Genome-wide RNA structure changes during human neurogenesis modulate gene regulatory networks.

The distribution, dynamics, and function of RNA structures in human development are under-explored. Here, we systematically assayed RNA structural dynamics and their relationship with gene expression, translation, and decay during human neurogenesis. We observed that the human ESC transcriptome is globally more structurally accessible than differentiated cells and undergoes extensive RNA structure changes, particularly in the 3' UTR. Additionally, RNA structure changes during differentiation are associated with translation and decay. We observed that RBP and miRNA binding is associated with RNA structural changes during early neuronal differentiation, and splicing is associated during later neuronal differentiation. Furthermore, our analysis suggests that RBPs are major factors in structure remodeling and co-regulate additional RBPs and miRNAs through structure. We demonstrated an example of this by showing that PUM2-induced structure changes on LIN28A enable miR-30 binding. This study deepens our understanding of the widespread and complex role of RNA-based gene regulation during human development.

RNA structure profiling at single-cell resolution reveals new determinants of cell identity.

RNA structure is critical for multiple steps in gene regulation. However, how the structures of transcripts differ both within and between individual cells is unknown. Here we develop a SHAPE-inspired method called single-cell structure probing of RNA transcripts that enables simultaneous determination of transcript secondary structure and abundance at single-cell resolution. We apply single-cell structure probing of RNA transcripts to human embryonic stem cells and differentiating neurons. Remarkably, RNA structure is more homogeneous in human embryonic stem cells compared with neurons, with the greatest homogeneity found in coding regions. More extensive heterogeneity is found within 3' untranslated regions and is determined by specific RNA-binding proteins. Overall RNA structure profiles better discriminate cell type identity and differentiation stage than gene expression profiles alone. We further discover a cell-type variable region of 18S ribosomal RNA that is associated with cell cycle and translation control. Our method opens the door to the systematic characterization of RNA structure-function relationships at single-cell resolution.

Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA.

The exonuclease ISG20L2 has been initially characterized for its role in the mammalian 5.8S rRNA 3' end maturation, specifically in the cleavage of ITS2 of 12S precursor ribosomal RNA (pre-rRNA). Here, we show that human ISG20L2 is also involved in 18S pre-rRNA maturation through removing the ITS1 region, and contributes to ribosomal biogenesis and cell proliferation. Furthermore, we determined the crystal structure of the ISG20L2 nuclease domain at 2.9 Å resolution. It exhibits the typical αßα fold of the DEDD 3'-5' exonuclease with a catalytic pocket located in the hollow near the center. The catalytic residues Asp183, Glu185, Asp267, His322 and Asp327 constitute the DEDDh motif in ISG20L2. The active pocket represents conformational flexibility in the absence of an RNA substrate. Using structural superposition and mutagenesis assay, we mapped RNA substrate binding residues in ISG20L2. Finally, cellular assays revealed that ISG20L2 is aberrantly up-regulated in colon adenocarcinoma and promotes colon cancer cell proliferation through regulating ribosome biogenesis. Together, these results reveal that ISG20L2 is a new enzymatic member for 18S pre-rRNA maturation, provide insights into the mechanism of ISG20L2 underlying pre-rRNA processing, and suggest that ISG20L2 is a potential therapeutic target for colon adenocarcinoma.

Structural and biochemical insights into the molecular mechanism of TRPT1 for nucleic acid ADP-ribosylation.

Nucleic acid ADP-ribosylation has been established as a novel modification found in a wide diversity of prokaryotic and eukaryotic organisms. tRNA 2'-phosphotransferase 1 (TRPT1/TPT1/KptA) possesses ADP-ribosyltransferase (ART) activity and is able to ADP-ribosylate nucleic acids. However, the underlying molecular mechanism remains elusive. Here, we determined crystal structures of TRPT1s in complex with NAD+ from Homo sapiens, Mus musculus and Saccharomyces cerevisiae. Our results revealed that the eukaryotic TRPT1s adopt common mechanisms for both NAD+ and nucleic acid substrate binding. The conserved SGR motif induces a significant conformational change in the donor loop upon NAD+ binding to facilitate the catalytic reaction of ART. Moreover, the nucleic acid-binding residue redundancy provides structural flexibility to accommodate different nucleic acid substrates. Mutational assays revealed that TRPT1s employ different catalytic and nucleic acid-binding residues to perform nucleic acid ADP-ribosylation and RNA 2'-phosphotransferase activities. Finally, cellular assays revealed that the mammalian TRPT1 is able to promote endocervical HeLa cell survival and proliferation. Together, our results provide structural and biochemical insights into the molecular mechanism of TRPT1 for nucleic acid ADP-ribosylation.

