Multiplexed immunofluorescence identifies high stromal CD68+PD‑L1+ macrophages as a predictor of improved survival in triple negative breast cancer

Triple negative breast cancer (TNBC) comprises 10–15% of all breast cancers and has a poor prognosis with a high risk of recurrence within 5 years. PD-L1 is an important biomarker for patient selection for immunotherapy but its cellular expression and co-localization within the tumour immune microenvironment and associated prognostic value is not well defined. We aimed to characterise the phenotypes of immune cells expressing PD-L1 and determine their association with overall survival (OS) and breast cancer-specific survival (BCSS). Using tissue microarrays from a retrospective cohort of TNBC patients from St George Hospital, Sydney (n = 244), multiplexed immunofluorescence (mIF) was used to assess staining for CD3, CD8, CD20, CD68, PD-1, PD-L1, FOXP3 and pan-cytokeratin on the Vectra Polaris™ platform and analysed using QuPath. Cox multivariate analyses showed high CD68+PD-L1+ stromal cell counts were associated with improved prognosis for OS (HR 0.56, 95% CI 0.33–0.95, p = 0.030) and BCSS (HR 0.47, 95% CI 0.25–0.88, p = 0.018) in the whole cohort and in patients receiving chemotherapy, improving incrementally upon the predictive value of PD-L1+ alone for BCSS. These data suggest that CD68+PD-L1+ status can provide clinically useful prognostic information to identify sub-groups of patients with good or poor prognosis and guide treatment decisions in TNBC

Comparison of Clinician Suspicion Versus a Clinical Prediction Rule in Identifying Children at Risk for Intra‐abdominal Injuries After Blunt Torso Trauma

ObjectivesEmergency department (ED) identification and radiographic evaluation of children with intra‐abdominal injuries who need acute intervention can be challenging. To date, it is unclear if a clinical prediction rule is superior to unstructured clinician judgment in identifying these children. The objective of this study was to compare the test characteristics of clinician suspicion with a derived clinical prediction rule to identify children at risk of intra‐abdominal injuries undergoing acute intervention following blunt torso trauma.MethodsThis was a planned subanalysis of a prospective, multicenter observational study of children (50% prior to knowledge of abdominal computed tomography (CT) scanning (if performed). Intra‐abdominal injuries undergoing acute intervention were defined by a therapeutic laparotomy, angiographic embolization, blood transfusion for abdominal hemorrhage, or intravenous fluid administration for 2 or more days in those with pancreatic or gastrointestinal injuries. Patients were considered to be positive for clinician suspicion if suspicion was documented as ≥1%. Suspicion ≥ 1% was compared to the presence of any variable in the prediction rule for identifying children with intra‐abdominal injuries undergoing acute intervention.ResultsClinicians