Structural atlas of human primary microRNAs generated by SHAPE-MaP.

MicroRNA (miRNA) maturation is critically dependent on structural features of primary transcripts (pri-miRNAs). However, the scarcity of determined pri-miRNA structures has limited our understanding of miRNA maturation. Here, we employed selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP), a high-throughput RNA structure probing method, to unravel the secondary structures of 476 high-confidence human pri-miRNAs. Our SHAPE-based structures diverge substantially from those inferred solely from computation, particularly in the apical loop and basal segments, underlining the need for experimental data in RNA structure prediction. By comparing the structures with high-throughput processing data, we determined the optimal structural features of pri-miRNAs. The sequence determinants are influenced substantially by their structural contexts. Moreover, we identified an element termed the bulged GWG motif (bGWG) with a 3' bulge in the lower stem, which promotes processing. Our structure-function mapping better annotates the determinants of pri-miRNA processing and offers practical implications for designing small hairpin RNAs and predicting the impacts of miRNA mutations.

A quantitative map of human primary microRNA processing sites.

Maturation of canonical microRNA (miRNA) is initiated by DROSHA that cleaves the primary transcript (pri-miRNA). More than 1,800 miRNA loci are annotated in humans, but it remains largely unknown whether and at which sites pri-miRNAs are cleaved by DROSHA. Here, we performed in vitro processing on a full set of human pri-miRNAs (miRBase version 21) followed by sequencing. This comprehensive profiling enabled us to classify miRNAs on the basis of DROSHA dependence and map their cleavage sites with respective processing efficiency measures. Only 758 pri-miRNAs are confidently processed by DROSHA, while the majority may be non-canonical or false entries. Analyses of the DROSHA-dependent pri-miRNAs show key cis-elements for processing. We observe widespread alternative processing and unproductive cleavage events such as "nick" or "inverse" processing. SRSF3 is a broad-acting auxiliary factor modulating alternative processing and suppressing unproductive processing. The profiling data and methods developed in this study will allow systematic analyses of miRNA regulation.

Genomic Clustering Facilitates Nuclear Processing of Suboptimal Pri-miRNA Loci.

Nuclear processing of most miRNAs is mediated by Microprocessor, comprised of RNase III enzyme Drosha and its cofactor DGCR8. Here, we uncover a hidden layer of Microprocessor regulation via studies of Dicer-independent mir-451, which is clustered with canonical mir-144. Although mir-451 is fully dependent on Drosha/DGCR8, its short stem and small terminal loop render it an intrinsically weak Microprocessor substrate. Thus, it must reside within a cluster for normal biogenesis, although the identity and orientation of its neighbor are flexible. We use DGCR8 tethering assays and operon structure-function assays to demonstrate that local recruitment and transfer of Microprocessor enhances suboptimal substrate processing. This principle applies more broadly since genomic analysis indicates suboptimal canonical miRNAs are enriched in operons, and we validate several of these experimentally. Proximity-based enhancement of suboptimal hairpin processing provides a rationale for genomic retention of certain miRNA operons and may explain preferential evolutionary emergence of miRNA operons.

Adenylation of maternally inherited microRNAs by Wispy.

Early development depends heavily on accurate control of maternally inherited mRNAs, and yet it remains unknown how maternal microRNAs are regulated during maternal-to-zygotic transition (MZT). We here find that maternal microRNAs are highly adenylated at their 3' ends in mature oocytes and early embryos. Maternal microRNA adenylation is widely conserved in fly, sea urchin, and mouse. We identify Wispy, a noncanonical poly(A) polymerase, as the enzyme responsible for microRNA adenylation in flies. Knockout of wispy abrogates adenylation and results in microRNA accumulation in eggs, whereas overexpression of Wispy increases adenylation and reduces microRNA levels in S2 cells. Wispy interacts with Ago1 through protein-protein interaction, which may allow the effective and selective adenylation of microRNAs. Thus, adenylation may contribute to the clearance of maternally deposited microRNAs during MZT. Our work provides mechanistic insights into the regulation of maternal microRNAs and illustrates the importance of RNA tailing in development.

ERH facilitates microRNA maturation through the interaction with the N-terminus of DGCR8.