ToxMPNN: A deep learning model for small molecule toxicity prediction.

Machine learning (ML) has shown a great promise in predicting toxicity of small molecules. However, the availability of data for such predictions is often limited. Because of the unsatisfactory performance of models trained on a single toxicity endpoint, we collected toxic small molecules with multiple toxicity endpoints from previous study. The dataset comprises 27 toxic endpoints categorized into seven toxicity classes, namely, carcinogenicity and mutagenicity, acute oral toxicity, respiratory toxicity, irritation and corrosion, cardiotoxicity, CYP450, and endocrine disruption. In addition, a binary classification Common-Toxicity task was added based on the aforementioned dataset. To improve the performance of the models, we added marketed drugs as negative samples. This study presents a toxicity predictive model, ToxMPNN, based on the message passing neural network (MPNN) architecture, aiming to predict the toxicity of small molecules. The results demonstrate that ToxMPNN outperforms other models in capturing toxic features within the molecular structure, resulting in more precise predictions with the ROC_AUC testing score of 0.886 for the Toxicity_drug dataset. Furthermore, it was observed that adding marketed drugs as negative samples not only improves the predictive performance of the binary classification Common-Toxicity task but also enhances the stability of the model prediction. It shows that the graph-based deep learning (DL) algorithms in this study can be used as a trustworthy and effective tool to assess small molecule toxicity in the development of new drugs.

Colposcopic accuracy in diagnosing squamous intraepithelial lesions: a systematic review and meta-analysis of the International Federation of Cervical Pathology and Colposcopy 2011 terminology.

BACKGROUND: Colposcopy is an important tool in diagnosing cervical cancer, and the International Federation of Cervical Pathology and Colposcopy (IFCPC) issued the latest version of the guidelines in 2011. This study aims to systematically assess the accuracy of colposcopy in predicting low-grade squamous intraepithelial lesions or worse (LSIL+) / high-grade squamous intraepithelial lesions or worse (HSIL+) under the 2011 IFCPC terminology. METHODS: We performed a systematic review and meta-analysis, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We searched for studies about the performance of colposcopy in diagnosing cervical intraepithelial neoplasia under the new IFCPC colposcopy terminology from PubMed, Embase, Web of Science and the Cochrane database. Data were independently extracted by two authors and an overall diagnostic performance index was calculated under two colposcopic thresholds. RESULTS: Totally, fifteen articles with 22,764 participants in compliance with the criteria were included in meta-analysis. When colposcopy was used to detect LSIL+, the combined sensitivity and specificity were 0.92 (95% CI 0.88-0.95) and 0.51 (0.43-0.59), respectively. When colposcopy was used to detect HSIL+, the combined sensitivity and specificity were 0.68 (0.58-0.76) and 0.93 (0.88-0.96), respectively. CONCLUSION: In accordance with the 2011 IFCPC terminology, the accuracy of colposcopy has improved in terms of both sensitivity and specificity. Colposcopy is now more sensitive with LSIL+ taken as the cut-off value and is more specific to HSIL+. These findings suggest we are avoiding under- or overdiagnosis both of which impact on patients' well-being.

Organic-Cation Modulated Assembly Behaviors of a Ureidopyrimidone-Grafting Cluster.

Ureidopyrimidone (UPy) is an important building block for constructing functional supramolecular polymers and soft materials based on their characteristic quadruple hydrogen bonds. While the evidence from the single-crystal X-ray diffraction data for the existence of linear hydrogen bonding has still been absent up to now. To obtain the crystals of UPy-containing molecules with high quality, enhanced rigidity and crystallinity are expected. Herein, an inorganic Anderson-Evans type cluster [Mn(OH)6Mo6O18]3-, which can provide suitable stiffness and charge, is used as a linker to covalently anchor two UPy units. The prepared organic-inorganic polyanion with three negative charges has a linear architecture, which is prone to form an infinite one-dimensional structure based on the supramolecular forces. The results indicate that the combination models of UPy units can be conveniently modulated by organic counter cations with different sizes, and therefore three unreported models are observed under various conditions. The present study gives a unique understanding of the intermolecular interactions in UPy-based supramolecular polymers and also provides a simple tuning method, which benefits the construction of functional materials and the adjustment of their properties.

Analysis and Validation of Human Targets and Treatments Using a Hepatocellular Carcinoma-Immune Humanized Mouse Model.

