RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.

RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.

Complement-Mediated Thrombotic Microangiopathy in a Patient With Antiphospholipid Syndrome and Anti-glomerular Basement Membrane Antibodies.

Thrombotic microangiopathy (TMA) is a range of diseases characterized by thrombocytopenia, microangiopathic hemolytic anemia, and organ injury. Complement-mediated TMA is a rare, life-threatening subtype of TMA that occurs due to the uncontrolled activation of the alternative complement pathway in the absence of normal regulation, often resulting from deficiencies of various regulatory proteins. Anti-glomerular basement membrane (anti-GBM) disease, previously known as Goodpasture syndrome, is a life-threatening form of vasculitis in which immunoglobulin G autoantibodies bind to the alpha-3 chain of type IV collagen in alveolar and glomerular basement membranes. We present the case of a patient with a history of antiphospholipid syndrome who was diagnosed with complement-mediated TMA during hospital admission for elevated anti-GBM antibody titers discovered during an outpatient evaluation for elevated creatinine levels. Upon admission, treatment was started for presumed anti-GBM disease, including high-dose intravenous methylprednisolone injections and multiple plasmapheresis sessions. However, renal biopsy results showed no evidence of anti-GBM disease, but rather evidence of TMA. Subsequent laboratory studies revealed decreased complement levels, suggestive of a diagnosis of complement-mediated TMA. The patient was started on rituximab and eculizumab infusions, and she was discharged in stable condition after a 15-day hospitalization with outpatient appointments scheduled for genetic testing and further infusions. This case illustrates the importance of recognizing the key clinical and diagnostic features of complement-mediated TMA to promptly initiate appropriate therapy.

SIGIRR/TIR8, an important regulator of TLR4 and IL-1R-mediated NF-κB activation, predicts biochemical recurrence after prostatectomy in low-grade prostate carcinomas.

Single Ig IL-1-related receptor (SIGIRR) is a negative regulator of toll-like receptor 4 and IL-1-mediated activation of nuclear factor κ-light-chain enhancer of activated B cells. The purpose of this study was to qualitatively and quantitatively determine SIGIRR protein expression in human prostate tissues and associate SIGIRR expression with clinical parameters. SIGIRR expression was quantified in glandular prostate tissue using immunohistochemistry and multispectral imaging, and expression was evaluated in relation to clinicopathological features of benign prostatic hyperplasia and prostate cancer (PCa). Subgroupings of low Gleason score (≤ 6 and 3 + 4) and high Gleason score (4 + 3 and ≥ 8) were used for patient outcomes. SIGIRR was predominantly expressed in the cytoplasm and nucleus of the prostatic epithelium with little expression within the stroma. Compared with normal prostate, cytoplasmic SIGIRR expression was similar in benign prostatic hyperplasia, high-grade prostatic intraepithelial neoplasia, PCa, and metastases. A decrease in nuclear expression was found in metastasis samples (P = .04). Changes in SIGIRR expression were not associated with Gleason score, pathological stage, tumor volume, surgical margin status, or serum prostate-specific antigen (P > .05). Nuclear (P = .96) and cytoplasmic (P = .89) SIGIRR expressions were not related to patient outcomes in univariable analysis, but in the analysis of patients with low Gleason scores, high cytoplasmic SIGIRR expression was associated with biochemical recurrence in both univariable (P = .01) and multivariable (hazard ratio, 2.31 [95% confidence interval 1.05-5.06]; P = .04) analyses. Similarly, in multivariable analysis of only low-stage (pT2) tumors, SIGIRR independently predicted biochemical recurrence (P = .009). We conclude that SIGIRR predicts biochemical recurrence in patients with low Gleason score and low pathological stage PCa.