The microprocessor complex cleaves the primary transcript of microRNA (pri-miRNA) to initiate miRNA maturation. Microprocessor is known to consist of RNase III DROSHA and dsRNA-binding DGCR8. Here, we identify Enhancer of Rudimentary Homolog (ERH) as a new component of Microprocessor. Through a crystal structure and biochemical experiments, we reveal that ERH uses its hydrophobic groove to bind to a conserved region in the N-terminus of DGCR8, in a 2:2 stoichiometry. Knock-down of ERH or deletion of the DGCR8 N-terminus results in a reduced processing of suboptimal pri-miRNAs in polycistronic miRNA clusters. ERH increases the processing of suboptimal pri-miR-451 in a manner dependent on its neighboring pri-miR-144. Thus, the ERH dimer may mediate 'cluster assistance' in which Microprocessor is loaded onto a poor substrate with help from a high-affinity substrate in the same cluster. Our study reveals a role of ERH in the miRNA biogenesis pathway.

A cone-beam computed tomography evaluation of posterior available space in both arches relative to various skeletal patterns.

INTRODUCTION: This study aimed to evaluate the posterior available space (PAS) in both dental arches of adult patients with varying skeletal patterns using cone-beam computed tomography. METHODS: A sample of 114 adult patients (56 males and 58 females) was divided into 3 groups according to ANB angle and facial height ratio. Using C-mode cone-beam computed tomography images from these patients, maxillary PAS (MxPAS) and mandibular PAS (MnPAS) were measured in the distobuccal and palatal roots of the maxillary second molars and the distal roots of the mandibular second molars, respectively. The planes perpendicular to the tooth axes of the second molars in the coronal views and parallel to the posterior occlusal planes in the sagittal views were set at 3 heights of furcation, middle, and apex of the roots. For each plane, the shortest posterior distances from the roots to the inner and outer cortices were measured parallel to the furcation line connecting the furcations of the molars in the axial views. Posterior cortical bone thickness, defined as the distance from the inner cortex to the outer cortex, was measured. RESULTS: PAS was significantly greater in males than in females and in the maxilla than in the mandible (P <0.01). All MxPAS gradually increased from the furcation to the apex with significance (P <0.05), but there was no difference in MnPAS. MxPAS was significantly greater (P <0.05) in subjects with Class II and III malocclusion than subjects with Class I malocclusion, whereas MnPAS showed no difference. MxPAS showed no significant differences in facial height ratio, whereas MnPAS was significantly greater (P <0.05) at furcation in normovergent subjects than in others. Posterior cortical bone thickness was greater (P <0.001) in the mandible than in the maxilla. CONCLUSIONS: PAS was different according to sex and skeletal patterns. It would be helpful to evaluate PAS when distalizing the molars in either arch.

Quality of Recovery of Patients Who Underwent Curative Pancreatectomy: Comparison of Total Intravenous Anesthesia Versus Inhalation Anesthesia Using the QOR-40 Questionnaire.

BACKGROUND: There has been increasing attention on the subjective recovery of patients undergoing cancer surgery. Total intravenous anesthesia (TIVA) and inhaled anesthesia with volatile anesthetics (INHA) are safe and common anesthetic techniques. Currently, TIVA and INHA have only been compared for less invasive and less complex surgeries. This prospective randomized trial aimed to compare the quality of recovery between TIVA and INHA in patients undergoing pancreatoduodenectomy (PD) or distal pancreatectomy (DP) using the Quality of Recovery (QOR)-40 questionnaire. METHODS: We enrolled 132 patients who were randomly assigned to either the desflurane (DES) (INHA, balanced anesthesia with DES and remifentanil infusion) or TIVA (effect-site target-controlled infusion of propofol and remifentanil) groups and completed the QOR-40 questionnaire postoperatively. RESULTS: The mean global QOR-40 score on postoperative day 3 was significantly higher in the TIVA group than in the DES group. In the PD group, the total QOR-40 score was significantly higher in the TIVA group than in the DES group. Moreover, the TIVA group had significantly higher scores in the physical comfort and psychological support QOR-40 dimensions than the DES group. CONCLUSION: TIVA provides better quality of recovery scores on POD 3 for patients undergoing curative pancreatectomy. CLINICAL TRIAL REGISTRATION NUMBER: NCT03447691.

Bias-minimized quantification of microRNA reveals widespread alternative processing and 3' end modification.