BACKGROUND AND AIMS: Recent development of multiple treatments for human hepatocellular carcinoma (HCC) has allowed for the selection of combination therapy to enhance the effectiveness of monotherapy. Optimal selection of therapies is based on both HCC and its microenvironment. Therefore, it is critical to develop and validate preclinical animal models for testing clinical therapeutic solutions. APPROACH AND RESULTS: We established cell line-based or patient-derived xenograft-based humanized-immune-system mouse models with subcutaneous and orthotopic HCC. Mice were injected with human-specific antibodies (Abs) to deplete human immune cells. We analyzed the transcription profiles of HCC cells and human immune cells by using real-time PCR and RNA sequencing. The protein level of HCC tumor cells/tissues or human immune cells was determined by using flow cytometry, western blotting, and immunohistochemistry. The HCC tumor size was measured after single, dual-combination, and triple-combination treatment using N-(1',2-Dihydroxy-1,2'-binaphthalen-4'-yl)-4-methoxybenzenesulfonamide (C188-9), bevacizumab, and pembrolizumab. In this study, human immune cells in the tumor microenvironment were strongly selected and modulated by HCC, which promoted the activation of the IL-6/Janus kinase 2 (JAK2)/signal transducer and activator of transcription 3 (STAT3) signaling pathway in tumor cells and led to augmented HCC proliferation and angiogenesis by releasing angiogenic cytokines in humanized-immune-system mice with HCC. In particular, intratumor human cluster of differentiation-positive (hCD14+ ) cells could produce IL-33 through damage-associated molecular pattern/Toll-like receptor 4/activator protein 1, which up-regulated IL-6 in other intratumor immune cells and activated the JAK2/STAT3 pathway in HCC. Specific knockdown of the CD14 gene in human monocytes could impair IL-33 production induced by cell lysates. Subsequently, we evaluated the in vivo anti-HCC effect of C188-9, bevacizumab, and pembrolizumab. The results showed that the anti-HCC effect of triple-combination therapy was superior to that of single or dual treatments. CONCLUSIONS: Humanized-immune-system HCC mouse models are suitable for identifying targets from cancer and immune components and for testing combinational therapies.

Improving colposcopic accuracy for cervical precancer detection: a retrospective multicenter study in China.

BACKGROUND: Colposcopy alone can result in misidentification of high-grade squamous intraepithelial or worse lesions (HSIL +), especially for women with Type 3 transformation zone (TZ) lesions, where colposcopic assessment is particularly imprecise. This study aimed to improve HSIL + case identification by supplementing referral screening results to colposcopic findings. METHODS: This is an observational multicenter study of 2,417 women, referred to colposcopy after receiving cervical cancer screening results. Logistic regression analysis was conducted under uni- and multivariate models to identify factors which could be used to improve HSIL + case identification. Histological diagnosis was established as the gold standard and is used to assess accuracy, sensitivity, and specificity, as well as to incrementally improve colposcopy. RESULTS: Multivariate analysis highlighted age, TZ types, referral screening, and colposcopists' skills as independent factors. Across this sample population, diagnostic accuracies for detecting HSIL + increased from 72.9% (95%CI 71.1-74.7%) for colposcopy alone to 82.1% (95%CI 80.6-83.6%) after supplementing colposcopy with screening results. A significant increase in colposcopic accuracy was observed across all subgroups. Although, the highest increase was observed in women with a TZ3 lesion, and for those diagnosed by junior colposcopists. CONCLUSION: It appears possible to supplement colposcopic examinations with screening results to improve HSIL + detection, especially for women with TZ3 lesions. It may also be possible to improve junior colposcopists' diagnoses although, further psychological research is necessary. We need to understand how levels of uncertainty influence diagnostic decisions and what the concept of "experience" actually is and what it means for colposcopic practice.

External validation of the BEST-J score and a new risk prediction model for ESD delayed bleeding in patients with early gastric cancer.

