rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data.

Pre-mRNA alternative splicing is a prevalent mechanism for diversifying eukaryotic transcriptomes and proteomes. Regulated alternative splicing plays a role in many biological processes, and dysregulated alternative splicing is a feature of many human diseases. Short-read RNA sequencing (RNA-seq) is now the standard approach for transcriptome-wide analysis of alternative splicing. Since 2011, our laboratory has developed and maintained Replicate Multivariate Analysis of Transcript Splicing (rMATS), a computational tool for discovering and quantifying alternative splicing events from RNA-seq data. Here we provide a protocol for the contemporary version of rMATS, rMATS-turbo, a fast and scalable re-implementation that maintains the statistical framework and user interface of the original rMATS software, while incorporating a revamped computational workflow with a substantial improvement in speed and data storage efficiency. The rMATS-turbo software scales up to massive RNA-seq datasets with tens of thousands of samples. To illustrate the utility of rMATS-turbo, we describe two representative application scenarios. First, we describe a broadly applicable two-group comparison to identify differential alternative splicing events between two sample groups, including both annotated and novel alternative splicing events. Second, we describe a quantitative analysis of alternative splicing in a large-scale RNA-seq dataset (~1,000 samples), including the discovery of alternative splicing events associated with distinct cell states. We detail the workflow and features of rMATS-turbo that enable efficient parallel processing and analysis of large-scale RNA-seq datasets on a compute cluster. We anticipate that this protocol will help the broad user base of rMATS-turbo make the best use of this software for studying alternative splicing in diverse biological systems.

TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing.

Long-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read sequencing platforms limits transcript coverage. One strategy for overcoming this bottleneck is targeted long-read RNA-seq for preselected gene panels. We present TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA-seq utilizing isothermally linear-amplified capture probes. When performed on the Oxford nanopore platform with multiple gene panels of varying sizes, TEQUILA-seq consistently and substantially enriches transcript coverage while preserving transcript quantification. We profile full-length transcript isoforms of 468 actionable cancer genes across 40 representative breast cancer cell lines. We identify transcript isoforms enriched in specific subtypes and discover novel transcript isoforms in extensively studied cancer genes such as TP53. Among cancer genes, tumor suppressor genes (TSGs) are significantly enriched for aberrant transcript isoforms targeted for degradation via mRNA nonsense-mediated decay, revealing a common RNA-associated mechanism for TSG inactivation. TEQUILA-seq reduces the per-reaction cost of targeted capture by 2-3 orders of magnitude, as compared to a standard commercial solution. TEQUILA-seq can be broadly used for targeted sequencing of full-length transcripts in diverse biomedical research settings.

Synergy of Regenerative Periodontal Surgery and Orthodontics Improves Quality of Life of Patients with Stage IV Periodontitis: 24-Month Outcomes of a Multicenter RCT.

In stage IV periodontitis patients with pathologic tooth migration (PTM), interdisciplinary treatment includes regenerative periodontal surgery (RPS) with an application of biomaterials and orthodontic therapy (OT) to restore function, esthetics and thereby quality of life (QoL). In a 24-month randomized trial we explored the synergy between regenerative medicine and biomechanical force application. The following methods were used: Forty-three patients had been randomized to a combined treatment comprising RPS and subsequent OT starting either 4 weeks (early OT) or 6 months (late OT) post-operatively. Clinical periodontal parameters and oral health-related QoL (GOHAI) were recorded up to 24 months. We obtained the following results: Mean clinical attachment gain (∆CAL ± SD) was significantly higher with early OT (5.96 ± 2.1 mm) versus late OT (4.65 ± 1.76 mm) (p = 0.034). Pocket closure (PPD ≤ 4 mm) was obtained in 91% of defects with early OT compared to 90% with late OT. GOHAI-scores decreased significantly from 26.1 ± 7.5 to 9.6 ± 4.7 (early OT) and 25.1 ± 7.1 to 12.7 ± 5.6 (late OT). Inconclusion, teeth severely compromised by intrabony defects and PTM can be treated successfully by RPS followed by early OT with the advantage of an overall reduced treatment time. As a result of the combined periodontal-orthodontic therapy, the oral health-related QoL of patients was significantly improved. Early stimulation of wound healing with orthodontic forces had a favorable impact on the outcomes of regenerative periodontal surgery.

IRIS: Discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing.