MicroRNAs (miRNAs) modulate diverse biological and pathological processes via post-transcriptional gene silencing. High-throughput small RNA sequencing (sRNA-seq) has been widely adopted to investigate the functions and regulatory mechanisms of miRNAs. However, accurate quantification of miRNAs has been limited owing to the severe ligation bias in conventional sRNA-seq methods. Here, we quantify miRNAs and their variants (known as isomiRs) by an improved sRNA-seq protocol, termed AQ-seq (accurate quantification by sequencing), that utilizes adapters with terminal degenerate sequences and a high concentration of polyethylene glycol (PEG), which minimize the ligation bias during library preparation. Measurement using AQ-seq allows us to correct the previously misannotated 5' end usage and strand preference in public databases. Importantly, the analysis of 5' terminal heterogeneity reveals widespread alternative processing events which have been underestimated. We also identify highly uridylated miRNAs originating from the 3p strands, indicating regulations mediated by terminal uridylyl transferases at the pre-miRNA stage. Taken together, our study reveals the complexity of the miRNA isoform landscape, allowing us to refine miRNA annotation and to advance our understanding of miRNA regulation. Furthermore, AQ-seq can be adopted to improve other ligation-based sequencing methods including crosslinking-immunoprecipitation-sequencing (CLIP-seq) and ribosome profiling (Ribo-seq).

Hemimandibular hyperplasia treatment with condylectomy and orthodontic camouflage treatment using miniplate.

A 13-year-old growing female patient presented with hemimandibular hyperplasia of the right side, Class III hypodivergent skeletal pattern, and severe facial asymmetry. Corrective surgery was deferred until her growth had been completed. When the patient was 16 years old, a low condylectomy was performed on the hyperplastic side of her mandible to prevent its progressive condylar hyperplasia, while simultaneous orthodontic camouflage treatment was performed with the intrusion of the maxillary right posterior teeth using temporary skeletal anchorage devices without additional orthognathic surgery. A low condylectomy caused anterior and lateral open bite after the downward and backward movement of the chin, which improved Class III appearance. The intrusion of the maxillary right posterior teeth followed by compensating extrusion of the mandibular posterior teeth contributed to improve the patient's facial asymmetry with correction of the transverse occlusal plane and lip canting. After 30 months of treatment, an acceptable esthetic outcome and functional occlusion were achieved. The treatment results were well maintained for 1-year retention.

SRSF3 recruits DROSHA to the basal junction of primary microRNAs.

The Microprocessor complex, consisting of an RNase III DROSHA and the DGCR8 dimer, cleaves primary microRNA transcripts (pri-miRNAs) to initiate microRNA (miRNA) maturation. Pri-miRNAs are stem-loop RNAs, and ∼79% of them contain at least one of the three major and conserved RNA motifs, UG, UGU, and CNNC. We recently demonstrated that the basal UG and apical UGU motifs of pri-miRNAs interact with DROSHA and DGCR8, respectively. They help orient Microprocessor on pri-miRNA in a proper direction in which DROSHA and DGCR8 localize to the basal and apical pri-miRNA junctions, respectively. In addition, CNNC, located at ∼17 nucleotides (nt) from the Microprocessor cleavage site, interacts with SRSF3 (SRp20) to stimulate Microprocessor to process pri-miRNAs. The mechanism underlying this stimulation, however, is unknown. In this study, we discovered that SRSF3 recruits DROSHA to the basal junction in a CNNC-dependent manner, thereby enhancing Microprocessor activity. Furthermore, by generating various pri-miRNA substrates containing CNNC at different locations, we demonstrated that such stimulation only occurs when CNNC is located at ∼17 nt from the Microprocessor cleavage site. Our findings reveal the molecular mechanism of SRSF3 in pri-miRNA processing and support the previously proposed explanation for the highly conserved position of CNNC in SRSF3-enhanced pri-miRNA processing.

The added value of pelvic surveillance by MRI during postoperative follow-up of rectal cancer, with a focus on abbreviated MRI.

OBJECTIVES: To assess the added value of MRI over CT for the detection of pelvic recurrence during postoperative surveillance after rectal cancer surgery and to compare the diagnostic accuracy for pelvic recurrence achieved with abbreviated MRI (aMRI) with that of conventional enhanced MRI (cMRI). METHODS: Patients who underwent rectal cancer surgery followed by MRI in addition to the standard CT follow-up protocol were evaluated retrospectively. Two readers independently scored images from CT, cMRI, and aMRI, which consisted of T2-weighted and diffusion-weighted imaging, to rate the likelihood of recurrence. Diagnostic accuracy and ROC curves were calculated. The patients were divided into two groups for risk-adapted surveillance according to risk of recurrence: high-risk (n = 157) and low-risk (n = 169) groups. RESULTS: In total, 579 MRIs from 326 patients were assessed. A total of 48 pelvic recurrences occurred in 33 patients. The AUC in cMRI, aMRI, and CT were 0.98, 0.99, and 0.84, respectively. The difference in performance between CT and cMRI or aMRI for identifying recurrence was statistically significant (p < 0.001). Both cMRI and aMRI showed superior performance compared with CT in the high-risk group (p < 0.001), but this was not the case in the low-risk group (p = 0.13). Furthermore, the diagnostic accuracy of aMRI was similar to that of cMRI. CONCLUSIONS: The addition of MRI to the postoperative surveillance protocol may result in an improvement in the detection of pelvic recurrence after rectal cancer surgery. For patients at high risk of recurrence, an aMRI surveillance may be justified to improve the diagnostic yield. KEY POINTS: • The addition of MRI to the postoperative surveillance protocol improved the diagnostic yield in patients at a high risk of recurrence. • Abbreviated non-enhanced MRI with DWI allows detection of pelvic recurrence with a diagnostic accuracy that is similar to that of contrast-enhanced MRI (AUC, 0.99 and 0.98, respectively; p = 0.12). • Abbreviated MRI that is restricted to high spatial resolution structural imaging and diffusion-weighted imaging takes less time and can be carried out without the need for injection of a contrast agent.