BACKGROUND: Delayed bleeding is an important adverse event after gastric endoscopic submucosal dissection (ESD). We aimed to externally validate the Bleeding after ESD Trend from Japan (BEST-J) score and subsequently develop a risk prediction model for bleeding in Chinese patients with early gastric cancer (EGC) after ESD. METHODS: The clinical data of patients who underwent ESD for EGC in Beijing Friendship Hospital from June 2013 to December 2019 were collected retrospectively. The BEST-J score was evaluated according to the clinical data. Through univariate and multivariate logistic regression analyses of the clinical data, the factors affecting delayed bleeding were identified, and a new risk prediction model for bleeding was established. Receiver operating characteristic (ROC) curves were used to evaluate the predictive value of the two prediction models. RESULTS: A total of 444 patients with EGC undergoing ESD were included, of whom 27 patients had delayed bleeding (6.1%). Multivariate logistic regression analysis showed that a history of smoking (P = 0.029), tumor size > 20 mm (P = 0.022), intraoperative use of hemoclips (P = 0.025), resection of multiple tumors (P = 0.027), and prolongation of activated partial thromboplastin time (APTT) (P = 0.020) were independent influencing factors for delayed bleeding. ROC curve analysis showed that the areas under the curves (AUCs) were different between the BEST-J score and the newly built prediction model (0.624 vs. 0.749, P = 0.012). CONCLUSIONS: The BEST-J score has moderately good discrimination for Chinese patients with EGC. However, for patients with EGC without severe comorbidities, the new risk prediction model may predict delayed bleeding better than the BEST-J score.

Assessing colposcopic accuracy for high-grade squamous intraepithelial lesion detection: a retrospective, cohort study.

BACKGROUND: Inappropriate management of high-grade squamous intraepithelial lesions (HSIL) may be the result of an inaccurate colposcopic diagnosis. The aim of this study was to assess colposcopic performance in identifying HSIL+ cases and to analyze the associated clinical factors. METHODS: Records from 1130 patients admitted to Shenzhen Maternal and Child Healthcare Hospital from 12th January, 2018 up until 30th December, 2018 were retrospectively collected, and included demographics, cytological results, HPV status, transformation zone type, number of cervical biopsy sites, colposcopists' competencies, colposcopic impressions, as well as histopathological results. Colposcopy was carried out using 2011 colposcopic terminology from the International Federation of Cervical Pathology and Colposcopy. Logistic regression modelling was implemented for uni- and multivariate analyses. A forward stepwise approach was adopted in order to identify variables associated with colposcopic accuracy. Histopathologic results were taken as the comparative gold standard. RESULTS: Data from 1130 patient records were collated and analyzed. Colposcopy was 69.7% accurate in identifying HSIL+ cases. Positive predictive value, negative predictive value, sensitivity and specificity of detecting HSIL or more (HSIL+) were 35.53%, 64.47%, 42.35% and 77.60%, respectively. Multivariate analysis highlighted the number of biopsies, cytology, and transformation zone type as independent factors. Age and HPV subtype did not appear to statistically correlate with high-grade lesion/carcinoma. CONCLUSION: Evidence presented here suggests that colposcopy is only 69.7% accurate at diagnosing HSIL. Even though not all HSIL will progress into cancer it is considered pre-cancerous and therefore early identification will save lives. The number of biopsies, cytology and transformation zone type appear to be predictors of misdiagnosis and therefore should be considered during clinical consultations and by way of further research.

Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons.

The stochastic dynamics and regulatory mechanisms that govern differentiation of individual human neural precursor cells (NPC) into mature neurons are currently not fully understood. Here, we used single-cell RNA-sequencing (scRNA-seq) of developing neurons to dissect/identify NPC subtypes and critical developmental stages of alternative lineage specifications. This study comprises an unsupervised, high-resolution strategy for identifying cell developmental bifurcations, tracking the stochastic transcript kinetics of the subpopulations, elucidating regulatory networks, and finding key regulators. Our data revealed the bifurcation and developmental tracks of the two NPC subpopulations, and we captured an early (24 h) transition phase that leads to alternative neuronal specifications. The consequent up-regulation and down-regulation of stage- and subpopulation-specific gene groups during the course of maturation revealed biological insights with regard to key regulatory transcription factors and lincRNAs that control cellular programs in the identified neuronal subpopulations.

Crystal structure and biochemical features of dye-decolorizing peroxidase YfeX from Escherichia coli O157 Asp143 and Arg232 play divergent roles toward different substrates.

YfeX from Escherichia coli O157 is a bacterial dye-decolorizing peroxidase that represents both dye-decoloring activity and typical peroxidase activity. We reported the crystal structure of YfeX bound to heme at 2.09 Å resolution. The YfeX monomer resembles a ferredoxin-like fold and contains two domains. The three conserved residues surrounding the heme group are His215, Asp143 and Arg232. His215 functions as the proximal axial ligand of the heme iron atom. Biochemical data show that the catalytic significance of the conserved Asp143 and Arg232 depends on the substrate types and that YfeX may adopt various catalytic mechanisms toward divergent substrates. In addition, it is observed that an access tunnel spans from the protein molecular surface to the heme distal region, it serves as the passageway for the entrance and binding of the H2O2.

