circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA

Circular RNAs (circRNAs) represent a class of widespread endogenous RNAs that regulate gene expression and thereby influence cell biological decisions with implications for the pathogenesis of several diseases. Here, we disclose a novel gene-regulatory role of circHIPK3 by combining analyses of large genomics datasets and mechanistic cell biological follow-up experiments. Specifically, we use temporal depletion of circHIPK3 or specific RNA binding proteins (RBPs) and identify several perturbed genes by RNA sequencing analyses. Using expression-coupled motif analyses of mRNA expression data from various knockdown experiments, we identify an 11-mer motif within circHIPK3, which is also enriched in genes that become downregulated upon circHIPK3 depletion. By mining eCLIP datasets, we find that the 11-mer motif constitutes a strong binding site for IGF2BP2 and validate this circHIPK3-IGF2BP2 interaction experimentally using RNA-immunoprecipitation and competition assays in bladder cancer cell lines. Our results suggest that circHIPK3 and IGF2BP2 mRNA targets compete for binding. Since the identified 11-mer motif found in circHIPK3 is enriched in upregulated genes following IGF2BP2 knockdown, and since IGF2BP2 depletion conversely globally antagonizes the effect of circHIPK3 knockdown on target genes, our results suggest that circHIPK3 can sequester IGF2BP2 as a competing endogenous RNA (ceRNA), leading to target mRNA stabilization. As an example of a circHIPK3-regulated gene, we focus on the STAT3 mRNA as a specific substrate of IGF2BP2 and validate that manipulation of circHIPK3 regulates IGF2BP2-STAT3 mRNA binding and thereby STAT3 mRNA levels. However, absolute copy number quantifications demonstrate that IGF2BP2 outnumbers circHIPK3 by orders of magnitude, which is inconsistent with a simple 1:1 ceRNA hypothesis. Instead, we show that circHIPK3 can nucleate multiple copies of IGF2BP2, potentially via phase separation, to produce IGF2BP2 condensates. Finally, we show that circHIPK3 expression correlates with overall survival of patients with bladder cancer. Our results are consistent with a model where relatively few cellular circHIPK3 molecules function as inducers of IGF2BP2 condensation thereby regulating STAT3 and other key factors for cell proliferation and potentially cancer progression.

Different tumor growth pattern of clinically nonfunctioning pituitary neuroendocrine tumor according to sex and age: a longitudinal study

PURPOSE

Asymptomatic patients with clinically non-functional pituitary neuroendocrine tumors (CNF-PitNETs) are usually followed up. However, the natural course of CNF-PitNETs according to sex and age remains unclear. Therefore, this study assessed growth patterns of CNF-PitNETs according to sex and age.

METHODS

In this longitudinal study, we enrolled 431 consecutive patients with CNF-PitNETs who were treated at Seoul National University Hospital from 1997 to 2021. The patients underwent hormone function testing and visual field testing, and were subsequently followed up with imaging over a median duration of 66 months.

RESULTS

The median age of the patients was 53.0 years, and 37.1% (n = 160) were men. Men were older and harbored more macroadenomas than women. The annual tumor volume change was higher in men than in women (0.21 vs. 0.04 cm3/year, P < 0.001). The estimated cutoff value of age for significant tumor growth was 51 years. In men, the annual tumor volume change was similar across all age groups. In women, those aged ≤ 50 years showed significantly lower annual tumor volume change than those aged > 50 years (0.01, 0.11, and 0.17 cm3/year, P = 0.001). When comparing sexes within the same age group, the annual tumor volume changes was significantly lower for women than for men, only in patients aged ≤ 50 years (0.01 vs. 0.15 cm3/year, P < 0.001).

CONCLUSIONS

Among patients with CNF-PitNET, tumor growth was slower in women aged ≤ 50 years than in men and women aged > 50. These findings may guide the customization of surveillance strategies for CNF-PitNETs according to sex and age.

Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies

RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize fusions of RNA base-editors (rBEs) to RBPs to circumvent the limitations of immunoprecipitation (CLIP)-based methods that require enzymatic digestion and large amounts of input material. To broaden the repertoire of rBEs suitable for editing-based RBP-RNA interaction studies, we have devised experimental and computational assays in a framework called PRINTER (protein-RNA interaction-based triaging of enzymes that edit RNA) to assess over thirty A-to-I and C-to-U rBEs, allowing us to identify rBEs that expand the characterization of binding patterns for both sequence-specific and broad-binding RBPs. We also propose specific rBEs suitable for dual-RBP applications. We show that the choice between single or multiple rBEs to fuse with a given RBP or pair of RBPs hinges on the editing biases of the rBEs and the binding preferences of the RBPs themselves. We believe our study streamlines and enhances the selection of rBEs for the next generation of RBP-RNA target discovery.

Comparing Acute Oral Mucosa Toxicity Associated with Minibeam and Conventional Radiotherapy

PURPOSE/OBJECTIVE(S)

Acute oral mucosa toxicity is associated with ulceration, severe pain, and nutritional deficiencies that may lead to treatment interruptions and a decreased quality of life for head and neck cancer patients. Minibeam radiotherapy (MRT) is a type of spatially fractionated radiotherapy that delivers an alternating pattern of sub-millimeter wide peaks of high dose immediately adjacent to much lower valley doses. By delivering a non-uniform dose distribution, MRT allows for elevated peak doses while maintaining extraordinary normal tissue tolerance. In this study, we used an acute oral mucosa toxicity mouse model to test the hypothesis that MRT provides superior tissue sparing compared to conventional radiotherapy (CRT).

MATERIALS/METHODS

A total of 33 female C57BLJ6 mice were randomized by body weight (BW) across two CRT groups (n = 4/group) receiving open field radiation of 16 and 20 Gy and five MRT groups (n = 5/group) receiving peak:valley doses of 48:8, 72:12, 96:16, 96:8, and 152:8 Gy. All radiation was given in one fraction. The CRT groups were irradiated with a 10 mm circular field using a 225 kVp PA x-ray beam encompassing the oral cavity and oropharynx. The MRT groups were irradiated with the same arrangement, but the beam was collimated into 0.5 mm wide minibeams spaced 1.1 mm center-to-center using tungsten collimators of 0.5, 1, and 2.5 mm thickness to deliver peak-to-valley ratios (PVRs) of 6:1, 12:1, and 19:1. Acute effects in the oral mucosa were studied using changes in BW as a surrogate for clinically significant oral mucositis. BWs were measured daily starting on the day of treatment, and BW changes were computed relative to the day of treatment. The toxicity endpoint was defined such that mice losing >20% BW were humanely euthanized.

RESULTS

Doses of 20 Gy CRT and 96:16 Gy MRT were highly toxic, with all animals in these groups reaching the toxicity endpoint between 9-11 days post-RT, compared to only one animal in the 16 Gy CRT group, and no animals in the other MRT groups. The BWs of all surviving animals returned to baseline within 15 days post-RT. The groups 48:8, 96:8, and 152:8 Gy showed similar BW loss and full recovery patterns. Additionally, the groups 48:8, 72:12, and 96:16 Gy showed that, for the same PVR, increasing the valley dose resulted in increased BW loss. Lastly, animals did not tolerate 96:16 Gy, but those in the 96:8 Gy group fully recovered.

CONCLUSION

Despite the extreme toxicity caused by 20 Gy CRT, animals in the MRT groups tolerated peak doses up to 152 Gy when the valley dose was 8 Gy. These results confirm the superior normal tissue sparing capacity of MRT compared to CRT in an oral mucosa mouse model. We delivered tolerable MRT peak doses an order of magnitude larger than toxic CRT doses. Importantly, our results suggest that valley dose is the most useful parameter to assess acute toxicity when using MRT. Our data may prove useful for eventual clinical applications of MRT in head and neck cancers.

Physician and Patient-Reported Outcomes of a Phase III Trial of Ultra-Hypofractionated vs. Moderate Hypofractionated Radiotherapy to the Whole Breast after Breast-Conserving Surgery

PURPOSE/OBJECTIVE(S)

To report a final analysis evaluating physician and patient-reported outcomes of early breast cancer patients receiving moderate hypofractionation or ultra-hypofractionated whole breast radiotherapy (RT).