Posterior Available Space for Uprighting Horizontally Impacted Mandibular Second Molars Using Orthodontic Microimplant Anchorage.

Treatment of horizontally and deeply impacted mandibular molars is challenging for both orthodontists and oral surgeons because of the limited access and anchorage control. We report on two patients who had horizontally and mesially impacted mandibular second molars (MM2s). Both patients were treated by a surgical orthodontic approach, and the crowns of the impacted teeth were brought into the arches by closed forced eruption. Mesially impacted MM2s were uprighted with orthodontic microimplants, inserted in the retromolar area, and then moved into their ideal position. The first patient was in an active growing stage, while the second patient was beyond the active growing stage. Therefore posterior available space (PAS) should be analyzed before treatment of impacted MM2s to prevent periodontal problems after uprighting of impacted teeth. If PAS is not enough for uprighting impacted MM2s, alternative treatment should be considered based on the stage of growth.

Usefulness of feature analysis of breast-specific gamma imaging for predicting malignancy.

OBJECTIVES: The purpose of this study was to investigate which feature of the breast-specific gamma imaging (BSGI) uptake in women who were recently diagnosed with breast cancer was associated with malignancy. METHODS: Data on 231 newly diagnosed breast cancer patients who underwent preoperative BSGI were retrospectively reviewed. Feature analysis was done by classifying BSGI uptake into mass, non-mass, or focus/foci. Descriptors for mass, non-mass, or focus/foci were shape, distribution, number, and intensity. BSGI features of known malignancies and lesions that were additionally found by BSGI were correlated with mammographic breast density, histology, hormonal status, and clinical follow-up data obtained over at least 2 years. RESULTS: Among 372 breast lesions from 231 patients, 241 malignancies had been pathologically confirmed prior to BSGI and 131 additional lesions were found on BSGI. Irregular shape was more predictive of malignancy than oval shape (p=0.004) in mass uptake. Linear/ductal distribution was more predictive of malignancy than focal, regional, and segmental distribution (p<0.05) in non-mass uptake. Mammographic breast density was not associated with BSGI features. The lesion to normal ratio (LNR) was higher in the postmenopausal patients than that in the premenopausal patients (p=0.003). CONCLUSIONS: The feature analysis of radiotracer uptake in BSGI is useful in predicting whether breast lesions are malignant or benign. KEY POINTS: • The feature analysis of BSGI uptake is useful in predicting malignancy. • Irregular shape was predictive of malignancy in mass uptake. • Linear/ductal distribution was predictive of malignancy in non-mass uptake.

Mandibular condyle bone density in adolescents with varying skeletal patterns evaluated using cone-beam computed tomography: A potential predictive tool.

INTRODUCTION: The aim of this study was to evaluate the bone density of mandibular condyles in adolescents with varying skeletal patterns using cone-beam computed tomography. The null hypothesis was that there is no difference in the bone density of mandibular condyles in adolescents across various facial height ratios, ANB angle classifications, sexes, and age categories. METHODS: We divided 120 adolescent patients, 56 boys and 64 girls, into 3 groups according to 3 criteria: (1) age (early, 10 to <14 years; middle, 14 to <17 years; late, 17 to <20 years); (2) facial height ratio or Jarabak quotient (hyperdivergent: facial height ratio, <62%; normovergent: facial height ratio, 62% to ≤65%; and hypodivergent: facial height ratio, >65%); and (3) ANB angle classification (Class I, 1° to ≤4°; Class II, (>4°); and Class III, <1°). The total, cortical, and cancellous bone densities were measured and compared on the axial slice with the largest mediolateral diameter of the mandibular condyle using C-mode cone-beam computed tomography. RESULTS: Cortical bone density increased as age increased and showed statistically significant differences between the early and middle (P = 0.041) and the early and late adolescent groups (P = 0.031). Condylar bone density increased as facial height ratio decreased, and cancellous bone density showed statistically significant differences between the hyperdivergent and hypodivergent groups (P = 0.038). The cortical, cancellous, and total bone densities increased as ANB angle increased and showed statistically significant differences between the Class II and Class III groups (P = 0.022, P = 0.006, and P = 0.003, respectively). CONCLUSIONS: The null hypothesis was rejected. Condylar bone density increased as facial height ratio decreased and ANB angle increased. These findings may be useful in predicting the vertical and horizontal skeletal growth patterns of growing adolescents.