Gap junction protein connexin43 deregulation contributes to bladder carcinogenesis via targeting MAPK pathway.

High expression of connexins was found in a variety of cancers, but their role is still controversial. We investigated whether connexin43 (Cx43) contributed to bladder carcinogenesis through MAPK activation. In this study, we found that Cx43 expression was significantly increased in bladder cancer tissues and cell line. Overexpression of Cx43 in bladder cancer 5637 cells increased cell proliferation, promoted cell cycle progression, and inhibited apoptosis. Western blot showed that JNK and ERK pathways were dramatically activated in Cx43-overexpressed cells. Conversely, knockdown of Cx43 inhibited cell proliferation by increasing apoptosis and causing cell cycle arrest, concomitant with inhibition of JNK and ERK signaling. In addition, JNK and ERK pathways were also activated in bladder cancer tissues. In conclusion, abnormal high expression and cytoplasmic localization of Cx43 contributed to bladder cancer. Inhibition of Cx43 activity could be a potential therapeutic strategy for preventing the progression of bladder cancer.

Pluripotency Activity of Nanog Requires Biochemical Stabilization by Variant Histone Protein H2A.Z.

The variant histone protein H2A.Z plays a critical role in early development. Likewise, Nanog, a master regulator of embryonic stem cells (ESCs), is essential for proper development in early embryogenesis. In this study, we establish that these two factors work together to maintain pluripotency. It is shown that H2A.Z influences the protein level of Nanog through the ubiquitin-proteasome pathway. Knockdown of H2A.Z causes differentiation of mouse ESCs and disrupts the reprogramming of somatic cells, which can be partially rescued by overexpression of Nanog. We conclude that the H2A.Z-Nanog partnership is involved in ESC pluripotency and reprogramming of somatic cells. Stem Cells 2015;33:2126-2134.

Regulation of L-threonine dehydrogenase in somatic cell reprogramming.

Increasing evidence suggests that metabolic remodeling plays an important role in the regulation of somatic cell reprogramming. Threonine catabolism mediated by L-threonine dehydrogenase (TDH) has been recognized as a specific metabolic trait of mouse embryonic stem cells. However, it remains unknown whether TDH-mediated threonine catabolism could regulate reprogramming. Here, we report TDH as a novel regulator of somatic cell reprogramming. Knockdown of TDH inhibits, whereas induction of TDH enhances reprogramming efficiency. Moreover, microRNA-9 post-transcriptionally regulates the expression of TDH and thereby inhibits reprogramming efficiency. Furthermore, protein arginine methyltransferase (PRMT5) interacts with TDH and mediates its post-translational arginine methylation. PRMT5 appears to regulate TDH enzyme activity through both methyltransferase-dependent and -independent mechanisms. Functionally, TDH-facilitated reprogramming efficiency is further enhanced by PRMT5. These results suggest that TDH-mediated threonine catabolism controls somatic cell reprogramming and indicate the importance of post-transcriptional and post-translational regulation of TDH.

Core-shell PLGA/collagen nanofibers loaded with recombinant FN/CDHs as bone tissue engineering scaffolds.

Poly(lactic-co-glycolic acid) (PLGA)/collagen nanofibrous scaffolds have been utilized in the tissue engineering field. It has been shown that both fibronectin (FN) and cadherin 11 (CDH) play important roles in the progress of osteogenesis and cell adhesion. The aim of this study was to fabricate recombinant FN/CDHs (rFN/CDHs)-loaded PLGA/collagen nanofibrous scaffolds and evaluate their effects on the adhesion and differentiation of human bone marrow mesenchymal stem cells (hMSCs). PLGA/collagen nanofibers were made by coaxial electrospinning. The morphology and mechanical properties of PLGA/collagen nanofibrous mats were analyzed by scanning electron microscopy and mechanical testing, respectively. The performance of scaffolds was evaluated in terms of the viability, morphology, and osteogenic gene expression levels of hMSCs. rFN/CDHs was successfully incorporated into the PLGA/collagen nanofibers. The release of rFN/CDHs from PLGA nanofibers was investigated by liquid chromatography-mass spectrometry. rFN/CDHs improved the mechanical properties of the PLGA/collagen nanofibers. The controlled release of rFN/CDHs can enhance the proliferation of hMSCs and induce osteogenic gene expression (alkaline phosphatase, RUNX2, and osteocalcin). Our data imply that rFN/CDHs may induce hMSCs differentiation into osteoblasts and PLGA/collagen nanofibers loaded with rFN/CDHs have potential in bone tissue engineering.