MATERIALS/METHODS

Between April 4, 2018, and February 11, 2020, patients with localized breast cancer (T1-T3, N0-N1, and M0) managed with breast-conserving surgery (BCS) were enrolled. Patients were randomized to receive whole breast RT with moderate hypofractionation to 40 Gy in 15 fractions (Arm A) or ultra-hypofractionation to 25 Gy in 5 fractions (Arm B). An optional concurrent integrated boost to 48 Gy on Arm A or 30 Gy on Arm B was allowed. Early toxicity (<3 months), late toxicity (> 3 months), quality of life (QOL), cosmesis, Patient-Reported Outcomes version of the Common Terminology Criteria for Adverse Events (PRO-CTCAE), and deterioration of cosmesis were analyzed.

RESULTS

One hundred and seven patients were randomized to moderate hypofractionation (n = 54) or ultra-hypofractionation (n = 53). With a median follow-up of 36 months, no significant differences in patient characteristics were noted between the two arms. There were no patients with a grade ≥3 or higher toxicity. Grade 2 toxicities were 7.4% in Arm A and 7.5% in Arm B, and primarily consisted of radiation dermatitis (6 patients), fibrosis (1 patient) and lymphedema (1 patient). The average Harvard Cosmesis score and overall QoL were similar between arms at all time points, with no patients developing cosmetic deterioration. Patient-reported moderate to severe radiation skin burns were more commonly reported in Arm A (21.05%) vs. Arm B (6.25%) at the end of treatment (EOT) (p = 0.078). At EOT, patients receiving moderate hypofractionation had higher mean toxicity scores in breast tenderness (2.66 vs. 1.5, p = 0.018), skin flaking or peeling (0.63 vs. 0.06, p = 0.035), blistering (0.74 vs. 0.06, p = 0.028), pruritis (2.53 vs. 0.87, p < 0.001), erythema (4.24 vs. 2.0, p <0.001), telangiectasias (1.0 vs. 0.28, p = 0.021). Additionally, patients receiving moderate hypofractionation reported significantly worse changes from baseline at EOT in breast tenderness (-2.25 vs. -.86, p = 0.02), telangiectasia (-0.81 vs. 0.18, p = 0.012), skin discoloration (-4.31 vs. -1.04, p < 0.001), skin flaking or peeling (-.55 vs. 0.04, p = 0.053), blistering (-0.82 vs. -0.07, p = 0.033), and pruritus (-2.27 vs. -.67, p = 0.002). There was a return to baseline in all patient-reported breast domains by 3 months (p >0.05) in both arms.

CONCLUSION

Ultra-hypofractionated whole breast irradiation, consisting of 25 Gy in 5 fractions, provided comparable provider assessed toxicity and cosmetic outcomes to 40 Gy in 15 fractions. At the EOT assessment, ultra-hypofractionation had a better patient reported toxicity profile. Our findings provide further evidence to support daily ultra-hypofractionated whole breast radiotherapy as an appropriate treatment option for early-stage breast cancer.

Local Control after Re-Irradiation of Spinal Metastases with Stereotactic Body Radiation Therapy

PURPOSE/OBJECTIVE(S)

Determine local control (LC) rate and risk of vertebral compression fractures (VCFs) and radiation myelitis (RM) for patients receiving re-irradiation of spinal metastases (SMs) using stereotactic body radiation therapy (SBRT) from large single-institutional experience with long follow-up.

MATERIALS/METHODS

Retrospectively identified patients receiving re-irradiation SBRT (rSBRT, 1, 3, or 5 fractions) to SMs previously treated with radiation therapy (RT) and having follow up imaging to assess local control. 1 fraction patients typically received 20-24 Gy and 16-18 Gy to the high- and low-risk planning target volumes (PTVs), respectively, and 27-39 Gy and 21-24 Gy for the 3 fraction patients, with a single level of 50 Gy for 5 fractions. Patient and treatment characteristics for previous RT (pRT) and rSBRT were collected, including histology and dose-volume histogram statistics (DVH). Kaplan-Meier estimates of overall survival (OS), and cumulative incidence (competing with death) of local failure with death as a competing risk was computed for the whole cohort and stratified by radioresistance of histology, and risk of VCF for RM (for treatments at L1 and above) and 95% confidence intervals. Equivalent dose in 2 Gy fractions (EQD2) for PTV and spinal cord (SC) DVH statistics was computed for each individual course and cumulatively, using a/b = 10 Gy for tumor and 2 Gy for SC.

RESULTS

Identified 107 lesions in 91 patients. 48 (45%) had radioresistant histologies. For all patients, at 1 and 2 years, respectively OS was 64% (55-74%) and 43% (34-55%), LC was 88% (81-94%) and 85% (78-91%) with median follow-up of 52 months (Table 1). OS and LC were not significantly different between radiosensitivity groups (p>0.05). Risk of VCF at 1 and 2 years was 7% (3-13%) and 9% (4-16%). RM was identified in 1 patient, who received 30 Gy in 5 fractions to T1, and had 1-fraction rSBRT 21 months later. SC Dmax was 31.5 Gy for pRT and 10.4 Gy, for rSBRT, resulting in total SC EQD2 of 73 Gy. RM was confirmed on MRI 8 months after rSBRT. Cumulative RM risk at 8 months after rSBRT was estimated at 1% (0-4%). Median EQD2 for the minimum dose to the high and low risk PTVs were 17.7 Gy (interquartile range, IQR, 13.0-27.6 Gy) and 13.7 Gy (IQR, 10.8-19.3 Gy) for rSBRT, and maximum EQD to SC for previous RT, rSBRT, and cumulatively was 38 Gy (IQR, 30-41 Gy), 27 Gy (IQR, 22-36 Gy), and 65 Gy (IQR, 54-73 Gy).Re-irradiation of spinal metastasis with SBRT can be delivered safely and provide high rates of local control, including for radioresistant tumors, as demonstrated with the longest reported follow-up in this setting.

CONCLUSION

Re-irradiation of SM with SBRT provides high rates of LC even for radioresistant tumors, and low risk of VCF and RM, based on the longest reported follow-up in this setting.

Assessment of Minimum Dose as a Strong Predictor of Local Failure after Spine SBRT

PURPOSE/OBJECTIVE(S)

Stereotactic body radiation therapy (SBRT) has demonstrated robust clinical benefits in carefully selected patients, improving local control and even overall survival (OS). Even so, a wide range of dose-fractionation schemes are used in clinical practice. We seek to assess a large database to determine clinical and dosimetric predictors of local failure after spine SBRT.

MATERIALS/METHODS

From a large institutional database, spine SBRT treatments with subsequent imaging follow-up to assess local control were identified. Patients were treated with a simultaneous integrated boost technique using 1 or 3 fractions, generally delivering 20-24 Gy in 1 fraction to the high dose volume and 16 Gy to the low dose volume (or 30-36 Gy and 24 Gy for 3 fraction treatments). Exclusions included: lack of imaging follow-up, proton therapy, and benign primary histologies. Statistical analyses included Cox proportional hazards analyses and the robust log-rank statistic for cut-point analysis. The cumulative incidence of local failure with death as a competing risk was considered as the primary endpoint.

RESULTS

A total of 522 eligible spine SBRT treatments (68% single fraction) were identified in 377 unique patients. Patients had a median OS of 43.7 months (95% confidence interval: 34.3-54.4). The cumulative incidence of local failure was 19.3% (15.3-23.2) at 1 year and 25.6% (21.1-29.9) at 2 years. Univariate analysis identified that the minimum dose (normalized for the prescription dose) was a strong predictor of local failure (p = 0.0093). Among patients treated with a single fraction, statistical significance was maintained (p = 0.024). No other dosimetric factors were predictive of local failure. In a cut point analysis, the log-rank statistic was maximized at 15.8 Gy minimum dose for single-fraction treatment (HR = 0.51, 95% CI: 0.34 - 0.75, p = 0.0009). Cumulative incidence of local failure was 15.1% (9.8-20.2) vs. 24.7% (17.2-31.5) at 1 year using this cut-off. Comparable local control was demonstrated with a minimum dose of 14 Gy (HR = 0.57, 95%: 0.37 - 0.87, p = 0.009), with reduced local control with lower minimum doses. Among a range of clinical factors assessed, only epidural and soft tissue involvement were predictive of local failure (HR = 1.80 and 1.98, respectively). Multivariable analyses incorporating soft tissue involvement, epidural extension, and multilevel disease confirmed the 15.8 Gy cutoff for single fraction cases (HR = 0.58, 95% CI: 0.38-0.88, p = 0.011).