Alternative splicing (AS) is prevalent in cancer, generating an extensive but largely unexplored repertoire of novel immunotherapy targets. We describe Isoform peptides from RNA splicing for Immunotherapy target Screening (IRIS), a computational platform capable of discovering AS-derived tumor antigens (TAs) for T cell receptor (TCR) and chimeric antigen receptor T cell (CAR-T) therapies. IRIS leverages large-scale tumor and normal transcriptome data and incorporates multiple screening approaches to discover AS-derived TAs with tumor-associated or tumor-specific expression. In a proof-of-concept analysis integrating transcriptomics and immunopeptidomics data, we showed that hundreds of IRIS-predicted TCR targets are presented by human leukocyte antigen (HLA) molecules. We applied IRIS to RNA-seq data of neuroendocrine prostate cancer (NEPC). From 2,939 NEPC-associated AS events, IRIS predicted 1,651 epitopes from 808 events as potential TCR targets for two common HLA types (A*02:01 and A*03:01). A more stringent screening test prioritized 48 epitopes from 20 events with "neoantigen-like" NEPC-specific expression. Predicted epitopes are often encoded by microexons of ≤30 nucleotides. To validate the immunogenicity and T cell recognition of IRIS-predicted TCR epitopes, we performed in vitro T cell priming in combination with single-cell TCR sequencing. Seven TCRs transduced into human peripheral blood mononuclear cells (PBMCs) showed high activity against individual IRIS-predicted epitopes, providing strong evidence of isolated TCRs reactive to AS-derived peptides. One selected TCR showed efficient cytotoxicity against target cells expressing the target peptide. Our study illustrates the contribution of AS to the TA repertoire of cancer cells and demonstrates the utility of IRIS for discovering AS-derived TAs and expanding cancer immunotherapies.

ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data.

Long-read RNA sequencing (RNA-seq) holds great potential for characterizing transcriptome variation and full-length transcript isoforms, but the relatively high error rate of current long-read sequencing platforms poses a major challenge. We present ESPRESSO, a computational tool for robust discovery and quantification of transcript isoforms from error-prone long reads. ESPRESSO jointly considers alignments of all long reads aligned to a gene and uses error profiles of individual reads to improve the identification of splice junctions and the discovery of their corresponding transcript isoforms. On both a synthetic spike-in RNA sample and human RNA samples, ESPRESSO outperforms multiple contemporary tools in not only transcript isoform discovery but also transcript isoform quantification. In total, we generated and analyzed ~1.1 billion nanopore RNA-seq reads covering 30 human tissue samples and three human cell lines. ESPRESSO and its companion dataset provide a useful resource for studying the RNA repertoire of eukaryotic transcriptomes.

The effect of timing of orthodontic therapy on the outcomes of regenerative periodontal surgery in patients with stage IV periodontitis: A multicenter randomized trial.

AIM: To compare the outcomes after early (4 weeks post surgery) or late (6 months post surgery) orthodontic therapy (OT) following regenerative surgery of intra-bony defects (IDs). MATERIALS AND METHODS: In a multi-center, parallel-group, randomized clinical trial, 43 patients with stage IV periodontitis were randomized to receive either early (n = 23) or late OT (n = 20) following regenerative surgery of IDs. Primary outcome was change in clinical attachment level (CAL) in one target ID at 12 months after surgery. Secondary outcomes were changes of probing pocket depth (PPD), bleeding on probing (BOP), and frequency of pocket closure. RESULTS: No statistically significant differences between groups could be observed for CAL gain (5.4 mm [±2.1 mm] for early; 4.5 mm [±1.7 mm] for late OT). PPD was reduced by 4.2 mm (±1.9 mm) in the early group and by 3.9 mm (±1.5 mm) in the late group (p > .05). Pocket closure (PPD ≤ 4 mm) was obtained in 91% of defects in early compared to 85% in late OT. CONCLUSION: In the inter-disciplinary treatment of periodontitis stage IV, OT can be initiated already 4 weeks after regenerative surgery of IDs with favourable results, thus reducing the overall treatment time.

Dimensional changes of the alveolar ridge contour of the premolar extraction site in adolescents.

PURPOSE: Premolar extraction in orthodontic therapy is common in adolescent patients. Knowledge of the tissue reaction in an extraction site is mainly based on studies with animal and adults. Thus, we aim to describe the time-dependent dimensional changes of the alveolar ridge contour of the premolar extraction site in adolescents. METHODS: Clinical data were obtained from a randomized controlled clinical trial (Universal Trial Number U1111-1132-6655), comparing treatment modalities with orthodontic space closure was initiated after 2-4 weeks (group A) and ≥ 12 weeks after tooth extraction (group B). Dental casts taken before the tooth extraction (T1) and before initiation of the space closure (T2) were digitalized with a 3D scanner and superimposed to analyze the dimensional changes of the alveolar ridge in early and later stage of wound healing. Linear mixed models were used for statistical analysis. RESULTS: Plaster models of 25 patients (mean age 15.2 years, 11 male and 14 female) with 66 extraction sites were enrolled. The average atrophic changes from tooth extraction to the early stage of wound healing (group A, n = 41) were in total 27.5% ± 11.8; labially 31.3% ± 15.1 and orally 23.6% ± 13.4. In group B (n = 25) the average atrophic changes were in total 38.6% ± 12.1; labially 46.2% ± 16.7; orally 31.3% ± 18.9. The atrophic changes between the groups in total (p = 0.031) and at the labial side (p = 0.012) were significant. The jaw affiliation was a significant parameter for all examined areas in regard to all cases (labial p = 0.019; oral p = 0.020; total p = 0.001). Atrophic changes between genders were not statistically different. CONCLUSIONS: Alveolar atrophy increased over time after extraction primarily in the lower jaw at the labial side. The main atrophy occurred in the first healing phase of the extraction socket. Thus, timely coordination is important to preserve sufficient bone levels. The atrophic changes of the alveolar ridge in adolescents parallel those reported for adults.

Incidence and severity of gingival invaginations associated with early versus late initiation of orthodontic space closure after tooth extraction : A multicenter pilot and randomized controlled trial.

OBJECTIVE: Gingival invaginations are a common side effect of orthodontic extraction-space closure. The timing of initiating the closure of an extraction space varies greatly in clinical practice. In this multicenter pilot and randomized controlled trial, we prospectively investigated whether initiating space closure in the early stage of wound healing would benefit the incidence and severity of invaginations developing in the extraction sites. METHODS: A total of 368 patients were screened for indications to extract at least one mandibular premolar. Those recruited were randomly assigned to one of two treatment arms: initiation of space closure either 2-4 weeks (arm A) or ≥12 weeks (arm B) after tooth extraction. Clinical data regarding treatment process and periodontal tissue response were recorded during and after space closure and analyzed by a specialized biometrics unit. The study was performed under continuous surveillance by an independent study control center. RESULTS: A total of 74 extraction sites were analyzed. Regarding the incidence of gingival invaginations, there were no significant intergroup differences [p = 0.13; group A comprising 37/44 (84.1%) and group B 29/30 (96.7%) invaginated sites]. The same was true based on either maxillary (p = 0.52) or mandibular (p = 0.21) sites only, and the severity of the invaginations did not differ between the treatment arms. CONCLUSIONS: As to the incidence and severity of gingival invaginations, we did not notice any statistically significant differences between the two timeframes. Our data do, however, provide a basis to identify additional confounders and to improve the accuracy of case-load estimations for future trials.

Effectiveness of early orthopaedic treatment with headgear: a systematic review and meta-analysis.

Background: Although the headgear appliance has been used extensively to correct anteroposterior discrepancies, its treatment effects have not yet been adequately assessed in an evidence-based manner. Objective: Aim of this systematic review was to assess the therapeutic and adverse effects of early headgear treatment from controlled clinical trials on human patients in an evidence-based manner. Search methods: An unrestricted electronic search of six databases from inception to December 2015. Selection criteria: Randomized and prospective non-randomized controlled trials assessing the effects of headgear treatment on human patients. Data collection and analysis: After duplicate study selection, data extraction, and risk of bias assessment according to the Cochrane guidelines, random-effects meta-analyses of mean differences (MDs) and relative risks (RRs), including their 95% confidence intervals (CIs) were performed, followed by subgroup and sensitivity analyses. Results: A total of 18 unique studies with a total of 930 (56% male/44% female) patients were included. Headgear treatment was associated with a posterior translation of the anterior maxilla border in the short term, as seen by the mean annualized change in the SNA angle (MD = -1.63°/year; 95% CI = -2.20 to -1.06°/year; high quality evidence) compared to untreated patients. This effect was independent of the rotation of the palatal plane and the inclination of the upper incisors, while a proportional relationship with the initial discrepancy in SNA was seen. The clinical significance of this improvement diminished in the long term, although only limited evidence existed. Additionally, early headgear treatment might decrease the risk of dental trauma during the following years (RR = 0.34; 95% CI = 0.14 to 0.80; moderate quality evidence). Low quality evidence on the effect of headgear on the rotation of the palatal plane, the nasolabial angle, the occlusal outcome, and signs of temporomandibular disorders precluded robust assessments, due to risk of bias, inconsistency, imprecision, and small-study effects. Conclusions: Based on existing trials, headgear is a viable treatment option to modify sagittal growth of the maxilla in the short term in Class II patients with maxillary prognathism. Registration: PROSPERO (CRD42015029837). Funding: None.