The Effects of Granulocyte-Colony Stimulating Factor on Regeneration in Nerve Crush Injuries in Rats.

Granulocyte-colony stimulating factor (G-CSF) is widely known to have a neuroprotective effect, but its effects on function and morphology in mechanical nerve injury are not well understood. The aim of this study was to confirm the time course of the functional changes and morphological effects of G-CSF in a rat model of nerve crush injury. Twelve-eight rats were divided into three group: sham-operated control group, G-CSF-treated group, and saline treated group. 2 weeks after the nerve crush injury, G-CSF was injected for 5 days. After 4 weeks, functional tests such as motor nerve conduction velocity (MNCV), mechanical and cold allodynia tests, and morphological studies were performed. G-CSF-treated rats had significantly improved nerve function including MNCV and mechanical and cold allodynia. In addition, G-CSF-treated rats had significantly higher the density of myelinated fibers than saline-treated rats. In conclusion, we found that 100 µg/kg administration of G-CSF promoted long-term functional recovery in a rat model of nerve crush injury.

RNA-guided RNA silencing by an Asgard archaeal Argonaute.

Argonaute proteins are the central effectors of RNA-guided RNA silencing pathways in eukaryotes, playing crucial roles in gene repression and defense against viruses and transposons. Eukaryotic Argonautes are subdivided into two clades: AGOs generally facilitate miRNA- or siRNA-mediated silencing, while PIWIs generally facilitate piRNA-mediated silencing. It is currently unclear when and how Argonaute-based RNA silencing mechanisms arose and diverged during the emergence and early evolution of eukaryotes. Here, we show that in Asgard archaea, the closest prokaryotic relatives of eukaryotes, an evolutionary expansion of Argonaute proteins took place. In particular, a deep-branching PIWI protein (HrAgo1) encoded by the genome of the Lokiarchaeon 'Candidatus Harpocratesius repetitus' shares a common origin with eukaryotic PIWI proteins. Contrasting known prokaryotic Argonautes that use single-stranded DNA as guides and/or targets, HrAgo1 mediates RNA-guided RNA cleavage, and facilitates gene silencing when expressed in human cells and supplied with miRNA precursors. A cryo-EM structure of HrAgo1, combined with quantitative single-molecule experiments, reveals that the protein displays structural features and target-binding modes that are a mix of those of eukaryotic AGO and PIWI proteins. Thus, this deep-branching archaeal PIWI may have retained an ancestral molecular architecture that preceded the functional and mechanistic divergence of eukaryotic AGOs and PIWIs.

Novel Porous Organic Polymer Catalyst with Phosphate and Sulfonic Acid Sites for Facile Esterification of Levulinic Acid.

Biomass-derived value-added materials such as levulinic acid (LA) are favorable natural resources for producing ester-based biolubricants owing to their biodegradability, nontoxicity, and excellent metal-adhering properties. However, highly active catalysts must be developed to carry out efficient esterification of LA with aliphatic alcohols, especially long-chain aliphatic alcohols. In this study, we developed a novel porous covalent organic polymer catalyst (BPOP-SO3H) with dual acid sites, phosphate and sulfonic acid sites, for the esterification of LA. The prepared BPOP-SO3H catalyst was verified using various surface analysis techniques. BPOP-SO3H exhibited 98% LA conversion with n-butanol and 99% selectivity for butyl levulinate ester within 30 min, which is superior to that of most reported catalysts. BPOP-SO3H also showed high LA conversion and ester selectivity when other aliphatic alcohols were used. Moreover, BPOP-SO3H showed good recyclability for five consecutive cycles. We believe that incorporating a high density of acid sites into a porous polymer with a large surface area and hierarchical pores is a promising approach for developing heterogeneous acid catalysts for the production of alkyl levulinate esters from LA.