CONCLUSION

Spine SBRT offers favorable local control using a range of dose-fractionation schemes; however, minimum dose has a strong association with local control, unlike any other dosimetric factors tested. Furthermore, statistical significance was maintained even when considering epidural extension and potential limitations from dose to the spinal cord. Our data suggests that the minimum dose should be prioritized during treatment planning, ideally to at least 14 - 15.8 Gy for single fraction.

PSMA-Positive Extracellular Vesicles Predict Disease Recurrence in Oligometastatic Castration-Sensitive Prostate Cancer Treated with Stereotactic Ablative Radiotherapy: Analysis of the ORIOLE trial

PURPOSE/OBJECTIVE(S)

Stereotactic ablative radiation therapy (SABR) can prolong progression free survival in oligometastatic prostate cancer (omPC) patients. However, predictive tools to identify those who will benefit from SABR are necessary. Our group was the first to demonstrate that plasma levels of prostate cancer-derived extracellular vesicles (ProstEVs) correlate with tumor burden and predict disease progression in omPC after SABR. Herein, we conducted a blinded validation study using plasma samples from the ORIOLE randomized phase 2 clinical trial in castration-sensitive patients.

MATERIALS/METHODS

Plasma samples from 46 omPC patients from the Baltimore ORIOLE trial: a 2:1 ratio randomization to SABR vs observation (NCT02680587). Baseline PSMA+ ProstEV levels were measured by standardized and calibrated nanoscale flow cytometry using fluorescent PSMA antibodies. Median ProstEV levels was used as cut-off for low and high levels. Kaplan-Meier curves and Cox regression models were used to determine the association of ProstEV levels with clinical outcomes [PSA progression-free survival (psaPFS) and radiographic distant progression free survival (rPFS)].

RESULTS

No association was observed between number of metastatic lesions or baseline PSA and plasma ProstEV levels. The rPFS for patients treated with SABR was 29.6 months. The rPFS for patients treated with SABR with high and low ProstEV levels were 11.1 months and 36 months, respectively (Hazard Ratio: 2.85; 95% CI, 1.01-7.48; P = 0.02). The psaPFS for patients treated with SABR was 11.9 months. The psaPFS for patients with high and low ProstEV levels were 5.9 months and 24.3 months, respectively (HR: 2.44; 95% CI, 1.00-5.94; P = 0.03).

CONCLUSION

ProstEVs is the first blood biomarker of tumor burden that can prognosticate the risk of disease recurrence in omPC patients treated with SABR. While biomarker-guided trials are warranted, our validation study strengthens the clinical value of ProstEVs for personalized radiation therapy.

Unique T-cell Sub-Population Shifts after SBPT and Nivolumab in Platinum Refractory HNC: Biomarker Correlates from ROR1771

PURPOSE/OBJECTIVE(S)

ROR1771 was a clinical trial investigating the use of stereotactic body proton radiotherapy (SBPT) and nivolumab in recurrent platinum refractory head and neck squamous cell carcinoma (HNSCC). The planned analysis of T-cell subpopulation and biomarker response is herein presented.

MATERIALS/METHODS

Patients with metastatic histologically confirmed HNSCC from any primary site received 2 cycles of nivolumab followed by SBPT to 1-2 selected target lesion(s) (hilar/lung: 8 of 12 patients), followed by maintenance nivolumab. Peripheral blood mononuclear cells were isolated pre-/post-treatment. Flow cytometry identified T-cell subpopulations. Single Cell 5' Gene Expression (GEX) and V(D)J T Cell Receptor libraries were prepared using Single Cell Immune Profiling. Seurat (v4.1.1) was used to identify cell type clusters, and differential expression post-filtration was evaluated using the Wilcoxon Rank Sum test.

RESULTS

A total of 12 patients were eligible for analysis, with one alive at time of analysis, 52 months from start of treatment. Median overall survival here was 12.5 months vs. 7.5-months on CheckMate 141. SBPT ranged from 35-50 Gy. Sequential changes in T-cell populations from baseline were noted with initiation of nivolumab, driving decrease in tumor-reactive (TTR; CD11ahighPD1+CD8+), central memory (TCM; CCR7+CD45RA-), and effector T-cells (TEF; CCR7-CD45RA-). TTR and TCM increased following SBPT, with greatest increase (3.5x TTR and 5.2x TCM) in the surviving patient. An average of 68 genes with significant differential expression between timepoints (p<0.0001) demonstrated RNA gene expression changes across all cell subtypes, including ribosomal (RPL and RPS) genes, ACTB, FTL, MALAT1, and others. This averaged 113 genes across all timepoints in the surviving patient, with peak following nivolumab induction. On T-cell receptor (TCR) analysis of this patient, the predominant clonotype diversity changed substantially following nivolumab. Following SBPT, clonotype diversity again changed to include a milieu seen neither at baseline nor with nivolumab alone. These TCRs persisted for approximately 2 weeks following SBPT before returning to resemble the nivolumab-induced TCR diversity alone, coinciding with disease recurrence.

CONCLUSION

ROR1771 demonstrated overall survival favorably comparable to CheckMate 141. Biomarker analysis of peripheral blood samples demonstrated significant shifts in T-cell subpopulations and underlying gene expression to nivolumab and then to SBPT administration. SBPT to a target lesion changed TCR clonotypes within the peripheral blood beyond those seen with nivolumab administration, with fading of these TCR clonotypes coinciding with recurrence. SBPT in combination with nivolumab may drive systemic immunologic change above that induced by nivolumab alone and warrants further investigation.

Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies

RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize fusions of RNA base-editors (rBEs) to RBPs to circumvent the limitations of immunoprecipitation (CLIP)-based methods that require enzymatic digestion and large amounts of input material. To broaden the repertoire of rBEs suitable for editing-based RBP-RNA interaction studies, we have devised experimental and computational assays in a framework called PRINTER (protein-RNA interaction-based triaging of enzymes that edit RNA) to assess over thirty A-to-I and C-to-U rBEs, allowing us to identify rBEs that expand the characterization of binding patterns for both sequence-specific and broad-binding RBPs. We also propose specific rBEs suitable for dual-RBP applications. We show that the choice between single or multiple rBEs to fuse with a given RBP or pair of RBPs hinges on the editing biases of the rBEs and the binding preferences of the RBPs themselves. We believe our study streamlines and enhances the selection of rBEs for the next generation of RBP-RNA target discovery.

HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence

RNA-binding proteins (RBPs) control RNA metabolism to orchestrate gene expression and, when dysfunctional, underlie human diseases. Proteome-wide discovery efforts predict thousands of RBP candidates, many of which lack canonical RNA-binding domains (RBDs). Here, we present a hybrid ensemble RBP classifier (HydRA), which leverages information from both intermolecular protein interactions and internal protein sequence patterns to predict RNA-binding capacity with unparalleled specificity and sensitivity using support vector machines (SVMs), convolutional neural networks (CNNs), and Transformer-based protein language models. Occlusion mapping by HydRA robustly detects known RBDs and predicts hundreds of uncharacterized RNA-binding associated domains. Enhanced CLIP (eCLIP) for HydRA-predicted RBP candidates reveals transcriptome-wide RNA targets and confirms RNA-binding activity for HydRA-predicted RNA-binding associated domains. HydRA accelerates construction of a comprehensive RBP catalog and expands the diversity of RNA-binding associated domains.

Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq

Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets plays a critical role in enabling our understanding of how these RBPs control RNA processing and regulation. Cross-linking and immunoprecipitation (CLIP) provides a generalizable, transcriptome-wide method by which RBP/RNA complexes are purified and sequenced to identify sites of intermolecular contact. By simplifying technical challenges in prior CLIP methods and incorporating the generation of and quantitative comparison against size-matched input controls, the single-end enhanced CLIP (seCLIP) protocol allows for the profiling of these interactions with high resolution, efficiency and scalability. Here, we present a step-by-step guide to the seCLIP method, detailing critical steps and offering insights regarding troubleshooting and expected results while carrying out the ~4-d protocol. Furthermore, we describe a comprehensive bioinformatics pipeline that offers users the tools necessary to process two replicate datasets and identify reproducible and significant peaks for an RBP of interest in ~2 d.

Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions

The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs in authentic virus-infected cells. SARS-CoV-2 proteins, NSP8, NSP12, and nucleocapsid display distinct preferences to specific regions in the RNA viral genome, providing evidence for their shared and separate roles in replication, transcription, and viral packaging. SARS-CoV-2 proteins expressed in human lung epithelial cells bind to 4773 unique host coding RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 and ORF9c, whose RNA substrates are associated with pathways in protein N-linked glycosylation ER processing and mitochondrial processes. Furthermore, siRNA knockdown of host genes targeted by viral proteins in human lung organoid cells identify potential antiviral host targets across different SARS-CoV-2 variants. Conversely, NSP9 inhibits host gene expression by blocking mRNA export and dampens cytokine productions, including interleukin-1α/β. Our viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.

Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions

The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs in authentic virus-infected cells. SARS-CoV-2 proteins, NSP8, NSP12, and nucleocapsid display distinct preferences to specific regions in the RNA viral genome, providing evidence for their shared and separate roles in replication, transcription, and viral packaging. SARS-CoV-2 proteins expressed in human lung epithelial cells bind to 4773 unique host coding RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 and ORF9c, whose RNA substrates are associated with pathways in protein N-linked glycosylation ER processing and mitochondrial processes. Furthermore, siRNA knockdown of host genes targeted by viral proteins in human lung organoid cells identify potential antiviral host targets across different SARS-CoV-2 variants. Conversely, NSP9 inhibits host gene expression by blocking mRNA export and dampens cytokine productions, including interleukin-1α/β. Our viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.

Integrative RNA-omics discovers GNAS alternative splicing as a phenotypic driver of splicing factor-mutant neoplasms

Mutations in splicing factors (SFs) are the predominant class of mutations in myelodysplastic syndrome (MDS), but convergent downstream disease drivers remain elusive. To identify common direct targets of mis-splicing by mutant U2AF1 and SRSF2, we performed RNA-Seq and eCLIP in human hematopoietic stem/progenitor cells (HSPCs) derived from isogenic induced pluripotent stem cell (iPSC) models. Integrative analyses of alternative splicing and differential binding converged on a long isoform of GNAS (GNAS-L), promoted by both mutant factors. MDS population genetics, functional and biochemical analyses support that GNAS-L is a driver of MDS and encodes a hyperactive long form of the stimulatory G protein alpha subunit, Gas-L, that activates ERK/MAPK signaling. SF-mutant MDS cells have activated ERK signaling and consequently are sensitive to MEK inhibitors. Our findings highlight an unexpected and unifying mechanism by which SRSF2 and U2AF1 mutations drive oncogenesis with potential therapeutic implications for MDS and other SF-mutant neoplasms.

Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

Background

Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions in different biological contexts.

Methods

We conduct an extensive screen of circRNA-RBP interactions in the ENCODE cell lines HepG2 and K562. We profile circRNAs in deep-sequenced total RNA samples and analyze circRNA-RBP interactions using a large set of eCLIP data with binding sites of 150 RBPs. We validate interactions for select circRNAs and RBPs by performing RNA immunoprecipitation and functionally characterize our most interesting candidates by conducting knockdown studies followed by RNA-Seq.

Results

We generate a comprehensive catalog of circRNA-RBP interactions in HepG2 and K562 cells. We show that KHSRP binding sites are enriched in flanking introns of circRNAs and that KHSRP depletion affects circRNA biogenesis. We identify circRNAs that are highly covered by RBP binding sites and experimentally validate individual circRNA-RBP interactions. We show that circCDYL, a highly expressed circRNA with clinical and functional implications in bladder cancer, is almost completely covered with GRWD1 binding sites in HepG2 cells, and that circCDYL depletion counteracts the effect of GRWD1 depletion. Furthermore, we confirm interactions between circCDYL and RBPs in bladder cancer cells and demonstrate that circCDYL depletion affects hallmarks of cancer and perturbs the expression of key cancer genes, e.g., TP53. Finally, we show that elevated levels of circCDYL are associated with overall survival of bladder cancer patients.

Conclusions

Our study demonstrates transcriptome-wide and cell-type-specific circRNA-RBP interactions that could play important regulatory roles in tumorigenesis.

Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins

BACKGROUND

A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis across datasets. The development of enhanced CLIP (eCLIP) enabled the mapping of targets for 150 RBPs in K562 and HepG2, creating a unique resource of RBP interactomes profiled with a standardized methodology in the same cell types.

RESULTS

Our analysis of 223 eCLIP datasets reveals a range of binding modalities, including highly resolved positioning around splicing signals and mRNA untranslated regions that associate with distinct RBP functions. Quantification of enrichment for repetitive and abundant multicopy elements reveals 70% of RBPs have enrichment for non-mRNA element classes, enables identification of novel ribosomal RNA processing factors and sites, and suggests that association with retrotransposable elements reflects multiple RBP mechanisms of action. Analysis of spliceosomal RBPs indicates that eCLIP resolves AQR association after intronic lariat formation, enabling identification of branch points with single-nucleotide resolution, and provides genome-wide validation for a branch point-based scanning model for 3' splice site recognition. Finally, we show that eCLIP peak co-occurrences across RBPs enable the discovery of novel co-interacting RBPs.

CONCLUSIONS

This work reveals novel insights into RNA biology by integrated analysis of eCLIP profiling of 150 RBPs with distinct functions. Further, our quantification of both mRNA and other element association will enable further research to identify novel roles of RBPs in regulating RNA processing.

Hydrothorax Due to Extravasation of Intravenous Contrast after Power Injection through Right Subclavian Catheter

We report a case of hydrothorax after receiving intravenous (IV) contrast material by power injector through right subclavian central venous catheter (CVC) line. A 38-year-old woman presented to the local emergency department with hypotension after a pedestrian accident. After resuscitation, CVC was inserted into her right subclavian vein and fluid was administered well before computed tomography (CT) enhancement. Contrast-enhanced CT scan showed a large amount of extravasation of contrast material and fluid collection in the thoracic and pericardial cavities which was not shown in non-enhanced CT scan. During operation, vascular perforation was found in right subclavian vein. This case highlights that emergency physicians must keep in mind the possibility of vessel injury after CVC insertion and contrast material is preferably injected via peripheral IV access.

A Randomised, Cross over Study Using a Mannequin Model to Evaluate the Effects on CPR Quality of Real-Time Audio-Visual Feedback Provided by a Smartphone Application

Objective

To evaluate the effect of real time feedback provided by smartphone application on cardiopulmonary resuscitation (CPR) performance.

Methods

Participants were randomised in two groups based on whether chest compression with or without the assistance of the smartphone application. Both groups performed hands-only CPR on a mannequin for 4 minutes. Data on CPR performance of both groups was compared. To assess the reliability the feedback value, we compared the CPR data from Skillmeter and data from smartphone. A questionnaire survey to participants about the usefulness of the application was also evaluated.

Results

Twenty-one subjects were recruited for the study. We found no significant difference in mean chest compression rate (103.3±5.0/min vs. 107.1±1.7/min; p=0.133) and depth between the two groups (47.3 [39.3, 56.2] mm vs. 45.8 [40.3, 49.9] mm; p=0.085). The proportion of adequate compression depth over the total compression was significantly higher in the group using the smartphone (38.1% vs. 22.2%; p=0.034). The CPR data displayed on smartphone application in mannequin's chest was not different from Skillmeter software. The majority of the participants considered the application easy to use, but holding the smartphone during CPR hampered compression.