[Ridge preservation with synthetic nanocrystalline hydroxyapatite reduces the severity of gingival invaginations-a prospective clinical study]. / Alveolenerhalt mit einem nanopartikulärem Hydroxylapatit verringert den Ausprägungsgrad von Gingivaduplikaturen - eine prospektive klinische Studie.

BACKGROUND AND OBJECTIVE: Gingival invaginations develop after tooth extraction and subsequent orthodontic space closure. Aetiological factors and long-term effects of gingival invaginations on oral health are nearly unknown. In addition, preventive or therapeutic strategies are rare. This prospective clinical study employing the split mouth technique was performed to investigate the effect of extraction socket augmentation with a synthetic nanocrystalline hydroxyapatite (NanoBone(®) Artoss, Rostock, Germany) on the incidence and degree of gingival invaginations. MATERIAL AND METHODS: A total of 10 orthodontic patients with need for symmetric premolar extractions offering a total of 28 extractions were included in this trial. The study plan provided one extraction site to be augmented with synthetic nanocrystalline hydroxyapatite (NanoBone(®)), the other served as control. After primary wound healing, space closure was performed under defined biomechanical conditions. After space closure was accomplished, occurrence and degree of gingival invaginations as well as probing depths of the adjacent teeth mesial and distal to the extractions were determined and dental radiographs were taken. RESULTS: The degree of gingival invaginations and probing depths mesial and distal of the extraction were significantly reduced on NanoBone(®) augmented extraction sites. In addition, 70% of the radiographs revealed translucent and hyperdense areas on the intervention side after space closure. Apical root resorption was found in 2 patients on both the NanoBone(®) side and the control side. CONCLUSION: Ridge preservation with NanoBone(®) appeared to reduce the severity of gingival invaginations. Further investigation on long-term effects is mandatory to eliminate the appearance of adverse effects.

Influence of time after extraction on the development of gingival invagination: study protocol for a multicenter pilot randomized controlled clinical trial.

BACKGROUND: Gingival invaginations are a common side effect of orthodontic therapy involving tooth extraction and subsequent space closure. Consequences of gingival invaginations are a jeopardized stability of the space closure and hampered oral hygiene. In a retrospective study, the factor time until initiation of orthodontic space closure after tooth extraction has been identified as a potential risk factor for the development of gingival invaginations. The aim of this pilot study is to proof this hypothesis and to enable a caseload calculation for further clinical trials. The referring question is: is it possible to reduce the number of developing gingival invaginations by initiation of orthodontic space closure after tooth extraction at an early point of time? DESIGN: The intended pilot study is designed as a multicenter randomized controlled clinical trial, comparing the impact of two different time intervals from tooth extraction to initiation of orthodontic space closure on the development of gingival invaginations.Forty participants, men and women in the age range of 11 to 30 years with orthodontically related indication for tooth extraction in the lower jaw, will be randomized 1:1 in one of two treatment groups. In group A the orthodontic tooth movement into the extraction area will be initiated in a time interval 2 to 4 weeks after tooth extraction. In group B the tooth movement will be initiated in a time interval >12 weeks after extraction. A possible effect of these treatment modalities on the development of gingival invaginations will be documented at the moment of space closure or 10 months +/- 14 days after initiation of space closure respectively, by clinical documentation of the primary (reduced number of gingival invagination) and the secondary endpoint (reduction of the severity of gingival invaginations). TRIAL REGISTRATION: Universal Trial Number U1111-1132-6655; German Clinical Trials Register DRKS00004248.