Impact of Lactiplantibacillus plantarum and casein fortification on angiotensin converting enzyme inhibitory peptides in yogurt: identification and in silico analysis.

In this study, the effects of Lactiplantibacillus plantarum M11 (Lb. plantarum M11) in conjunction with sodium caseinate on the characteristics and angiotensin converting enzyme (ACE) inhibitory activity of yogurt were investigated. ACE inhibitory peptides (ACEIPs) in yogurt were identified by nano-LC-MS/MS and potential ACEIPs were predicted by in silico and molecular docking methods. The results showed that the ACE-inhibitory activity of yogurt was significantly enhanced (p < 0.05), while maintaining the quality characteristics of the yogurt. Thirteen ACEIPs in the improved yogurt (883 + M11-CS group) were identified, which were more abundant than the other yogurt groups (control 883 group, 883 + M11 group and 883-CS group). Two novel peptides with potential ACE inhibitory activity, YPFPGPIH and NILRFF, were screened. The two peptides showed PeptideRanker scores above 0.8, small molecular weight and strong hydrophobicity, and were non-toxic after prediction. Molecular docking results showed that binding energies with ACE were -9.4 kcal mol-1 and -10.7 kcal mol-1, respectively, and could bind to the active site of ACE. These results indicated that yogurt with Lb. plantarum M11 and sodium caseinate has the potential to be utilized as a functional food with antihypertensive properties. The combination of ACEIP-producing strains and casein fortification could be an effective method to promote the release of ACEIPs from yogurt.

The efficacy of bracing in the treatment of progressive early-onset scoliosis.

Serial casting as one of the applications to treat early-onset scoliosis has been reported efficiently to improve deformity, but no report has focused on the efficacy of braces in the treatment of congenital early-onset scoliosis and comparison with progressive idiopathic early-onset scoliosis. Patients with progressive EOS treated with braces in our institution with a minimum of 4 years follow-up were reviewed. Two groups according to the etiological diagnosis were analyzed and compared: the congenital scoliosis (CS) group and idiopathic scoliosis (IS) group. The success cases and the failure cases were also compared. 27 patients with an average main Cobb angle of 38.19° (20-55) underwent initial bracing at an average age of 55.7 months (24-108), the average follow-up time was 76.19 months (49-117). In IS group the main Cobb angle was corrected to 18.69 ± 12.06° (48.61%) following the first bracing; the final Cobb angle was 23.08 ± 22.15°(38.76%) after brace removal. In CS group the main Cobb angle was corrected to 33.93 ± 10.31°(17.1%) following the first bracing and 37.93 ± 14.74°(3.53%) after brace removal. Both coronal chest width and T1-T12 height increased dramatically from pre-bracing to the last follow-up. Patients diagnosed as IS tended to have a better result in main Cobb angle correction than that of CS (P = 0.049). By the time of last follow-up, 8 patients had undergone surgery, and the operation time was postponed by 68.88 ± 26.43 months. For patients with progressive early-onset scoliosis, bracing is an efficient nonsurgical alternative to casting, and some of them can be cured; if not, eventual surgical intervention can be delayed for a period of time without restrictions on the thoracic cavity.

Direct RNA sequencing coupled with adaptive sampling enriches RNAs of interest in the transcriptome.

Abundant cellular transcripts occupy most of the sequencing reads in the transcriptome, making it challenging to assay for low-abundant transcripts. Here, we utilize the adaptive sampling function of Oxford Nanopore sequencing to selectively deplete and enrich RNAs of interest without biochemical manipulation before sequencing. Adaptive sampling performed on a pool of in vitro transcribed RNAs resulted in a net increase of 22-30% in the proportion of transcripts of interest in the population. Enriching and depleting different proportions of the Candida albicans transcriptome also resulted in a 11-13.5% increase in the number of reads on target transcripts, with longer and more abundant transcripts being more efficiently depleted. Depleting all currently annotated Candida albicans transcripts did not result in an absolute enrichment of remaining transcripts, although we identified 26 previously unknown transcripts and isoforms, 17 of which are antisense to existing transcripts. Further improvements in the adaptive sampling of RNAs will allow the technology to be widely applied to study RNAs of interest in diverse transcriptomes.