Conclusions

Real-time audio-visual feedback on CPR depth and rate using a smartphone application can help to maintain the adequate chest compression depth in prolonged CPR. A better method to hold the smartphone may maximise the feedback effect on CPR quality. (Hong Kong j.emerg.med. 2014;21:153-160)

The effect of low-volatile organic compounds, water-based paint on aggravation of allergic disease in schoolchildren

Whether indoor painting aggravates preexisting allergic diseases remains unclear. We aimed to evaluate the impact of new classroom painting on aggravation of asthma, allergic rhinitis (AR), and atopic dermatitis (AD) in children. Studied school was previously painted with conventional water-based paint 20 years ago and had natural ventilation system. We identified a total of 172 children aged 10-12 years with allergic diseases in 17 classrooms, which were allocated to newly painted rooms with low-volatile organic compounds (VOC), water-based paint, or existing rooms. After painting, there was no intervention or internal airflow to influence indoor air environment in both classrooms. We prospectively assessed the symptom severity and serious events of allergic diseases between both classrooms at baseline and after one and eight weeks after painting. At one and eight weeks, there were no significant changes in the Childhood Asthma Control Test scores, the fractional nitric oxide levels, lung function in asthmatic children in either classroom. There were also no significant changes in the severity score of AR or AD, or serious events in all allergic diseases. These findings suggest classroom painting with this new paint at the levels encountered in this study might not be a major aggravating factor for school-aged children with allergic diseases.

Abstract OT2-03-03: A randomized trial of 15 fraction vs 25 fraction pencil beam scanning proton radiotherapy after mastectomy in patients requiring regional nodal irradiation

Background: Post-mastectomy radiotherapy improves survival in women with node-positive breast cancer. Pencil beam scanning proton therapy is attractive due to potential to reduce the dose to the heart and lungs compared with traditional photon techniques while improving conformality and limiting skin dose compared with passively scanned proton therapy. The optimal dose and fractionation for pencil-beam scanning proton therapy remains unknown.

Trial Design: This is a multi-center open label phase II randomized controlled trial to determine the safety of 15 fraction vs 25 fraction pencil beam scanning proton radiotherapy after mastectomy in patients requiring regional nodal irradiation.

Eligibility Criteria: Patients ≥ 18 years with primary, non-inflammatory invasive breast cancer who have undergone mastectomy with or without immediate reconstruction and chest wall and regional nodal irradiation planned.

Aims: To determine whether the 24 month complication rate (defined as grade 3 or greater late adverse events, and unplanned surgical intervention in patients who undergo mastectomy with reconstruction) of 15 fraction chest wall and regional node pencil beam scanning proton radiotherapy is acceptable relative to 25 fraction chest wall and regional nodal pencil beam scanning proton radiotherapy and worthy of further investigation.

Statistical methods: The study is designed as a non-inferiority/superiority “hybrid” design using the approach of Freidlin et al. It is Using a one-sided type I error rate of 0.05 (corresponding equivalently to constructing a 1-sided 95% confidence limit), 72 evaluable patients will have 80% power to reject the null hypothesis that the 24-month complication rate in the experimental arm is higher than that of the control arm by more than 10% (i.e. rule out inferiority) under the alternative hypothesis that the complication rate in the experimental arm is 5% less than that of the control arm (i.e. superiority). However, the design will have only 41% power when the two treatment arms are equivalent (i.e. the complication rate is 10% for both arms).

Accrual: The study opened in June 2016. Five of a planned eighty-two patients have been accrued to date.

Citation Format: Mutter RW, Park SS, Hieken TJ, Vargas CE, Mei-Yin PC, Kathryn RJ, Hector VR, Kimberly CS, Elizabeth YS, Daniel VW. A randomized trial of 15 fraction vs 25 fraction pencil beam scanning proton radiotherapy after mastectomy in patients requiring regional nodal irradiation [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT2-03-03.

Temporal and spatial discordance of programmed cell death-ligand 1 expression and lymphocyte tumor infiltration between paired primary lesions and brain metastases in lung cancer

The tumor microenvironments of paired primary lung cancers and brain metastases are significantly different, such that many of the metastases lose PD-L1 expression, lymphocyte infiltration or both with greater discrepancies over time. The spatial and temporal heterogeneity of PD-L1 expression may limit its use as a tissue-based predictive biomarker in lung cancer.

Background

The dynamics of PD-L1 expression may limit its use as a tissue-based predictive biomarker. We sought to expand our understanding of the dynamics of PD-L1 expression and tumor-infiltrating lymphocytes (TILs) in patients with lung cancer-related brain metastases.

Experimental design

Paired primary lung cancers and brain metastases were identified and assessed for PD-L1 and CD3 expression by immunohistochemistry. Lesions with 5% or greater PD-L1 expression were considered positive. Agreement statistics and the χ² or Fisher's exact test were used for analysis.

Results

We analyzed 146 paired lesions from 73 cases. There was disagreement of tumor cell PD-L1 expression in 10 cases (14%, κ = 0.71), and disagreement of TIL PD-L1 expression in 19 cases (26%, κ = 0.38). Most paired lesions with discordant tumor cell expression of PD-L1 were obtained 6 or more months apart. When specimens were categorized using a proposed tumor microenvironment categorization scheme based on PD-L1 expression and TILs, there were significant changes in the classifications because many of the brain metastases lacked either PD-L1 expression, tumor lymphocyte infiltration or both even when they were present in the primary lung cancer specimens (P = 0.009).

Conclusions

We identified that there are significant differences between the tumor microenvironment of paired primary lung cancers and brain metastases. When physicians decide to treat patients with lung cancer with a PD-1 or PD-L1 inhibitor, they must do so in the context of the spatial and temporal heterogeneity of the tumor microenvironment.

Counseling services for Asian, Latino/a, and White American students: Initial severity, session attendance, and outcome

OBJECTIVE

The current study examined racial/ethnic differences in initial severity, session attendance, and counseling outcomes in a large and diverse sample of Asian American, Latino/a, and White student clients who utilized university counseling services between 2008 and 2012.

METHOD

We used archival data of 5,472 clients (62% female; M age = 23.1, SD = 4.3) who self-identified their race/ethnicity as being Asian American (38.9%), Latino/a (14.9%), or White (46.2%). Treatment engagement was measured by the number of counseling sessions attended; initial severity and treatment outcome were measured using the Outcome Questionnaire-45.

RESULTS

Asian American clients, particularly Chinese, Filipino/a, Korean, and Vietnamese Americans, had greater initial severity compared with White clients. Asian Indian, Korean, and Vietnamese American clients used significantly fewer sessions of counseling than White clients after controlling for initial severity. All racial/ethnic minority groups continued to have clinically significant distress in certain areas (e.g., social role functioning) at counseling termination.

CONCLUSIONS

These findings highlight the need to devote greater attention to the counseling experiences of racial/ethnic minority clients, especially certain Asian American groups. Further research directions are provided. (PsycINFO Database Record

Effect of inhalers on the development of haemoptysis in patients with non-cystic fibrosis bronchiectasis

BACKGROUND

The association of inhaler use with haemoptysis has rarely been reported in patients with non-cystic fibrosis (CF) bronchiectasis.

OBJECTIVE

To elucidate the effect of inhaler use on the development of haemoptysis in patients with non-CF bronchiectasis.

METHODS

In a case-crossover study of 192 non-CF bronchiectasis patients with a history of haemoptysis and inhaler use, the risk of haemoptysis associated with the use of inhalers was elucidated. Two inhaled corticosteroids/long-acting β₂-agonists (ICS/LABA), one long-acting muscarinic antagonist and one short-acting β₂-agonist (SABA) were evaluated. The case and control periods were defined respectively as 030 and 180210 days before haemoptysis.

RESULTS

The risk of haemoptysis during the case period was 3.51 times higher than during the control period with any use of inhalers (95%CI 1.966.28). The results of clinically significant haemoptysis showed good agreement with those of total events. These associations were consistent with the sensitivity analyses. In the sub-analysis according to inhaler type, ICS/LABA and SABA were significantly associated with an increased risk of haemoptysis (aOR 2.62, 95%CI 1.255.45; aOR 2.51, 95%CI 2.235.15).

CONCLUSIONS

In patients with non-CF bronchiectasis, the use of inhalers, especially including 2-agonist, was associated with an increased risk of haemoptysis.

Disseminated mucormycosis with myocardial involvement in a renal transplant recipient

We report the case of a renal transplant recipient with pulmonary and splenic mucormycosis whose demise was accelerated by a myocardial abscess. Once pulmonary and splenic mucormycosis was diagnosed, liposomal amphotericin B was started and immunosuppressant treatments were discontinued. The pulmonary cavities regressed during treatment, but new myocardial and peri-allograft abscesses developed. The myocardial abscess diffusely infiltrated the left ventricular wall and was associated with akinesia, which led to sudden cardiac arrest. This case demonstrates a rare manifestation of mucormycosis and highlights the fatality and invasiveness of this infection.

Clinical applications of next-generation sequencing-based gene panel in patients with muscular dystrophy: Korean experience

Muscular dystrophy (MD) is a genetically and clinically heterogeneous group of disorders. Here, we performed targeted sequencing of 18 limb-girdle MD (LGMD)-related genes in 35 patients who were highly suspected of having MD. We identified one or more pathogenic variants in 23 of 35 patients (65.7%), and a genetic diagnosis was performed in 20 patients (57.1%). LGMD2B was the most common LGMD type, followed by LGMD1B, LGMD2A, and LGMD2G. Among the three major LGMD types in this group, LGMD1B was correlated with the lowest creatine kinase (CK) levels and the earliest onset, whereas LGMD2B was correlated with the highest CK levels and the latest onset. Thus, next-generation sequencing-based gene panels can be a helpful tool for the diagnosis of MDs, particularly in young children and those displaying atypical symptoms.

Abstract P4-04-12: Both metabolic syndrome and statin use are more common in women with breast inflammation

Background: Metabolic syndrome is associated with increased breast cancer (BC) risk. After menopause, obesity is associated with increased risk of hormone receptor (HR)-positive breast cancer. We demonstrated an obesity → inflammation → aromatase axis in breast white adipose tissue (WAT) where inflammation is defined by the presence of crown-like structures (CLS) consisting of a dead or dying adipocyte encircled by macrophages. CLS in the breast (CLS-B) are associated with elevated body mass index (BMI), postmenopausal status, increased adipocyte size, and increased tissue levels of proinflammatory mediators and aromatase. As obesity is a component of the metabolic syndrome and is associated with inflammation, we compared levels of relevant circulating factors in women with and without breast WAT inflammation.

Methods: We prospectively collected paired WAT and fasting serum and plasma from women undergoing mastectomy at MSKCC. WAT inflammation was detected by CD68 immunohistochemistry to identify CLS-B by light microscopy. Plasma levels of glucose, insulin, hsCRP, leptin, adiponectin, and IL-6 were measured by ELISA. Serum levels of total cholesterol, triglycerides (TG), HDL and LDL cholesterol were determined. Insulin resistance (IR) was assessed using fasting plasma glucose and insulin levels via the updated Homeostasis Model Assessment (HOMA2-IR). Associations between CLS-B and clinicopathologic features, including medication usage, were analyzed by logistic regression and Fisher’s exact test. Differences in serum/plasma endpoints between subjects with and without CLS-B were evaluated using Student t-test and nonparametric Wilcoxon rank-sum test.

Results: From 11/2011 – 3/2013 we accrued 100 patients (pts); median age 47 years (range 27 – 70). Overall, CLS-B were found in 52/100 (52%) pts: 18/19 (95%) obese pts, 17/33 (52%) overweight pts, and 17/48 (35%) normal BMI pts. A clinical diagnosis of dyslipidemia was present in 14/52 (27%) pts with CLS-B and 1/48 (2%) pts without CLS-B (P&lt;0.001). CLS-B were found in 10/11 (91%) statin users, but in only 42/89 (47%) non-users (P=0.008). Fasting glucose, insulin, LDL, TG, leptin, hsCRP, and IL-6 levels were higher in pts with CLS-B (Table). HOMA2-IR was greater in pts with CLS-B (mean 0.63 ±0.34) versus those without CLS-B (mean 0.46 ±0.23; P=0.006).

Fasting level, mean (SD)No CLS-B, N=48CLS-B +, N=52PGlucose, mg/dL73.2 (8.0)84.3 (37.6)0.04Insulin, mU/L4.3 (2.1)5.6 (2.9)0.01LDL cholesterol, mg/dL105.9 (31.0)119.4 (32.4)0.04HDL cholesterol, mg/dL71.9 (15.8)62.1 (16.1)0.003Triglycerides, mg/dL69.2 (26.3)104.9 (50.6)&lt;0.001Leptin, pg/mL12.0 (10.1)22.6 (19.7)&lt;0.001Adiponectin, ng/mL13.7 (5.2)10.4 (5.4)0.002hsCRP, ng/mL1.0 (1.4)2.3 (2.7)0.003

Conclusions: Breast WAT inflammation, which we have previously linked to increased aromatase activity, is associated with biochemical changes that occur in the metabolic syndrome, a risk factor for BC. Statin use is more common in patients with breast WAT inflammation and metabolic syndrome. Clinically, statin use may be a surrogate identifier of a population that is at increased baseline risk of BC. These findings may account for the variability in results of prior studies examining statin use and breast cancer risk due to elevated risk in users compared to non-users.

Citation Format: Neil M Iyengar, Ayca Gucalp, Xi K Zhou, Louise R Howe, Patrick G Morris, Dilip Giri, Kotha Subbaramaiah, Priya Bhardwaj, Samuel S Park, Michael Pollak, Monica Morrow, Clifford A Hudis, Andrew J Dannenberg. Both metabolic syndrome and statin use are more common in women with breast inflammation [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-04-12.

Unintentional secondary exogenous corticosteroid exposure and central serous chorioretinopathy

PURPOSE

The purpose of this study is to describe a possible association between unintentional secondary exogenous corticosteroid exposure and central serous chorioretinpathy (CSCR).

METHODS

A retrospective review of three patients diagnosed with CSCR in one or both eyes and a history of possible unintentional secondary corticosteroid exposure. Clinical history, exam findings, optical coherence tomography, fluorescein angiography, and clinical course were reviewed.

RESULTS

Three patients, who did not use corticosteroids, reported suspected unintentional secondary corticosteroid exposure from living with family members or partners using dermatologic corticosteroid cream and/or inhalers frequently. Two of the three patients had a history of recurrent CSCR, one patient involving both eyes. After taking precautions to avoid secondary corticosteroid exposure, all three patients had complete resolution of CSCR without further recurrence during follow-up ranging from 2 to 4 years.

CONCLUSIONS

Patients with CSCR should be queried for both primary and possible unintentional secondary routes of corticosteroid exposure, which may contribute to this condition.

Wound infections and healing: are they contributing factors for carcinogenesis?

The link between inflammation and tumourisation has long been considered as a key event in clinical cancer development. Inflammation and inflammatory diseases can be caused by many factors including infectious agents, altered genetics and various degrees of injuries from simple cuts to traumatic wounds, such as those suffered in battlefield. Improved management of all wound types is critical in protecting affected individuals against the development of tumourisation cues, which may potentially lead to cancer development. There have been numerous studies on the mechanism of inflammation-induced tumourisation. Thus, in this mini review, we summarised evidence demonstrating the potential link between infectious agents and their moonlight proteins, wounding, trauma, overactive repair mechanisms, and carcinogenesis.

Identification of novel mutations in the VPS33B gene involved in arthrogryposis, renal dysfunction, and cholestasis syndrome

Arthrogryposis, renal dysfunction, and cholestasis (ARC) syndrome is an autosomal recessive disorder caused by mutations in the VPS33B and VIPAS39. Here, we report novel mutations identified in four patients with ARC syndrome. We analyzed the entire coding regions of the VPS33B and VIPAS39 genes by direct sequencing. To detect novel splice site mutations, mRNA transcripts were analyzed by reverse transcription-polymerase chain reaction (RT-PCR) and sequencing. All four patients had compound heterozygous variants in the VPS33B gene. One patient had a previously reported splice site variant with unknown significance, c.239+5G>A, and a novel nonsense mutation, c.621G>A. The other three patients had the c.403+2T>A mutation, and each of them carried one of the splice site variants, c.239+5G>A or c.499-11G>A. c.239+5G>A and c.499-11G>A created novel splice sites which resulted in abnormal transcripts. No significant VIPAS39 mutation was detected in all patients. In patients suspected with ARC syndrome, mutation analysis of the VPS33B gene should be employed as a primary diagnostic test before performing invasive testing procedures such as organ biopsies. Performing mRNA analysis can be useful in predicting the pathogenic phenotype when the mutation seems to affect a normal splicing mechanism.