recorded their suspicion in 11,919 (99%) of 12,044 patients enrolled in the parent study. Intra‐abdominal injuries undergoing acute intervention were diagnosed in 203 (2%) patients. Abdominal CT scans were obtained in the ED in 2,302 of the 2,667 (86%, 95% confidence interval [CI] = 85% to 88%) enrolled patients with clinician suspicion ≥1% and in 3,016 of the 9,252 (33%, 95% CI = 32% to 34%) patients with clinician suspicion  50% previamente a conocer la tomografía computarizada (TC) abdominal (si fue realizada). La LIA con necesidad de intervención urgente se definió como laparotomía terapéutica, embolización angiográfica, transfusión de sangre por hemorragia intrabdominal o administración de fluidos intravenosos durante 2 o más días en aquéllos con lesiones pancreáticas o gastrointestinales. Los pacientes se consideraron positivos para la sospecha clínica si la sospecha se documentó como ≥1%. La sospecha > 1% se comparó con la presencia de cualquier variable en la regla de predicción para la identificación de niños con LIA con necesidad de una intervención urgente.ResultadosLos clínicos documentaron su sospecha en 11.919 (99%) de los 12.044 pacientes incluidos en el estudio original. La LIA con necesidad de intervención urgente se diagnosticó en 203 (2%) pacientes. Las TC abdominales se obtuvieron en el SU en 2.302 de los 2.667 pacientes (86%, IC95% = 85% a 88%) incluidos con sospecha clínica ≥1%; y en 3.016 de los 9.252 pacientes (33%, IC95% = 32% a 34%) con sospecha clínica < 1%. La sensibilidad de la regla de predicción para LIA con necesidad de intervención aguda fue mayor que la sospecha clínica ≥1% (197 de 203, 97,0%, IC95% = 93,7% a 98,9%, frente a 168 de 203, 82,8%, IC95% = 76,9% a 87,7%, respectivamente; diferencia de 14,2%, IC95% = 8,6% a 20,0%). La especificidad de la regla de predicción, sin embargo, fue menor que la sospecha clínica (4,979 de los 11.716, 42,5%, IC95% = 41,6% a 43,4%, frente a 9,217 de los 11.716, 78,7%, IC95% = 77,9% a 79,4%, respectivamente; diferencia de –36,2%, IC95% = –37,3% a –35,0%). Treinta y cinco de los pacientes con sospecha clínica < 1% (0,4%, IC95% = 0,3% a 0,5%) tuvieron LIA con necesidad de intervención urgente.ConclusionesLa regla de predicción clínica derivada tuvo una sensibilidad mayor de forma significativa, pero menor especificidad que la sospecha clínica para la identificación de niños con necesidad de una intervención urgente. La mayor especificidad de la sospecha clínica, sin embargo, no se tradujo en la práctica clínica, ya que los clínicos obtuvieron más frecuentemente TC abdominales en los pacientes que consideraron de muy bajo riesgo. Si se validase, esta regla de predicción puede ayudar en la toma de decisiones clínicas sobre el uso de TC abdominal en los niños con traumatismo torácico cerrado.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/113736/1/acem12739.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/113736/2/acem12739_am.pd

