatus

The invasive freshwater mollusc Dreissena bugensis (quagga mussel) sticks to underwater surfaces via a proteinacious ‘anchor’ (byssus), consisting of a series of threads linked to adhesive plaques. This adhesion results in the biofouling of crucial underwater industry infrastructure, yet little is known about the proteins responsible for the adhesion. Here the identification of byssal proteins extracted from freshly secreted byssal material is described. Several new byssal proteins were observed by gel electrophoresis. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to characterize proteins in different regions of the byssus, particularly those localized to the adhesive interface. Byssal plaques and threads contain in common a range of low molecular weight proteins, while several proteins with higher mass were observed only in the plaque. At the adhesive interface, a plaque-specific ~8.1 kDa protein had a relative increase in signal intensity compared to the bulk of the plaque, suggesting it may play a direct role in adhesion.     

Change in knee contact force with simulated change in body weight

The relationship between obesity, weight gain and progression of knee osteoarthritis is well supported, suggesting that excessive joint loading may be a mechanism responsible for cartilage deterioration. Examining the influence of weight gain on joint compressive forces is difficult, as both muscles and ground reaction forces can have a significant impact on the forces experienced during gait. While previous studies have examined the relationship between body weight and knee forces, these studies have used models that were not validated using experimental data. Therefore, the objective of this study was to evaluate the relationship between changes in body weight and changes in knee joint contact forces for an individual's gait pattern using musculoskeletal modeling that is validated against known internal compressive forces. Optimal weighting constants were determined for three subjects to generate valid predictions of knee contact forces (KCFs) using in vivo data collection with instrumented total knee arthroplasty. A total of five simulations per walking trial were generated for each subject, from 80% to 120% body weight in 10% increments, resulting in 50 total simulations. The change in peak KCF with respect to body weight was found to be constant and subject-specific, predominantly determined by the peak force during the baseline condition at 100% body weight. This relationship may be further altered by any change in kinematics or body mass distribution that may occur as a result of a change in body weight or exercise program.     

Induction of Krüppel‐like factor 2 reduces K/BxN serum‐induced arthritis

Krüppel‐like factor 2 (KLF2) critically regulates activation and function of monocyte, which plays important pathogenic role in progressive joint destruction in rheumatoid arthritis (RA). It is yet to be established the molecular basis of KLF2‐mediated regulation of monocytes in RA pathogenesis. Herein, we show that a class of compound, HDAC inhibitors (HDACi) induced KLF2 expression in monocytes both in vitro and in vivo. KLF2 level was also elevated in tissues, such as bone marrow, spleen and thymus in mice after infusion of HDACi. Importantly, HDACi significantly reduced osteoclastic differentiation of monocytes with the up‐regulation of KLF2 and concomitant down‐regulation of matrixmetalloproteinases both in the expression level as well as in the protein level. In addition, HDACi reduced K/BxN serum‐induced arthritic inflammation and joint destruction in mice in a dose‐dependent manner. Finally, co‐immunoprecipitation and overexpression studies confirmed that KLF2 directly interacts with HDAC4 molecule in cells. These findings provide mechanistic evidence of KLF2‐mediated regulation of K/BxN serum‐induced arthritic inflammation.     

Ti3C2Tx (MXene)‐Silicon Heterojunction for Efficient Photovoltaic Cells

A novel type of solar cell has been developed based on charge separation at the heterojunction formed by a transparent conducting MXene electrode and an n‐type silicon (n‐Si) wafer. A thin layer of the native silicon dioxide plays an important role in suppressing the recombination of charge carriers. A two‐step chemical treatment can increase the device efficiency by about 40%. Promisingly, an average power conversion efficiency of over 10% under simulated full sunlight is achieved for this novel class of solar cell with the application of an antireflection layer. The efficiencies of these novel solar cells based on a MXene‐Si heterojunction achieved in this work point to great promise in emerging photovoltaic technology. In addition to their high efficiency, the excellent reproducibility of such devices establishes a solid base for possible future commercialization.     

Identification and Quantitative Determination of Resin Acids from Corsican Pinus pinaster Aiton Oleoresin Using 13C‐NMR Spectroscopy

Twenty‐three resin samples have been obtained by tapping from individual Pinus pinaster adult trees grown in Corsica and submitted to acido‐basic partition. Identification and quantitative determination of resin acids has been carried out using ¹³C‐NMR spectroscopy following a method developed by our group. The main components were dehydroabietic acid (up to 37.6 %), levopimaric acid (up to 35.5 %) and abietic acid (up to 24.7 %). A lignan, pinoresinol, has been identified in some samples. Within the 23 compositions, submitted to k‐means analysis and Principal Component Analysis, two clusters have been perfectly differentiated, whose compositions were dominated by dehydroabietic acid (Group I, M=23.5 %, SD=6.3) and levopimaric acid (Group II, M=21.2 %; SD=6.2), respectively. Both compositions have been observed in the three locations of harvest.     

A computational framework to investigate retinal haemodynamics and tissue stress

Biomechanics and Modeling in Mechanobiology - The process of vision begins in the retina, yet the role of biomechanical forces in the retina is relatively unknown and only recently being explored....