Effects of combination of rice straw with alfalfa pellet on milk productivity and chewing activity in lactating dairy cows

An experiment was conducted to determine the effects of diets containing coarse-texture rice straw and small particle size alfalfa pellets as a part of total mixed ration (TMR) on milk productivity and chewing activity in lactating dairy cows. Sixteen multiparous Holstein dairy cows (670±21 kg body weight) in mid-lactation (194.1±13.6 days in milk) were randomly assigned to TMR containing 50% of timothy hay (TH) or TMR containing 20% of rice straw and 30% of alfalfa pellet mixture (RSAP). Geometric mean lengths of TH and RSAP were found to be 5.8 and 3.6, respectively. Dry matter intake, milk yield and milk composition were measured. Moreover, eating and ruminating times were recorded continuously using infrared digital camcorders. Milk yield and milk composition were not detected to have significant differences between TH and RSAP. Dry matter intake (DMI) did not significantly differ for cows fed with TH or RSAP. Although particle size of TH was larger than RSAP, eating, ruminating and total chewing time (min/d or min/kg of DMI) on TH and RSAP were similar. Taken together, our results suggest that using a proper amount of coarse-texture rice straw with high value nutritive alfalfa pellets may stimulate chewing activity in dairy cows without decreasing milk yield and composition even though the quantity of rice straw was 40% of TH.

Systematic review and meta-analysis of robotic surgery compared with conventional laparoscopic and open resections for gastric carcinoma

BACKGROUND

Robot-assisted gastrectomy (RAG) has been developed in the hope of improving surgical quality and overcoming the limitations of conventional laparoscopically assisted gastrectomy (LAG) and open gastrectomy (OG) for gastric cancer. The aim of this study was to determine the extent of evidence in support of these ideals.

METHODS

A systematic review of the three operation types (RAG, LAG and OG) was carried out to evaluate short-term outcomes including duration of operation, retrieved lymph nodes, estimated blood loss, resection margin status, technical postoperative complications and hospital stay.

RESULTS

Nine non-randomized observational clinical studies involving 7200 patients satisfied the eligibility criteria. RAG was associated with longer operating times than LAG and OG (weighted mean difference 61.99 and 65.73 min respectively; P ≤ 0.001). The number of retrieved lymph nodes and the resection margin length in RAG were comparable with those of LAG and OG. Estimated blood loss as significantly less in RAG than in OG (P = 0.002), but not LAG. Mean hospital stay for RAG was similar to that for LAG (P = 0.14). In contrast, hospital stay was significantly shorter, by a mean of 2.18 days, for RAG compared with OG (P < 0.001). Postoperative complications were similar for all three operative approaches.

CONCLUSION

Short-term oncological outcomes of RAG were comparable with those of the other approaches. LAG was a shorter procedure and less expensive than RAG. Future studies involving RAG should focus on minimizing duration of operation and reducing cost.

Germline mutations and genotype-phenotype correlations in patients with apparently sporadic pheochromocytoma/paraganglioma in Korea

The aim of our study was to assess the frequency of germline mutations and develop the genetic testing strategy in patients with apparently sporadic pheochromocytoma/paraganglioma (PPGL) in Korea. We included 53 patients diagnosed with non-syndromic PPGL without a family history of PPGLs in three referral centers from 2004 to 2011. Succinate dehydrogenase complex B (SDHB), SDHD, Von Hippel-Lindau (VHL), and rearranged during transfection (RET) genes were examined by direct sequencing and multiple ligation-dependent probe amplification. The study patients were composed of 26 men and 27 women, and mean age was 50.1 ± 13.5 years. The frequency of germline mutations was 13.2% (7/53): RET (n = 2), VHL (n = 1), SDHB (n = 2), and SDHD (n = 2). Six of seven mutation carriers were diagnosed before the age of 50. One of two patients harboring an SDHB mutation had malignant PPGLs. One patient with multifocal head and neck paraganglioma (PGL) and pheochromocytoma (PHEO) carried a SDHD mutation. The carriers of germline mutations in patients with apparently sporadic PPGL were 13.2% in our study. We recommend genetic testing in patients below 50 years and SDHD genetic testing in patients with multifocal PPGLs. In malignant PPGLs, SDHB genetic testing may be performed.

Enhancement of the stabilization in white organic light-emitting diodes utilizing a color conversion layer containing CdSe/ZnS quantum dots

White organic light emitting diodes (WOLEDs) were fabricated utilizing blue emitting organic light emitting diodes and color conversion layers containing CdSe/ZnS quantum dots (QDs). The best color purity of the WOLEDs was achieved by using the red and green QDs ratio of 1:9.5. Commission Internationale de l'Eclairage coordinates of the WOLEDs slightly shifted from (0.35, 0.33) to (0.35, 0.32) with increasing applied voltage from 9 to 14 V, indicative of a deep stabilized white color. Color tunable mechanisms of WOLEDs with a color conversion layer containing CdSe/ZnS QDs are described on the basis of the experimental results.

Total artificial heart in the pediatric patient with biventricular heart failure

Mechanical circulatory support emerged for the pediatric population in the late 1980s as a bridge to cardiac transplantation. The Total Artificial Heart (TAH-t) (SynCardia Systems Inc., Tuscon, AZ) has been approved for compassionate use by the Food and Drug Administration for patients with end-stage biventricular heart failure as a bridge to heart transplantation since 1985 and has had FDA approval since 2004. However, of the 1,061 patients placed on the TAH-t, only 21 (2%) were under the age 18. SynCardia Systems, Inc. recommends a minimum patient body surface area (BSA) of 1.7 m(2), thus, limiting pediatric application of this device. This unique case report shares this pediatric institution's first experience with the TAH-t. A 14-year-old male was admitted with dilated cardiomyopathy and severe biventricular heart failure. The patient rapidly decompensated, requiring extracorporeal life support. An echocardiogram revealed severe biventricular dysfunction and diffuse clot formation in the left ventricle and outflow tract. The decision was made to transition to biventricular assist device. The biventricular failure and clot formation helped guide the team to the TAH-t, in spite of a BSA (1.5 m(2)) below the recommendation of 1.7 m(2). A computed tomography (CT) scan of the thorax, in conjunction with a novel three-dimensional (3D) modeling system and team, assisted in determining appropriate fit. Chest CT and 3D modeling following implantation were utilized to determine all major vascular structures were unobstructed and the bronchi were open. The virtual 3D model confirmed appropriate device fit with no evidence of compression to the left pulmonary veins. The postoperative course was complicated by a left lung opacification. The left lung anomalies proved to be atelectasis and improved with aggressive recruitment maneuvers. The patient was supported for 11 days prior to transplantation. Chest CT and 3D modeling were crucial in assessing whether the device would fit, as well as postoperative complications in this smaller pediatric patient.

The failing Fontan: what’s NEXT…?

The Fontan procedure represents the final stage of the transition to single ventricle physiology. Conversion of very complex congenital heart anatomy, such as hypoplastic left heart syndrome, double-outlet right ventricle or double-inlet left ventricle, to a single ventricle has grown in popularity as morbidity and mortality have improved. As these patients grow, survivors are at risk for impaired ventricular dysfunction, plastic bronchitis, protein-losing enteropathy and late failure. Late failing Fontan patients represent a particularly vexing scenario for clinicians, as the only durable treatment option is cardiac transplantation. However, in the short-term, some of these patients require support beyond medical management, with mechanical circulatory support via extracorporeal life support or a ventricular assist device. We report the successful bridge of an adolescent female post-Fontan conversion with late severe cardiac failure. The patient was initially resuscitated with extracorporeal life support, transitioned to a single Berlin Heart EXCOR® ventricular assist device and, subsequently, underwent successful cardiac transplantation.

Diagnostic accuracy of Xpert® MTB/RIF on bronchoscopy specimens in patients with suspected pulmonary tuberculosis

OBJECTIVE

To determine the diagnostic accuracy of the Xpert® MTB/RIF assay using samples obtained through bronchoscopy in patients with suspected pulmonary tuberculosis (PTB).

DESIGN

We retrospectively reviewed the records of patients with suspected PTB for whom the Xpert MTB/RIF assay was performed on bronchoscopy specimens. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) for the diagnosis of active PTB were calculated for acid-fast bacilli (AFB) smear microscopy and the Xpert assay using culture of Mycobacterium tuberculosis from sputum or bronchoscopy specimens as a reference standard.

RESULTS

A total of 132 patients were included in the final analysis. Of these, 38 had culture-confirmed PTB. The sensitivity of the Xpert assay using bronchial washing or bronchoalveolar lavage (BAL) fluid for the diagnosis of PTB was 81.6%, and specificity was 100%. The PPV and NPV were 100% and 92.1%, respectively. The sensitivity and specificity of AFB smear microscopy were respectively 13.2% and 98.8%.

CONCLUSION

The Xpert assay on bronchoscopy specimens provided an accurate diagnosis of PTB in patients who had a negative AFB smear or who could not produce sputum.

Transcriptome correlation analysis identifies two unique craniosynostosis subtypes associated with IRS1 activation

The discovery of causal mechanisms associated with nonsyndromic craniosynostosis has proven to be a difficult task due to the complex nature of the disease. In this study, differential transcriptome correlation analysis was used to identify two molecularly distinct subtypes of nonsyndromic craniosynostosis, termed subtype A and subtype B. In addition to unique correlation structure, subtype A was also associated with high IGF pathway expression, whereas subtype B was associated with high integrin expression. To identify a pathologic link between altered gene correlation/expression and the disease state, phosphorylation assays were performed on primary osteoblast cell lines derived from cases within subtype A or subtype B, as well as on primary osteoblast cell lines with novel IGF1R variants previously reported by our lab (Cunningham ML, Horst JA, Rieder MJ, Hing AV, Stanaway IB, Park SS, Samudrala R, Speltz ML. Am J Med Genet A 155A: 91-97, 2011). Elevated IRS1 (pan-tyr) and GSK3β (ser-9) phosphorylation were observed in two novel IGF1R variants with receptor L domain mutations. In subtype A, a hypomineralization phenotype coupled with decreased phosphorylation of IRS1 (ser-312), p38 (thr-180/tyr-182), and p70S6K (thr-412) was observed. In subtype B, decreased phosphorylation of IRS1 (ser-312) as well as increased phosphorylation of Akt (ser-473), GSK3β (ser-9), IGF1R (tyr-1135/tyr-1136), JNK (thr-183/tyr-187), p70S6K (thr-412), and pRPS6 (ser-235/ser-236) was observed, thus implicating the activation of IRS1-mediated Akt signaling in potentiating craniosynostosis in this subtype. Taken together, these results suggest that despite the stimulation of different pathways, activating phosphorylation patterns for IRS1 were consistent in cell lines from both subtypes and the IGF1R variants, thus implicating a key role for IRS1 in the pathogenesis of nonsyndromic craniosynostosis.

The Xpert® MTB/RIF assay evaluation in South Korea, a country with an intermediate tuberculosis burden

SETTING

A central hospital laboratory in South Korea.

OBJECTIVE

To evaluate the usefulness of the Xpert® MTB/RIF assay in a country with an intermediate tuberculosis burden.

DESIGN

A total of 71 real-time polymerase chain reaction-positive sputum sediments were tested within 24 h by the Xpert MTB/RIF assay. Mycobacterium tuberculosis detection was compared with smear microscopy and culture. Rifampicin (RMP) resistance was compared with a culture-based method and rpoB gene sequencing. We also assessed the limit of detection for mutant proportions and time savings in diagnosis.

RESULTS

The Xpert MTB/RIF assay detected M. tuberculosis in 71 (100%) specimens (32 smear-positive, 39 smear-negative). This assay showed 100% (62/62) concordance with drug resistance confirmed by culture and 98.4% (61/62) concordance with sequencing. A specimen containing approximately 50% of mutant p.His526Tyr was falsely interpreted as wild-type bacilli by this assay. The minimal detection ratio was 5:1 of mutant vs. wild-type cells. The median time saved was 18.5 days (range 9-30) for the diagnosis of M. tuberculosis and 81.5 days (65-136) for RMP susceptibility in smear-negative, culture-positive patients.

CONCLUSIONS

The Xpert MTB/RIF assay showed high sensitivity in detecting M. tuberculosis with information on RMP resistance, and had a more rapid time to diagnosis compared to conventional tests; however, the location and amount of mutation may affect test sensitivity.

Paradoxical response in HIV-negative patients with pleural tuberculosis: a retrospective multicentre study

OBJECTIVE

To evaluate the incidence, clinical characteristics and predicting factors for the development of paradoxical response in human immunodeficiency virus negative patients with isolated pleural tuberculosis (TB).

DESIGN

A multicentre, retrospective cohort study including 458 patients who were diagnosed and treated with isolated pleural TB between March 2005 and February 2010.

RESULTS

Paradoxical response developed in 72 patients (16%) with isolated pleural TB. The mean time to development of paradoxical response was 8.8 ± 6.4 weeks after initiation of anti-tuberculosis treatment. The main presentation of paradoxical response was aggravation of pre-existing pleural effusion in 58 patients (81%). However, the majority of the patients who developed paradoxical response had no associated symptoms (n = 49, 68%). In multiple logistic regression analysis, development of paradoxical response was independently associated with the proportion of eosinophils (adjusted OR 1.293, 95%CI 1.077-1.553) and protein concentrations (adjusted OR 0.590, 95%CI 0.397-0.878) in the pleural fluid at the time of diagnosis.

CONCLUSION

Paradoxical response developed in 16% of the patients approximately 2 months after initiation of anti-tuberculosis treatment, presenting with aggravation of pre-existing pleural effusion. Development of paradoxical response was associated with the proportion of eosinophils and protein concentrations in the pleural fluid at the time of diagnosis.

Prediction of atomic force microscope probe dynamics through the receptance coupling method

The increased growth in the use of tip-based sensing, manipulations, and fabrication of devices in atomic force microscopy (AFM) necessitates the accurate prediction of the dynamic behavior of the AFM probe. The chip holder, to which the micro-sensing device is attached, and the rest of the AFM system can affect the overall dynamics of the probe. In order to consider these boundary effects, we propose a novel receptance coupling method to mathematically combine the dynamics of the AFM setup and probe, based on the equilibrium and compatibility conditions at the joint. Once the frequency response functions of displacement over force at the tool tip are obtained, the dynamic interaction forces between the tip and the sample in nanoscale can be determined by measuring the probe tip displacement.

Distal metatarsal osteotomy for hallux varus following surgery for hallux valgus

We reviewed the outcome of distal chevron metatarsal osteotomy without tendon transfer in 19 consecutive patients (19 feet) with a hallux varus deformity following surgery for hallux valgus. All patients underwent distal chevron metatarsal osteotomy with medial displacement and a medial closing wedge osteotomy along with a medial capsular release. The mean hallux valgus angle improved from -11.6° pre-operatively to 4.7° postoperatively, the mean first-second intermetatarsal angle improved from -0.3° to 3.3° and the distal metatarsal articular angle from 9.5° to 2.3° and the first metatarsophalangeal joints became congruent post-operatively in all 19 feet. The mean relative length ratio of the metatarsus decreased from 1.01 to 0.99 and the mean American Orthopaedic Foot and Ankle Society score improved from 77 to 95 points. In two patients the hallux varus recurred. One was symptom-free but the other remained symptomatic after a repeat distal chevron osteotomy. There were no other complications. We consider that distal chevron metatarsal osteotomy with a medial wedge osteotomy and medial capsular release is a useful procedure for the correction of hallux varus after surgery for hallux valgus.

A case of systemic polyarteritis nodosa involving bronchial artery

Polyarteritis nodosa (PAN) is a systemic necrotizing vasculitis involving predominantly medium-sized muscular arteries. It commonly involves skin, kidney, cardiovascular system, gastrointestinal system, and neurological system. But bronchial artery involvement of PAN is rarely identified. We report a case of PAN with initial presentation of hemoptysis. On admission, chest radiograph and chest CT angiography revealed no focus of bleeding. Angiography showed a bronchial artery aneurysm and multiple arterial aneurysms in both renal, hepatic, mesenteric and branches of small bowel arteries. These findings were compatible with the diagnosis of PAN. The patient was started on steroid and cyclophosphamide.