Occult Pneumothoraces in Children With Blunt Torso Trauma

Objectives Plain chest x‐ray (CXR) is often the initial screening test to identify pneumothoraces in trauma patients. Computed tomography (CT) scans can identify pneumothoraces not seen on CXR (“occult pneumothoraces”), but the clinical importance of these radiographically occult pneumothoraces in children is not well understood. The objectives of this study were to determine the proportion of occult pneumothoraces in injured children and the rate of treatment with tube thoracostomy among these children. Methods This was a planned substudy from a large prospective multicenter observational cohort study of children younger than 18 years old evaluated in emergency departments (EDs) in the Pediatric Emergency Care Applied Research Network (PECARN) for blunt torso trauma from May 2007 to January 2010. Children with CXRs as part of their trauma evaluations were included for analysis. The faculty radiologist interpretations of the CXRs and any subsequent imaging studies, including CT scans, were reviewed for the absence or presence of pneumothoraces. An “occult pneumothorax” was defined as a pneumothorax that was not identified on CXR, but was subsequently demonstrated on cervical, chest, or abdominal CT scan. Rates of pneumothoraces and placement of tube thoracostomies and rate differences with 95% confidence intervals (CIs) were calculated. Results Of 12,044 enrolled in the parent study, 8,020 (67%) children (median age = 11.3 years, interquartile range [IQR] = 5.3 to 15.2 years) underwent CXRs in the ED, and these children make up the study population. Among these children, 4,276 had abdominal CT scans performed within 24 hours. A total of 372 of 8,020 children (4.6%; 95% CI = 4.2% to 5.1%) had pneumothoraces identified by CXR and/or CT. The CXRs visualized pneumothoraces in 148 patients (1.8%; 95% CI = 1.6% to 2.2%), including one false‐positive pneumothorax, which was identified on CXR, but was not demonstrated on CT. Occult pneumothoraces were present in 224 of 372 (60.2%; 95% CI = 55.0% to 65.2%) children with pneumothoraces. Tube thoracostomies were performed in 85 of 148 (57.4%; 95% CI = 49.0% to 65.5%) children with pneumothoraces on CXR and in 35 of 224 (15.6%; 95% CI = 11.1% to 21.1%) children with occult pneumothoraces (rate difference = –41.8%; 95% CI = –50.8 to –32.3%). Conclusions In pediatric patients with blunt torso trauma, pneumothoraces are uncommon, and most are not identified on the ED CXR. Nearly half of pneumothoraces, and most occult pneumothoraces, are managed without tube thoracostomy. Observation, including in children requiring endotracheal intubation, should be strongly considered during the initial management of children with occult pneumothoraces. Resumen Objetivos La radiografía de tórax simple (RXT) es a menudo la prueba de despistaje inicial para identificar los neumotórax en los pacientes con traumatismo. La tomografía computarizada (TC) puede identificar neumotórax no vistos en la RXT (“neumotórax ocultos”), aunque la importancia clínica de estos neumotórax radiográficamente ocultos en los niños no está muy estudiada. Los objetivos de este estudio fueron determinar la proporción de neumotórax ocultos en los niños accidentados y el porcentaje de tratamiento con tubo de toracostomía en estos niños. Metodología Subestudio diseñado a partir de un gran estudio observacional de cohorte prospectivo multicéntrico de niños menores de 18 años atendidos en los servicios de urgencias (SU) de la Pediatric Emergency Care Applied Research Network (PECARN) que habían sido evaluados por traumatismo torácico cerrado de mayo de 2007 a enero de 2010. Se incluyeron en el análisis los niños en los que la RXT fue parte de la evaluación inicial del traumatismo. Las interpretaciones del radiólogo de las RXT y de cualquier estudio de imagen posterior, incluyendo a TC, se revisaron para la ausencia o presencia de neumotórax. Se definió “neumotórax oculto” como un neumotórax que no fue identificado en la RXT pero que fue posteriormente visualizado en la TC abdominal, torócica o cervical. Se calcularon los porcentajes de neumotórax e inserción de tubo de toracostomía y las diferencias de sus porcentajes con los intervalos de confianza (IC) al 95%. Resultados De los 12.044 incluidos en el estudio principal, se llevo a cabo una RXT en el SU en 8.020 (67%) niños (mediana de edad 11,3 años, rango intercuartílico 5,3 a 15,2), que constituyeron la población de estudio. De estos niños, 4.276 tuvieron una TC realizada en las primeras 24 horas. En 372 de los 8.020 niños (4,6%; IC 95% = 4,2% a 5,1%) se identificó un neumotórax en la RXT y/o la TC. La RXT mostró neumotórax en 148 pacientes (1,8%; IC 95% = 1,6% a 2,2%), incluyendo un falso positivo de neumotórax, que fue identificado en la RXT pero que no fue demostrado en la TC. Los neumotórax ocultos estuvieron presentes en 224 de los 372 niños con neumotórax (60,2%; IC 95% = 55,0% a 65,2%). Se insertaron tubos de toracostomía en 85 de los 148 niños con neumotórax en la RXT (57,4%; IC 95% = 49,0% a 65,5%), y en 35 de los 224 niños con neumotórax oculto (15,6%; IC 95% = 11,1% a 21,1%; diferencia de porcentajes ‐41,8%; IC 95% = ‐50,8 a ‐32,3%). Conclusiones En los pacientes pediátricos con traumatismo torácico cerrado, los neumotórax son poco frecuentes, y la mayoría no son identificados en la RXT en el SU. Casi la mitad de los neumotórax, y la mayoría de los neumotórax ocultos son manejados sin tubo de toracostomía. La observación, incluyendo en los niños que requieren intubación endotraqueal, debería ser especialmente considerada durante el manejo inicial de los niños con neumotórax ocultos.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106913/1/acem12344.pd

Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes

T lymphocytes utilize amoeboid migration to navigate effectively within complex microenvironments. The precise rearrangement of the actin cytoskeleton required for cellular forward propulsion is mediated by actin regulators, including the actin‐related protein 2/3 (Arp2/3) complex, a macromolecular machine that nucleates branched actin filaments at the leading edge. The consequences of modulating Arp2/3 activity on the biophysical properties of the actomyosin cortex and downstream T cell function are incompletely understood. We report that even a moderate decrease of Arp3 levels in T cells profoundly affects actin cortex integrity. Reduction in total F‐actin content leads to reduced cortical tension and disrupted lamellipodia formation. Instead, in Arp3‐knockdown cells, the motility mode is dominated by blebbing migration characterized by transient, balloon‐like protrusions at the leading edge. Although this migration mode seems to be compatible with interstitial migration in three‐dimensional environments, diminished locomotion kinetics and impaired cytotoxicity interfere with optimal T cell function. These findings define the importance of finely tuned, Arp2/3‐dependent mechanophysical membrane integrity in cytotoxic effector T lymphocyte activities

Challenges Enrolling Children Into Traumatic Brain Injury Trials: An Observational Study

ObjectivesIn preparation for a clinical trial of therapeutic agents for children with moderate‐to‐severe blunt traumatic brain injuries (TBIs) in emergency departments (EDs), we conducted this feasibility study to (1) determine the number and clinical characteristics of eligible children, (2) determine the timing of patient and guardian arrival to the ED, and (3) describe the heterogeneity of TBIs on computed tomography (CT) scans.MethodsWe conducted a prospective observational study at 16 EDs of children ≤ 18 years of age presenting with blunt head trauma and Glasgow Coma Scale scores of 3–12. We documented the number of potentially eligible patients, timing of patient and guardian arrival, patient demographics and clinical characteristics, severity of injuries, and cranial CT findings.ResultsWe enrolled 295 eligible children at the 16 sites over 6 consecutive months. Cardiac arrest and nonsurvivable injuries were the most common characteristics that would exclude patients from a future trial. Most children arrived within 2 hours of injury, but most guardians did not arrive until 2–3 hours after the injury. There was a substantial range in types of TBIs, with subdural hemorrhages being the most common.ConclusionEnrolling children with moderate‐to‐severe TBI into time‐sensitive clinical trials will require large numbers of sites and meticulous preparation and coordination and will prove challenging to obtain informed consent given the timing of patient and guardian arrival. The Federal Exception from Informed Consent for Emergency Research will be an important consideration for enrolling these children.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135996/1/acem13085_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135996/2/acem13085.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135996/3/acem13085-sup-0001-DataSupplementS1.pd

A New Isoform of the Histone Demethylase JMJD2A/KDM4A Is Required for Skeletal Muscle Differentiation

In proliferating myoblasts, muscle specific genes are silenced by epigenetic modifications at their promoters, including histone H3K9 methylation. Derepression of the promoter of the gene encoding the myogenic factor myogenin (Myog) is key for initiation of muscle differentiation. The mechanism of H3K9 demethylation at the Myog promoter is unclear, however. Here, we identify an isoform of the histone demethylase JMJD2A/KDM4A that lacks the N-terminal demethylase domain (ΔN-JMJD2A). The amount of ΔN-JMJD2A increases during differentiation of C2C12 myoblasts into myotubes. Genome-wide expression profiling and exon-specific siRNA knockdown indicate that, in contrast to the full-length protein, ΔN-JMJD2A is necessary for myotube formation and muscle-specific gene expression. Moreover, ΔN-JMJD2A promotes MyoD-induced conversion of NIH3T3 cells into muscle cells. ChIP-on-chip analysis indicates that ΔN-JMJD2A binds to genes mainly involved in transcriptional control and that this binding is linked to gene activation. ΔN-JMJD2A is recruited to the Myog promoter at the onset of differentiation. This binding is essential to promote the demethylation of H3K9me2 and H3K9me3. We conclude that induction of the ΔN-JMJD2A isoform is crucial for muscle differentiation: by directing the removal of repressive chromatin marks at the Myog promoter, it promotes transcriptional activation of the Myog gene and thus contributes to initiation of muscle-specific gene expression

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN