Safety and Adverse Events During Primary Care Paramedic Interfacility Transfer of Stable STEMI Patients

OBJECTIVE

Current guidelines recommend that patients presenting with ST-elevation myocardial infarction (STEMI) to hospitals not capable of performing primary percutaneous coronary intervention (PCI) be transferred to a PCI-capable hospital if reperfusion can be accomplished within 120 min. Most STEMI patients are accompanied by an advanced care paramedic (ACP, equivalent to EMT-P), nurse, or physician who can manage complications should they arise. In our region, stable STEMI patients are transported by primary care paramedics (PCPs, similar scope of practice to advanced EMT) in cases where a nurse, physician, or ACP paramedic is not available. Our goal was to describe adverse events and need for advanced interventions among initially stable STEMI patients during interfacility transfer by PCPs.

METHODS

We reviewed ambulance and hospital records of initially stable STEMI patients (as determined by first set of vital signs documented by paramedics) transferred to a PCI-capable hospital by PCPs between March 1, 2014, and December 31, 2019. We identified whether pre-determined adverse clinical events occurred during the transport as well as the potential need for advanced care interventions not within the PCP scope of practice. Adverse events upon arrival in the PCI lab were also identified.

RESULTS

Of 346 STEMI patients transferred, 179 met inclusion criteria. The mean age of included patients was 61 years (SD 12.1) and 74.9% (134/179) were male. Median transport interval was 36 min (IQR 3.0). During transport, 47/179 (26.0%) patients experienced pre-defined adverse events; for 16/47 (34%), one or more adverse events was major. Three patients met criteria for ACP interventions. One patient suffered a cardiac arrest and was promptly resuscitated with defibrillation by the PCPs.

CONCLUSIONS

We found PCP-interfacility transport of initially stable STEMI patients was safe and associated with a moderate proportion of adverse events, the majority of which did not require an advanced care intervention. These findings may help decision-making to avoid delays transferring stable patients to PCI-capable centers.

Preresidency research output among US neurological surgery residents

OBJECTIVE

Research productivity is often used to evaluate candidates for neurosurgery residency. Official annual reports describe the mean total number of research products of successful applicants for each match cycle; however, the average number of indexed publications, the highest-valued research product, is not reported separately from other research products. The primary objectives of this study were to describe the distribution of preresidency indexed publication quantity among successful neurosurgery applicants from 2017 to 2021 and determine whether any change in publication quantity across application cycles existed. Secondary objectives included determining the rate at which the average publication quantity is increasing across application cycles, whether this increase is driven by high-output applicants alone, and if a performance ceiling has been reached.

METHODS

US doctor of medicine seniors applying to the senior author's institution between 2017 and 2021 and who successfully matched into any US neurosurgery program were included. Publication quantities were extracted using Scopus. Additional variables were extracted from residency applications. Mean (SD) and median (IQR) publication quantities were used to describe the distribution and compare across years. Applicants were ranked by descending publication count and divided into quartiles. Averages within each quartile were compared with respective quartiles across years. Averages of the top 10% most productive applicants were compared across years to determine if a performance ceiling existed.

RESULTS

Overall, 93.2% of matched applicants were captured. The mean and median total numbers of publications for applicants who matched from 2017 to 2021 were 5.6 ± 8.3 and 3.0 (1.0, 7.0), respectively. The mean and median numbers of publications increased from 3.7 ± 5.3 and 2.0 (0.0, 5.0) in 2016-2017 to 8.1 ± 10.0 and 5.0 (2.0, 11.0) in 2020-2021 (p < 0.001). The distribution of publication quantity was right-skewed. Multivariable analysis determined the application year to be independently and positively correlated with publication quantity (β 1.07 [95% CI 0.71-1.42], p < 0.001). All quartiles observed an increased average number of publications across years (p < 0.001). The mean and median numbers for the top 10% increased from 15.8 ± 8.7 and 13.0 (10.8, 15.5) in 2016-2017, respectively, to 31.3 ± 16.0 and 25.0 (21.0, 35.5) in 2020-2021 (p < 0.001).

CONCLUSIONS

Indexed publications account for a small portion of the total research products that successful neurosurgery candidates list on applications. A high number of publications is not necessary for candidates to match, with approximately 50% of all applicants who successfully matched having ≤ 5 publications and 25% having ≤ 2 publications. The average preresidency publication quantity has been increasing yearly among neurosurgery applicants. This increase was present across the applicant pool. Additionally, no performance ceiling was observed.

Rare subclonal sequencing of breast cancers indicates putative metastatic driver mutations are predominately acquired after dissemination

BACKGROUND

Evolutionary models of breast cancer progression differ on the extent to which metastatic potential is pre-encoded within primary tumors. Although metastatic recurrences often harbor putative driver mutations that are not detected in their antecedent primary tumor using standard sequencing technologies, whether these mutations were acquired before or after dissemination remains unclear.

METHODS

To ascertain whether putative metastatic driver mutations initially deemed specific to the metastasis by whole exome sequencing were, in actuality, present within rare ancestral subclones of the primary tumors from which they arose, we employed error-controlled ultra-deep sequencing (UDS-UMI) coupled with FFPE artifact mitigation by uracil-DNA glycosylase (UDG) to assess the presence of 132 "metastasis-specific" mutations within antecedent primary tumors from 21 patients. Maximum mutation detection sensitivity was ~1% of primary tumor cells. A conceptual framework was developed to estimate relative likelihoods of alternative models of mutation acquisition.

RESULTS

The ancestral primary tumor subclone responsible for seeding the metastasis was identified in 29% of patients, implicating several putative drivers in metastatic seeding including LRP5 A65V and PEAK1 K140Q. Despite this, 93% of metastasis-specific mutations in putative metastatic driver genes remained undetected within primary tumors, as did 96% of metastasis-specific mutations in known breast cancer drivers, including ERRB2 V777L, ESR1 D538G, and AKT1 D323H. Strikingly, even in those cases in which the rare ancestral subclone was identified, 87% of metastasis-specific putative driver mutations remained undetected. Modeling indicated that the sequential acquisition of multiple metastasis-specific driver or passenger mutations within the same rare subclonal lineage of the primary tumor was highly improbable.

CONCLUSIONS

Our results strongly suggest that metastatic driver mutations are sequentially acquired and selected within the same clonal lineage both before, but more commonly after, dissemination from the primary tumor, and that these mutations are biologically consequential. Despite inherent limitations in sampling archival primary tumors, our findings indicate that tumor cells in most patients continue to undergo clinically relevant genomic evolution after their dissemination from the primary tumor. This provides further evidence that metastatic recurrence is a multi-step, mutation-driven process that extends beyond primary tumor dissemination and underscores the importance of longitudinal tumor assessment to help guide clinical decisions.

Emerging Landscape of Targeted Therapy of Breast Cancers With Low Human Epidermal Growth Factor Receptor 2 Protein Expression

CONTEXT.—

Human epidermal growth factor receptor 2 (HER2) status in breast cancer is currently classified as negative or positive for selecting patients for anti-HER2 targeted therapy. The evolution of the HER2 status has included a new HER2-low category defined as an HER2 immunohistochemistry score of 1+ or 2+ without gene amplification. This new category opens the door to a targetable HER2-low breast cancer population for which new treatments may be effective.

OBJECTIVE.—

To review the current literature on the emerging category of breast cancers with low HER2 protein expression, including the clinical, histopathologic, and molecular features, and outline the clinical trials and best practice recommendations for identifying HER2-low-expressing breast cancers by immunohistochemistry.

DATA SOURCES.—

We conducted a literature review based on peer-reviewed original articles, review articles, regulatory communications, ongoing and past clinical trials identified through ClinicalTrials.gov, and the authors' practice experience.

CONCLUSIONS.—

The availability of new targeted therapy potentially effective for patients with breast cancers with low HER2 protein expression requires multidisciplinary recognition. In particular, pathologists need to recognize and identify this category to allow the optimal selection of patients for targeted therapy.

Adjusting the distance

This paper describes the anxiety evoked in a patient threatened by invasion or engulfment by his object on the one hand, and the fears of isolation and abandonment on the other. The author illustrates the patient's strugles to find a distance between himself and his object he can tolerate. The analyst has also to cope with the anxieties evoked by the patient's projections, and find a distance between himself and his patient that enables him to think and work.

Cost considerations for vestibular schwannoma screening and imaging: a systematic review

Vestibular schwannomas (VS) account for approximately 8% of all intracranial neoplasms. Importantly, the cost of the diagnostic workup for VS, including the screening modalities most commonly used, has not been thoroughly investigated. Our aim is to conduct a systematic review of the published literature on costs associated with VS screening. A systematic review of the literature for cost of VS treatment was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The terms "vestibular schwannoma," "acoustic neuroma," and "cost" were queried using the PubMed and Embase databases. Studies from all countries were considered. Cost was then corrected for inflation using the US Bureau of Labor Statistics Inflation Calculator, correcting to April 2022. The search resulted in an initial review of 483 articles, of which 12 articles were included in the final analysis. Screening criteria were used for non-neurofibromatosis type I and II patients who complained of asymmetric hearing loss, tinnitus, or vertigo. Patients included in the studies ranged from 72 to 1249. The currency and inflation-adjusted mean cost was $418.40 (range, $21.81 to $487.03, n = 5) for auditory brainstem reflex and $1433.87 (range, $511.64 to $1762.15, n = 3) for non-contrasted computed tomography. A contrasted magnetic resonance imaging (MRI) scan was found to have a median cost of $913.27 (range, $172.25-$2733.99; n = 8) whereas a non-contrasted MRI was found to have a median cost of $478.62 (range, $116.61-$3256.38, n = 4). In terms of cost reporting, of the 12 articles, 1 (8.3%) of them separated out the cost elements, and 10 (83%) of them used local prices, which include institutional costs and/or average costs of multiple institutions. Our findings describe the limited data on published costs for screening and imaging of VS. The paucity of data and significant variability of costs between studies indicates that this endpoint is relatively unexplored, and the cost of screening is poorly understood.

Chimeric kinase ALK induces expression of NAMPT and selectively depends on this metabolic enzyme to sustain its own oncogenic function

As we show in this study, NAMPT, the key rate-limiting enzyme in the salvage pathway, one of the three known pathways involved in NAD synthesis, is selectively over-expressed in anaplastic T-cell lymphoma carrying oncogenic kinase NPM1::ALK (ALK + ALCL). NPM1::ALK induces expression of the NAMPT-encoding gene with STAT3 acting as transcriptional activator of the gene. Inhibition of NAMPT affects ALK + ALCL cells expression of numerous genes, many from the cell-signaling, metabolic, and apoptotic pathways. NAMPT inhibition also functionally impairs the key metabolic and signaling pathways, strikingly including enzymatic activity and, hence, oncogenic function of NPM1::ALK itself. Consequently, NAMPT inhibition induces cell death in vitro and suppresses ALK + ALCL tumor growth in vivo. These results indicate that NAMPT is a novel therapeutic target in ALK + ALCL and, possibly, other similar malignancies. Targeting metabolic pathways selectively activated by oncogenic kinases to which malignant cells become "addicted" may become a novel therapeutic approach to cancer, alternative or, more likely, complementary to direct inhibition of the kinase enzymatic domain. This potential therapy to simultaneously inhibit and metabolically "starve" oncogenic kinases may not only lead to higher response rates but also delay, or even prevent, development of drug resistance, frequently seen when kinase inhibitors are used as single agents.

Serotonin reduction in post-acute sequelae of viral infection

Post-acute sequelae of COVID-19 (PASC, "Long COVID") pose a significant global health challenge. The pathophysiology is unknown, and no effective treatments have been found to date. Several hypotheses have been formulated to explain the etiology of PASC, including viral persistence, chronic inflammation, hypercoagulability, and autonomic dysfunction. Here, we propose a mechanism that links all four hypotheses in a single pathway and provides actionable insights for therapeutic interventions. We find that PASC are associated with serotonin reduction. Viral infection and type I interferon-driven inflammation reduce serotonin through three mechanisms: diminished intestinal absorption of the serotonin precursor tryptophan; platelet hyperactivation and thrombocytopenia, which impacts serotonin storage; and enhanced MAO-mediated serotonin turnover. Peripheral serotonin reduction, in turn, impedes the activity of the vagus nerve and thereby impairs hippocampal responses and memory. These findings provide a possible explanation for neurocognitive symptoms associated with viral persistence in Long COVID, which may extend to other post-viral syndromes.

Biallelic BRCA Loss and Homologous Recombination Deficiency in Nonbreast/Ovarian Tumors in Germline BRCA1/2 Carriers

PURPOSE

Breast and ovarian tumors in germline BRCA1/2 carriers undergo allele-specific loss of heterozygosity, resulting in homologous recombination deficiency (HRD) and sensitivity to poly-ADP-ribose polymerase (PARP) inhibitors. This study investigated whether biallelic loss and HRD also occur in primary nonbreast/ovarian tumors that arise in germline BRCA1/2 carriers.

METHODS

A clinically ascertained cohort of BRCA1/2 carriers with a primary nonbreast/ovarian cancer was identified, including canonical (prostate and pancreatic cancers) and noncanonical (all other) tumor types. Whole-exome sequencing or clinical sequencing results (n = 45) were analyzed. A pan-cancer analysis of nonbreast/ovarian primary tumors from germline BRCA1/2 carriers from The Cancer Genome Atlas (TCGA, n = 73) was used as a validation cohort.

RESULTS

Ages of nonbreast/ovarian cancer diagnosis in germline BRCA1/2 carriers were similar to controls for the majority of cancer types. Nine of 45 (20%) primary nonbreast/ovarian tumors from germline BRCA1/2 carriers had biallelic loss of BRCA1/2 in the clinical cohort, and 23 of 73 (32%) in the TCGA cohort. In the combined cohort, 35% and 27% of primary canonical and noncanonical BRCA tumor types, respectively, had biallelic loss. High HRD scores (HRDex > 42) were detected in 81% of tumors with biallelic BRCA loss compared with 22% (P < .001) of tumors without biallelic BRCA loss. No differences in genomic profile, including mutational signatures, mutation spectrum, tumor mutational burden, or microsatellite instability, were found in primary nonbreast/ovarian tumors with or without biallelic BRCA1/2 loss.

CONCLUSION

A proportion of noncanonical primary tumors have biallelic loss and evidence of HRD. Our data suggest that assessment of biallelic loss and HRD could supplement identification of germline BRCA1/2 mutations in selection of patients for platinum or PARP inhibitor therapy.

Angiographic analysis of ophthalmic artery flow direction in children undergoing chemosurgery for retinoblastoma compared to age-matched controls

PURPOSE

Catheter-based intra-arterial chemotherapy (IAC) has revolutionized the treatment of retinoblastoma (RB). Variability in ophthalmic artery (OA) flow, either retrograde from external carotid artery branches, or anterograde from the internal carotid artery, necessitates multiple IAC techniques. We evaluated the direction of OA flow and identify OA flow reversal events over the course of IAC treatment as well in comparison to OA flow direction in non-RB children.

MATERIALS AND METHODS

We performed a retrospective analysis of OA flow direction in all RB patients treated with IAC, along with an age-matched control group who underwent cerebral angiography at our center from 2014 to 2020.

RESULTS

IAC was administered to a total of 18 eyes (15 patients). Initial anterograde OA flow was demonstrated in 66% (n  =  12) of eyes. Five OA reversal events were identified (3/5 anterograde-to-retrograde). All five events were in patients receiving multiagent chemotherapy. No correlation was found between OA flow reversal events and the initial IAC technique. A control group of 88 angiograms representing 82 eyes (41 patients) was utilized. The anterograde flow was observed in 76 eyes (86.4%). Our control group included 19 patients with sequential angiograms. One OA flow reversal event was identified.

CONCLUSION

OA flow direction is dynamic in IAC patients. Anterograde and retrograde OA directional switches do occur and may necessitate delivery technique variation. In our analysis, all OA flow reversal events were associated with multiagent chemotherapy regimens. Both anterograde and retrograde OA flow patterns were observed in our control cohort, suggesting bidirectional flow can occur in non-RB children.

Abstract PD16-08: Title: Characterizing Changes in Tumor Heterogeneity via Radiomic Phenotyping for Predicting Response to Neoadjuvant Chemotherapy for Locally Advanced Breast Cancer: Preliminary Results from the ACRIN 6698/I-SPY 2 trial

Purpose: To predict pathologic complete response (pCR) in breast cancer patients undergoing neoadjuvant chemotherapy (NAC), from baseline and early-treatment DCE-MRI scans, in the context of the ACRIN 6698/I-SPY 2 BMMR2 challenge.

Materials and Methods: The BMMR2 dataset consists of 191 patients undergoing NAC for locally advanced breast cancer as part of the ACRIN 6698/I-SPY 2 trial. DCE-MRI was obtained at time points T0 (pre-NAC), T1 (3 weeks), and T2 (12 weeks). The BMMR2 challenge provided the MRI scans, tumor annotations, and limited clinical and demographic information. The data were split 60/40; using the 60% training data, the task was to develop models to predict pCR; the competition was for best area under the curve (AUC) when applied to the 40% unseen test data.

Using the publicly available CaPTk software we calculated 3 types of radiomic features within the segmented tumor volume: 1) texture of the signal enhancement ratio (SER) kinetic map of T0 images; 2) texture of the difference between the T1 kinetic maps (PE, WIS, WOS, and SER) and corresponding T0 maps; 3) texture of the difference between the T1 kinetic maps and the corresponding T0 maps, with T1 scans deformably registered to T0 scans. ComBat harmonization was applied to the extracted features to account for MRI acquisition differences. We computed the tumor longest diameter, functional tumor volume (FTV), and clinical tumor size each at T0 and T1.

We modeled pCR via logistic regression. Using the training data alone, with the criteria of performance in univariable modeling and low collinearity, we selected radiomic features and clinical, demographic, and size covariates. We then performed PCA on the combined set of selected radiomic features and size covariates. We evaluated multivariable models including the selected clinical covariates in combination with the first few PCs via cross-validated AUC (5-fold, 200 repetitions) on the training data. The best models were submitted for independent evaluation on the unseen test data of the BMMR2 challenge.

Results: Of the available clinical covariates, only hormone receptor (HR)± and human epidermal growth factor receptor 2 (HER2)± had any association with pCR. We retained these in all models, and performed PCA on the set combining the best-performing features and the size variables FTV at T0, FTV at T1, and longest diameter at T1. Models based on the first few PCs, HR, and HER2, had training AUCs in 0.78–0.81. Our best-performing model had an AUC on test data of 0.84, using the covariates PCs 1–5, HR, and HER2 (Table 1).

Conclusions: Our preliminary results suggest that radiomic phenotyping of changes in tumor heterogeneity can accurately predict pCR early in the course of NAC. Future analysis with larger samples from ISPY-2 could also examine the effect of different therapies, including targeted therapy and immunotherapy.

Table 1: Performance of candidate logistic regression models on training and test data. AUC: Area under receiver operating characteristic curve. * Mean 5-fold cross-validated AUC across 200 replicates. † Competition best-performing predictions.

Citation Format: Eric A. Cohen, Rhea D. Chitalia, Snekha Thakran, Walter C. Mankowski, Alex Anh-Tu Nguyen, Hannah Horng, Elizabeth S. McDonald, Michael Feldman, Angela DeMichele, Despina Kontos. Title: Characterizing Changes in Tumor Heterogeneity via Radiomic Phenotyping for Predicting Response to Neoadjuvant Chemotherapy for Locally Advanced Breast Cancer: Preliminary Results from the ACRIN 6698/I-SPY 2 trial [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD16-08.

Abstract P2-11-16: Computerized Measurements of Nuclear Morphology Features, Mitosis Rate, and Tubule Formation from H&E Images Predicts Disease-Free Survival in Patients with HR+ & LN+ Invasive Breast Cancer from SWOG S8814

Background: Lymph node (LN) involvement is a strong indicator of poor prognosis for breast cancer (BC), with adjuvant chemotherapy remaining fundamental to management of these patients. SWOG S8814 was a Phase III randomized trial of postmenopausal patients with pathologic LN-positive BC who were hormone receptor positive (HR+). The objectives of the clinical trial were to compare disease free survival (DFS) and overall survival (OS) of 1) these postoperative patients treated with a combination of cyclophosphamide, doxorubicin, fluorouracil (CAF) plus tamoxifen versus tamoxifen alone; and 2) patients treated with CAF followed by tamoxifen versus CAF plus concurrent tamoxifen. In this study we sought to evaluate the potential of applying computational image analysis on whole slide images (WSI) for predicting DFS and OS in SWOG S8814. Methods: A cohort of 135 patients (N=53 DFS event) diagnosed with HR+ & LN+ BC from clinical trial ECOG 2197 was utilized as training set D1. Validation set D2 comprised 630 patients (N=260 DFS event, N=195 death) with HR+& LN+ BC from SWOG S8814. Three deep learning models were employed to respectively detect nuclei, mitosis, and tubules in WSIs. Subsequently, a total of 1,810 features relating to nuclear morphology (e.g., spatial distribution, shape, texture, orientation), mitotic activity (e.g., mitosis hotspot, mitotic rates) and tubule formation (e.g., tubular nuclei distribution, ratio of tubule to non-tubule area) were extracted from each WSI. A lasso regularized Cox regression model (IbRiS) was trained on D1 to respectively identify four features from each of the feature categories (nuclei morphology, mitotic activity, and tubule formation) most strongly associated with DFS, a continuous risk score based on the selected features was then constructed. An optimal risk threshold was identified on D1 to dichotomize the risk scores into high vs. low risk of recurrence categories. Blinded validation of the machine learning model on SWOG S8814 using Cox regression was performed by SWOG to evaluate its performance in terms of DFS and OS. Results: In D2, patients identified as high risk of recurrence by IbRiS had a significantly worse prognosis in terms of DFS with hazard ratio=1.30 (p=0.039, 95% CI=1.01-1.66). IbRiS was also found to be significantly prognostic of OS with hazard ratio=1.38 (p=0.026, 95% CI=1.04-1.83). IbRiS was however, neither prognostic of DFS (HR = 1.20; 95% CI 0.93-1.54) nor OS (HR = 1.28; 95% CI 0.96-1.71) in multivariable analysis adjusting for treatment, tumor size, and number of positive nodes. IbRiS was also not a significant predictor of chemotherapy benefit (DFS p=0.45; OS p=0.25). Conclusion: We developed a prognostic model (IbRiS) based on the combined features of nuclear morphology, mitosis count, and tubule formation that can help further risk stratify HR+ & LN+ BC patients by only using H&E slides.

Citation Format: Yuli Chen, William E. Barlow, Haojia Li, Cheng Lu, Andrew Janowczyk, German Corredor, Shridar Ganesan, Michael Feldman, Pingfu Fu, Hannah Gilmore, Kathy S. Albain, Lajos Pusztai, James Rae, Daniel Hayes, Andrew K. Godwin, Alastair M. Thompson, Anant Madabhushi. Computerized Measurements of Nuclear Morphology Features, Mitosis Rate, and Tubule Formation from H&E Images Predicts Disease-Free Survival in Patients with HR+ & LN+ Invasive Breast Cancer from SWOG S8814 [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-11-16.

Flat-panel dual-energy head computed tomography in the angiography suite after thrombectomy for acute stroke: A clinical feasibility study

BACKGROUND

Management of large vessel occlusion (LVO) patients after thrombectomy is affected by the presence of intracranial hemorrhage (ICH) on post-procedure imaging. Differentiating contrast staining from hemorrhage on post-procedural imaging has been facilitated by dual-energy computed tomography (DECT), traditionally performed in dedicated computed tomography (CT) scanners with subsequent delays in treatment. We employed a novel method of DECT using the Siemens cone beam CT (DE-CBCT) in the angiography suite to evaluate for post-procedure ICH and contrast extravasation.

METHODS

After endovascular treatment for LVO was performed and before the patient was removed from the operating table, DE-CBCT was performed using the Siemens Q-biplane system, with two separate 20-second CBCT scans at two energy levels: 70 keV (standard) and 125 keV with tin filtration (nonstandard). Post-procedurally, patients also underwent a standard DECT using Siemens SOMATOM Force CT scanner. Two independent reviewers blindly evaluated the DE-CBCT and DECT for hemorrhage and contrast extravasation.

RESULTS

We successfully performed intra-procedural DE-CBCT in 10 subjects with no technical failure. The images were high-quality and subjectively useful to differentiate contrast from hemorrhage. The one hemorrhage seen on standard DECT was very small and clinically silent. The interrater reliability was 100% for both contrast and hemorrhage detection.

CONCLUSION

We demonstrate that intra-procedural DE-CBCT after thrombectomy is feasible and provides clinically meaningful images. There was close agreement between findings on DE-CBCT and standard DECT. Our findings suggest that DE-CBCT could be used in the future to improve stroke thrombectomy patient workflow and to more efficiently guide the postoperative management of these patients.

Race as a factor in adverse outcomes following unruptured aneurysm surgery

INTRODUCTION

Strong evidence demonstrates that race is associated with health outcomes. Previous neurosurgical research has focused predominantly on subjective data, such as patient satisfaction. Our objective was to assess whether racial disparities are present in primary objective outcomes for treatment of intracranial, unruptured aneurysms in the United States.

METHODS

Data from the 2012-2015 National Inpatient Sample (NIS) database was analyzed. Patients who underwent either open or endovascular treatment of unruptured intracranial aneurysms were included (n = 11663). Patients were stratified by race, and those of unknown race or whose race sample size was too underpowered for analysis were excluded (n = 1202), along with those who experienced head trauma (n = 110) or concurrent AVM (n = 71). Poor outcome was defined as in-hospital mortality, discharge to a nursing facility or hospice, placement of a tracheostomy tube, or placement of a gastrostomy tube. The associations between race and adverse outcomes were determined through multivariate logistic regression, corrected for potentially confounding variables such as age, sex, procedural type, elective procedure, obesity, diabetes, tobacco, severity of illness, and hospital type.

RESULTS

7478 White, 1460 Black, 1086 Hispanic, and 279 Asian patients were included in the final analysis. Complication rates were not significantly different between races, however Black patients experienced the highest proportion of complications (24 %). After adjusting for confounders, the odds of poor outcomes were significantly higher for Black patients (OR = 1.32 95 % CI: 1.07-1.62; p = 0.008) when compared to White patients. Black and Hispanic patients demonstrated a longer length of stay (Black, B: 0.04; 95 % CI: 0.03, 0.06; p < 0.001; Hispanic, B: 0.04; 95 % CI: 0.02, 0.05; p < 0.001) when compared to White patients.

CONCLUSION

Our nationwide analysis using the NIS suggests that Black patients treated for unruptured intracranial aneurysms experience worse outcomes and longer lengths of stay when compared to White patients. Recognizing the differences in objective outcomes and the presence of neurosurgical healthcare disparities is an important first step in providing equitable care to all patients. Future studies that carefully follow the social determinants of health and consider more confounding factors in the association between outcomes and determinants are needed.

The Penn Medicine BioBank: Towards a Genomics-Enabled Learning Healthcare System to Accelerate Precision Medicine in a Diverse Population

The Penn Medicine BioBank (PMBB) is an electronic health record (EHR)-linked biobank at the University of Pennsylvania (Penn Medicine). A large variety of health-related information, ranging from diagnosis codes to laboratory measurements, imaging data and lifestyle information, is integrated with genomic and biomarker data in the PMBB to facilitate discoveries and translational science. To date, 174,712 participants have been enrolled into the PMBB, including approximately 30% of participants of non-European ancestry, making it one of the most diverse medical biobanks. There is a median of seven years of longitudinal data in the EHR available on participants, who also consent to permission to recontact. Herein, we describe the operations and infrastructure of the PMBB, summarize the phenotypic architecture of the enrolled participants, and use body mass index (BMI) as a proof-of-concept quantitative phenotype for PheWAS, LabWAS, and GWAS. The major representation of African-American participants in the PMBB addresses the essential need to expand the diversity in genetic and translational research. There is a critical need for a "medical biobank consortium" to facilitate replication, increase power for rare phenotypes and variants, and promote harmonized collaboration to optimize the potential for biological discovery and precision medicine.

Defibrillation Strategies for Refractory Ventricular Fibrillation

BACKGROUND

Despite advances in defibrillation technology, shock-refractory ventricular fibrillation remains common during out-of-hospital cardiac arrest. Double sequential external defibrillation (DSED; rapid sequential shocks from two defibrillators) and vector-change (VC) defibrillation (switching defibrillation pads to an anterior-posterior position) have been proposed as defibrillation strategies to improve outcomes in patients with refractory ventricular fibrillation.

METHODS

We conducted a cluster-randomized trial with crossover among six Canadian paramedic services to evaluate DSED and VC defibrillation as compared with standard defibrillation in adult patients with refractory ventricular fibrillation during out-of-hospital cardiac arrest. Patients were treated with one of these three techniques according to the strategy that was randomly assigned to the paramedic service. The primary outcome was survival to hospital discharge. Secondary outcomes included termination of ventricular fibrillation, return of spontaneous circulation, and a good neurologic outcome, defined as a modified Rankin scale score of 2 or lower (indicating no symptoms to slight disability) at hospital discharge.

RESULTS

A total of 405 patients were enrolled before the data and safety monitoring board stopped the trial because of the coronavirus disease 2019 pandemic. A total of 136 patients (33.6%) were assigned to receive standard defibrillation, 144 (35.6%) to receive VC defibrillation, and 125 (30.9%) to receive DSED. Survival to hospital discharge was more common in the DSED group than in the standard group (30.4% vs. 13.3%; relative risk, 2.21; 95% confidence interval [CI], 1.33 to 3.67) and more common in the VC group than in the standard group (21.7% vs. 13.3%; relative risk, 1.71; 95% CI, 1.01 to 2.88). DSED but not VC defibrillation was associated with a higher percentage of patients having a good neurologic outcome than standard defibrillation (relative risk, 2.21 [95% CI, 1.26 to 3.88] and 1.48 [95% CI, 0.81 to 2.71], respectively).

CONCLUSIONS

Among patients with refractory ventricular fibrillation, survival to hospital discharge occurred more frequently among those who received DSED or VC defibrillation than among those who received standard defibrillation. (Funded by the Heart and Stroke Foundation of Canada; DOSE VF ClinicalTrials.gov number, NCT04080986.).

Association of Residual Ductal Carcinoma In Situ With Breast Cancer Recurrence in the Neoadjuvant I-SPY2 Trial

Importance

Pathologic complete response (pCR) after neoadjuvant chemotherapy (NAC) in breast cancer strongly correlates with overall survival and has become the standard end point in neoadjuvant trials. However, there is controversy regarding whether the definition of pCR should exclude or permit the presence of residual ductal carcinoma in situ (DCIS).

Objective

To examine the association of residual DCIS in surgical specimens after neoadjuvant chemotherapy for breast cancer with survival end points to inform standards for the assessment of pathologic complete response.

Design, Setting, and Participants

The study team analyzed the association of residual DCIS after NAC with 3-year event-free survival (EFS), distant recurrence-free survival (DRFS), and local-regional recurrence (LRR) in the I-SPY2 trial, an adaptive neoadjuvant platform trial for patients with breast cancer at high risk of recurrence. This is a retrospective analysis of clinical specimens and data from the ongoing I-SPY2 adaptive platform trial of novel therapeutics on a background of standard of care for early breast cancer. I-SPY2 participants are adult women diagnosed with stage II/III breast cancer at high risk of recurrence.

Interventions

Participants were randomized to receive taxane and anthracycline-based neoadjuvant therapy with or without 1 of 10 investigational agents, followed by definitive surgery.

Main Outcomes and Measures

The presence of DCIS and EFS, DRFS, and LRR.

Results

The study team identified 933 I-SPY2 participants (aged 24 to 77 years) with complete pathology and follow-up data. Median follow-up time was 3.9 years; 337 participants (36%) had no residual invasive disease (residual cancer burden 0, or pCR). Of the 337 participants with pCR, 70 (21%) had residual DCIS, which varied significantly by tumor-receptor subtype; residual DCIS was present in 8.5% of triple negative tumors, 15.6% of hormone-receptor positive tumors, and 36.6% of ERBB2-positive tumors. Among those participants with pCR, there was no significant difference in EFS, DRFS, or LRR based on presence or absence of residual DCIS.

Conclusions and Relevance

The analysis supports the definition of pCR as the absence of invasive disease after NAC regardless of the presence or absence of DCIS.

Trial Registration

ClinicalTrials.gov Identifier NCT01042379.

Impact of integrating genomic data into the electronic health record on genetics care delivery

PURPOSE

Integrating genomic data into the electronic health record (EHR) is key for optimally delivering genomic medicine.

METHODS

The PennChart Genomics Initiative (PGI) at the University of Pennsylvania is a multidisciplinary collaborative that has successfully linked orders and results from genetic testing laboratories with discrete genetic data in the EHR. We quantified the use of the genomic data within the EHR, performed a time study with genetic counselors, and conducted key informant interviews with PGI members to evaluate the effect of the PGI's efforts on genetics care delivery.

RESULTS

The PGI has interfaced with 4 genetic testing laboratories, resulting in the creation of 420 unique computerized genetic testing orders that have been used 4073 times to date. In a time study of 96 genetic testing activities, EHR use was associated with significant reductions in time spent ordering (2 vs 8 minutes, P < .001) and managing (1 vs 5 minutes, P < .001) genetic results compared with the use of online laboratory-specific portals. In key informant interviews, multidisciplinary collaboration and institutional buy-in were identified as key ingredients for the PGI's success.

CONCLUSION

The PGI's efforts to integrate genomic medicine into the EHR have substantially streamlined the delivery of genomic medicine.

Pulmonary vascular inflammation with fatal coronavirus disease 2019 (COVID-19): possible role for the NLRP3 inflammasome

Background

Pulmonary hyperinflammation is a key event with SARS-CoV-2 infection. Acute respiratory distress syndrome (ARDS) that often accompanies COVID-19 appears to have worse outcomes than ARDS from other causes. To date, numerous lung histological studies in cases of COVID-19 have shown extensive inflammation and injury, but the extent to which these are a COVID-19 specific, or are an ARDS and/or mechanical ventilation (MV) related phenomenon is not clear. Furthermore, while lung hyperinflammation with ARDS (COVID-19 or from other causes) has been well studied, there is scarce documentation of vascular inflammation in COVID-19 lungs.

Methods

Lung sections from 8 COVID-19 affected and 11 non-COVID-19 subjects, of which 8 were acute respiratory disease syndrome (ARDS) affected (non-COVID-19 ARDS) and 3 were from subjects with non-respiratory diseases (non-COVID-19 non-ARDS) were H&E stained to ascertain histopathological features. Inflammation along the vessel wall was also monitored by expression of NLRP3 and caspase 1.

Results

In lungs from COVID-19 affected subjects, vascular changes in the form of microthrombi in small vessels, arterial thrombosis, and organization were extensive as compared to lungs from non-COVID-19 (i.e., non-COVID-19 ARDS and non-COVID-19 non-ARDS) affected subjects. The expression of NLRP3 pathway components was higher in lungs from COVID-19 ARDS subjects as compared to non-COVID-19 non-ARDS cases. No differences were observed between COVID-19 ARDS and non-COVID-19 ARDS lungs.

Conclusion

Vascular changes as well as NLRP3 inflammasome pathway activation were not different between COVID-19 and non-COVID-19 ARDS suggesting that these responses are not a COVID-19 specific phenomenon and are possibly more related to respiratory distress and associated strategies (such as MV) for treatment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12931-022-01944-8.

PTEN Loss and BRCA1 Promoter Hypermethylation Negatively Predict for Immunogenicity in BRCA-Deficient Ovarian Cancer

PURPOSE

Ovarian cancers can exhibit a prominent immune infiltrate, but clinical trials have not demonstrated substantive response rates to immune checkpoint blockade monotherapy. We aimed to understand genomic features associated with immunogenicity in BRCA1/2 mutation-associated cancers.

MATERIALS AND METHODS

Using the Cancer Genome Atlas whole-exome sequencing, methylation, and expression data, we analyzed 66 ovarian cancers with either germline or somatic loss of BRCA1/2 and whole-exome sequencing, immunohistochemistry, and CyTOF in 20 ovarian cancers with germline BRCA1/2 pathogenic variants from Penn.

RESULTS

We found two groups of BRCA1/2 ovarian cancers differing in their immunogenicity: (1) 37 tumors significantly enriched for PTEN loss (11, 30%) and BRCA1 promoter-hypermethylated (10, 27%; P = .0016) and (2) PTEN wild-type (28 of 29 tumors) cancers, with the latter group having longer overall survival (OS; P = .0186, median OS not reached v median OS = 66.1 months). BRCA1/2-mutant PTEN loss and BRCA1 promoter-hypermethylated cancers were characterized by the decreased composition of lymphocytes estimated by gene expression (P = .0030), cytolytic index (P = .034), and cytokine expression but higher homologous recombination deficiency scores (P = .00013). Large-scale state transitions were the primary discriminating feature (P = .001); neither mutational burden nor neoantigen burden could explain differences in immunogenicity. In Penn tumors, PTEN loss and high homologous recombination deficiency cancers exhibited fewer CD3+ (P = .05), CD8+ (P = .012), and FOXP3+ (P = .0087) T cells; decreased PRF1 expression (P = .041); and lower immune costimulatory and inhibitory molecule expression.

CONCLUSION

Our study suggests that within ovarian cancers with genetic loss of BRCA1/2 are two subsets exhibiting differential immunogenicity, with lower levels associated with PTEN loss and BRCA hypermethylation. These genomic features of BRCA1/2-associated ovarian cancers may inform considerations around how to optimally deploy immune checkpoint inhibitors in the clinic.

Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes

Type 1 diabetes (T1D) is an autoimmune disease in which immune cells destroy insulin-producing beta cells. The aetiology of this complex disease is dependent on the interplay of multiple heterogeneous cell types in the pancreatic environment. Here, we provide a single-cell atlas of pancreatic islets of 24 T1D, autoantibody-positive and nondiabetic organ donors across multiple quantitative modalities including ~80,000 cells using single-cell transcriptomics, ~7,000,000 cells using cytometry by time of flight and ~1,000,000 cells using in situ imaging mass cytometry. We develop an advanced integrative analytical strategy to assess pancreatic islets and identify canonical cell types. We show that a subset of exocrine ductal cells acquires a signature of tolerogenic dendritic cells in an apparent attempt at immune suppression in T1D donors. Our multimodal analyses delineate cell types and processes that may contribute to T1D immunopathogenesis and provide an integrative procedure for exploration and discovery of human pancreatic function.

Anterior Cruciate Ligament Rehabilitation and Return to Sport: How Fast Is Too Fast?

This article summarizes the benefits and limitations of various approaches of anterior cruciate ligament (ACL) rehabilitation, more specifically a conservative or traditional rehabilitation approach versus a more accelerated approach. The conservative model is considered one with a return to sport at 9 months or later with more time-based criteria, and an accelerated approach is defined as one with a goal of return to sport by 6 months. Although there are some similarities between the 2 types of rehabilitation, key differences exist and will be highlighted. Additionally, we discuss a criteria-based return-to-sport model that we favor.

Level of Evidence

V, expert opinion.

Colorectal two-week wait service and quantitative FIT: it's not just about colon cancer

INTRODUCTION

The aim of this study was to assess faecal immunochemical test (FIT) negativity in terms of its effect on cancer risk in the local symptomatic two-week wait (2WW) population. FIT was introduced to the colorectal 2WW pathway at the start of the pandemic. This study analyses the FIT-negative (<10µg Hb/g) cohort and calculates the relative risk and odds ratio associated with a negative FIT test.

METHODS

FIT tests were sent to symptomatic 2WW patients without rectal bleeding, iron-deficient anaemia or palpable mass. Where FIT was <10µg Hb/g investigations were moved to a radiology protocol.

RESULTS

The test return rate was 91% with a FIT-negative (<10µg Hb/g) rate of 82%. The FIT-negative group in the symptomatic referral pathway in Cornwall have a low (1.4%) risk of colon cancer but a significant risk (6.6%) when all cancer types are considered. The impact of a negative quantitative FIT changes the odds ratio of a patient having a luminal cancer by 0.26. The odds ratio for 'all cancer' risk was affected by 0.83.

CONCLUSION

A negative FIT test within the local NG12 symptomatic patient group signifies a low risk of colon cancer and identifies patients who can be initially investigated with cross-sectional imaging. However, when all cancer types are considered, cancer prevalence in this group remains above 6%. In relative risk terms a negative FIT represents a small change in overall risk and this patient group still qualify for investigation through 2WW pathways.

Moderating effects of out-of-hospital cardiac arrest characteristics on the association between EMS response time and survival

BACKGROUND

Although several Utstein variables are known to independently improve survival, how they moderate the effect of emergency medical service (EMS) response times on survival is unknown.

OBJECTIVES

To quantify how public location, witnessed status, bystander CPR, and bystander AED shock individually and jointly moderate the effect of EMS response time delays on OHCA survival.

METHODS

This retrospective cohort study was a secondary analysis of the Resuscitation Outcomes Consortium Epistry-Cardiac Arrest database (December 2005 to June 2015). We included all adult, non-traumatic, non-EMS witnessed, and EMS-treated OHCAs from eleven sites across the US and Canada. We trained a logistic regression model with standard Utstein control variables and interaction terms between EMS response time and the four aforementioned OHCA characteristics.

RESULTS

102,216 patients were included. Three of the four characteristics - witnessed OHCAs (OR = 0.962), bystander CPR (OR = 0.968) and public location (OR = 0.980) - increased the negative effect of a one-minute delay on the odds of survival. In contrast, a bystander AED shock decreased the negative effect of a one-minute response time delay on the odds of survival (OR = 1.064). The magnitude of the effect of a one-minute delay in EMS response time on the odds of survival ranged from 1.3% to 9.8% (average: 5.3%), depending on the underlying OHCA characteristics.

CONCLUSIONS

Delays in EMS response time had the largest reduction in survival odds for OHCAs that did not receive a bystander AED shock but were witnessed, occurred in public, and/or received bystander CPR. A bystander AED shock appears to be protective against a delay in EMS response time.

Vascular Inflammation in Lungs of Patients with Fatal Coronavirus Disease 2019 (COVID-19): Possible Role for the NLRP3 Inflammasome.. [PMID: 34494018 PMCID: PMC8423225 DOI: 10.21203/rs.3.rs-842167/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Background:

Hyperinflammation is a key event that occurs with SARS-CoV-2 infection. In the lung, hyperinflammation leads to structural damage to tissue. To date, numerous lung histological studies have shown extensive alveolar damage, but there is scarce documentation of vascular inflammation in postmortem lung tissue.

Methods:

Lung sections from 8 COVID-19 affected and 11 non-COVID-19 subjects [of which 8 were acute respiratory disease syndrome (ARDS) affected and 3 were from subjects with non-respiratory diseases] were stained for H & E to ascertain histopathological features including presence of thrombi/microthrombi. Inflammation along the vessel wall was also monitored by quantification of the expression of moieties of the NLRP3 inflammasome pathway (NLRP3 and caspase-1).

Results:

In lungs from “fatal COVID-19”, vascular changes in the form of microthrombi in small vessels, arterial thrombosis, and organization were extensive as compared to lungs from “non-COVID-19 non respiratory disease” affected subjects. The NLRP3 pathway components were significantly higher in lungs from COVID-19 subjects as compared to non-COVID-19 fatal cases without respiratory disease. No significant differences were observed between COVID-19 lungs and non-COVID-19 ARDS lungs.

Conclusion:

We posit that inflammasome formation along the vessel wall is a characteristic of lung inflammation that accompanies COVID-19. Thus, the NLRP3 inflammasome pathway seems to be probable candidate that drives amplification of inflammation post SARS-CoV-2 infection.

Multiplexed detection of SARS-CoV-2 genomic and subgenomic RNA using in situ hybridization

The widespread Coronavirus Disease 2019 (COVID-19) is caused by infection with the novel coronavirus SARS-CoV-2. Currently, we have a limited toolset available for visualizing SARS-CoV-2 in cells and tissues, particularly in tissues from patients who died from COVID-19. Generally, single-molecule RNA FISH techniques have shown mixed results in formalin fixed paraffin embedded tissues such as those preserved from human autopsies. Here, we present a platform for preparing autopsy tissue for visualizing SARS-CoV-2 RNA using RNA FISH with amplification by hybridization chain reaction (HCR). We developed probe sets that target different regions of SARS-CoV-2 (including ORF1a and N) as well as probe sets that specifically target SARS-CoV-2 subgenomic mRNAs. We validated these probe sets in cell culture and tissues (lung, lymph node, and placenta) from infected patients. Using this technology, we observe distinct subcellular localization patterns of the ORF1a and N regions, with the ORF1a concentrated around the nucleus and the N showing a diffuse distribution across the cytoplasm. In human lung tissue, we performed multiplexed RNA FISH HCR for SARS-CoV-2 and cell-type specific marker genes. We found viral RNA in cells containing the alveolar type 2 (AT2) cell marker gene (SFTPC) and the alveolar macrophage marker gene (MARCO), but did not identify viral RNA in cells containing the alveolar type 1 (AT1) cell marker gene (AGER). Moreover, we observed distinct subcellular localization patterns of viral RNA in AT2 cells and alveolar macrophages, consistent with phagocytosis of infected cells. In sum, we demonstrate the use of RNA FISH HCR for visualizing different RNA species from SARS-CoV-2 in cell lines and FFPE autopsy specimens. Furthermore, we multiplex this assay with probes for cellular genes to determine what cell-types are infected within the lung. We anticipate that this platform could be broadly useful for studying SARS-CoV-2 pathology in tissues as well as extended for other applications including investigating the viral life cycle, viral diagnostics, and drug screening.

Collagen fiber orientation disorder from H&E images is prognostic for early stage breast cancer: clinical trial validation

Collagen fiber organization has been found to be implicated in breast cancer prognosis. In this study, we evaluated whether computerized features of Collagen Fiber Orientation Disorder in Tumor-associated Stroma (CFOD-TS) on Hematoxylin & Eosin (H&E) slide images were prognostic of Disease Free Survival (DFS) in early stage Estrogen Receptor Positive (ER+) Invasive Breast Cancers (IBC). A Cox regression model named M_CFOD-TS, was constructed using cohort S_t (N = 78) to predict DFS based on CFOD-TS features. The prognostic performance of M_CFOD-TS was validated on cohort S_v (N = 219), a prospective clinical trial dataset (ECOG 2197). M_CFOD-TS was prognostic of DFS in both S_t and S_v, independent of clinicopathological variables. Additionally, the molecular pathways regarding cell cycle regulation were identified as being significantly associated with M_CFOD-TS derived risk scores. Our results also found that collagen fiber organization was more ordered in patients with short DFS. Our study provided a H&E image-based pipeline to derive a potential prognostic biomarker for early stage ER+ IBC without the need of special collagen staining or advanced microscopy techniques.

A Natural Language Processing-Assisted Extraction System for Gleason Scores: Development and Usability Study

BACKGROUND

Natural language processing (NLP) offers significantly faster variable extraction compared to traditional human extraction but cannot interpret complicated notes as well as humans can. Thus, we hypothesized that an "NLP-assisted" extraction system, which uses humans for complicated notes and NLP for uncomplicated notes, could produce faster extraction without compromising accuracy.

OBJECTIVE

The aim of this study was to develop and pilot an NLP-assisted extraction system to leverage the strengths of both human and NLP extraction of prostate cancer Gleason scores.

METHODS

We collected all available clinical and pathology notes for prostate cancer patients in an unselected academic biobank cohort. We developed an NLP system to extract prostate cancer Gleason scores from both clinical and pathology notes. Next, we designed and implemented the NLP-assisted extraction system algorithm to categorize notes into "uncomplicated" and "complicated" notes. Uncomplicated notes were assigned to NLP extraction and complicated notes were assigned to human extraction. We randomly reviewed 200 patients to assess the accuracy and speed of our NLP-assisted extraction system and compared it to NLP extraction alone and human extraction alone.

RESULTS

Of the 2051 patients in our cohort, the NLP system extracted a prostate surgery Gleason score from 1147 (55.92%) patients and a prostate biopsy Gleason score from 1624 (79.18%) patients. Our NLP-assisted extraction system had an overall accuracy rate of 98.7%, which was similar to the accuracy of human extraction alone (97.5%; P=.17) and significantly higher than the accuracy of NLP extraction alone (95.3%; P<.001). Moreover, our NLP-assisted extraction system reduced the workload of human extractors by approximately 95%, resulting in an average extraction time of 12.7 seconds per patient (vs 256.1 seconds per patient for human extraction alone).

CONCLUSIONS

We demonstrated that an NLP-assisted extraction system was able to achieve much faster Gleason score extraction compared to traditional human extraction without sacrificing accuracy.

Abstract LB052: Cell cycle synchronization: Biomarker analysis in a phase I trial of alternating ribociclib and paclitaxel in advanced breast cancer

Background:Cyclin dependent kinase 4/6 inhibitors (CDK 4/6i) are standard of care for hormone receptor positive, HER2 negative metastatic breast cancer (MBC), alone or in combination with endocrine therapy. Combination with paclitaxel (P) is possible with an intermittent, alternating dosing schedule in order to synchronize (sync) the cell cycle (cc) with a short burst of CDKi. To optimize this strategy, we measured cc biomarkers before, during and after a 4 day run in of ribociclib (R) in patients (pts) receiving R with P in a phase I clinical trial (NCT02599363). Methods:Eligible pts with Rb-positive MBC of any subtype and measurable disease were treated with 200, 400 or 600 mg of R on Days (D) 2-5, 9-12 and 16-19, and P 80mg/m2 on D1, 8, 15 and 22 in 28-day cycles (C). Skin biopsies, blood samples and FLT-PET CT were assessed at baseline (pre- R burst), D-3 (post R burst) and C1D1 P (after cc re-entry). Skin biopsies were analyzed for Ki-67 (Dako Santa Clara, CA), phospho-Rb (Ser807/811; Cell Signaling, Danvers, MA) and Rb (clone 1F8, Thermo Scientific, Waltham, MA) by IHC. Serum and plasma were analyzed for thymidine kinase (TK, Biovica, Sweden) and R pharmacokinetics (PK, WuXi, China) respectively.P-Rb and Rb results were binned for intensity and pattern of staining.Intensity was defined as None (0), Weak (W, 1+), Moderate (M, 2+), Strong (S, 3+). Pattern was defined as: Rare (R, &lt;10%), Focal (F, 10-50%) and Diffuse (D, &gt;50%). SUV max was averaged over the 5 brightest lesions.Results:13 pts enrolled to the Phase I trial. Nine pts had at least 1 skin biopsy; 8 had ≥2. Five pts had at least one FLT-PET. Biomarker results are summarized in table. Ki-67 (skin) and TK and FLT (tumor) drop after 4 days of R treatment, when R PK levels are highest. Decreases in P-Rb, were less consistent, observed in 4/8 (50%) pts. While R PK levels drop after 2 days off treatment, only 2/8 (25%) subjects had higher cell cycle measurements on C1D1 compared to baseline.Conclusions:CC synchronization with intermittent dosing is possible, and allows safe administration of P. More time off R is needed for cc re-entry. Future trials should give more time off of R before P delivery.

Pt ID (Dose(mg))TKi-67 (%)P-RbIntensity- PatternRbIntensity- PatternR PKR PKTK (Du/L)FLT(SUV*)LEE011(ng/mL)LEQ803(ng/mL)002 (200)B22M-FM-D002045n/a004 (200)B8M-RM-D00190311.6D-34NM-D69.612.01459.55.2C1D15M-RM-D16.96.5165310005 (200)B11M-RW-F0083212.4D-32M-RW-D83.013.8122.55.1C1D161M-FM-F17.56.18234.514.8006 (200)Bn/an/an/a009030.512.3D-3n/an/an/a15412.37429.59.6013 (200)B19M-FM-D008566.0D-33M-FW-F15815.8767.55.2007 (400)B8M-FM-D003070.5n/aD-31NM-D33230.82009.5n/a010 (400)B23M-FM-D001964.7D-30.5NM-F35929.322.74.1C1D14M-RM-D78.516.4&lt;204.0016 (400)B30M-RW-Dn/an/a75.56.4D-312W-FW-Dn/an/an/a4.1C1D110M-FW-Dn/an/a21.65.1017 (400)B17M-RW-Fn/an/a46.6n/aD-314M-RW-Dn/an/a23n/aC1D116M-RW-Fn/an/a&lt;20n/a014 (600)B15M-RW-D0n/an/an/aD-312M-RW-Dn/a106&lt;20n/aC1D126M-FW-Dn/an/a&lt;20n/a

Citation Format: Amy Clark, Azadeh Elmi, Nicholas P. McAndrew, Paul Wileyto, Natalie Shih, Michael Feldman, Mark Rosen, Jessica Savage, Robin Holmes, Nancy Dinubile, Theresa Berger, Erin Schubert, Alice Matthai, Melissa Volpe, Payal Shah, Susan Domchek, David Mankoff, Angela DeMichele. Cell cycle synchronization: Biomarker analysis in a phase I trial of alternating ribociclib and paclitaxel in advanced breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB052.

Alpha-defensins: risk factor for thrombosis in COVID-19 infection

The inflammatory response to SARS/CoV-2 (COVID-19) infection may contribute to the risk of thromboembolic complications. α-Defensins, antimicrobial peptides released from activated neutrophils, are anti-fibrinolytic and prothrombotic in vitro and in mouse models. In this prospective study of 176 patients with COVID-19 infection, we found that plasma levels of α-defensins were elevated, tracked with disease progression/mortality or resolution and with plasma levels of interleukin-6 (IL-6) and D-dimers. Immunohistochemistry revealed intense deposition of α-defensins in lung vasculature and thrombi. IL-6 stimulated the release of α-defensins from neutrophils, thereby accelerating coagulation and inhibiting fibrinolysis in human blood, imitating the coagulation pattern in COVID-19 patients. The procoagulant effect of IL-6 was inhibited by colchicine, which blocks neutrophil degranulation. These studies describe a link between inflammation and the risk of thromboembolism, and they identify a potential new approach to mitigate this risk in patients with COVID-19 and potentially in other inflammatory prothrombotic conditions.

Abstract 2723: How BRCA1/2 mutations in TNBC affect TME and subsequently immune cell functions

Breast cancer type 1 and 2 susceptibility proteins (BRCA1/BRCA2) are well known breast cancer genes, mutations in which lead to defective homologous recombination repair (HRR). HR-based DNA repair deficiency (HRD) scores can be used to indicate DNA damage, genomic instability and may predict response to DNA damaging agents in BRCA1/2 mutated tumors. Tumors with a high HRD score caused by complete loss of BRCA1 or BRCA2 function locus-specific LOH are sensitive to DNA damage agents including platinum-based chemotherapy and poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi). To understand the relationship between BRCA1/2 mutations and DNA damage in the tumor microenvironment (TME), we have characterized 107 BRCA1/2 tumors to determine HRD score using whole exome sequencing (WES) and simultaneously measured markers of DNA damage, PARP expression, tumor-infiltrating lymphocytes (TILs) and immune checkpoints to identify potential treatment targets on matching samples (n=47) using highly multiplexed fluorescence microscopy CO-Detection by indEXing (CODEX). We have established and validated a 40-plex breast cancer specific antibody panel consisting of markers to detect DNA damage, TILs and immune checkpoints to deeply profile how the TME is affected by BRCA1/2 mutations using CODEX. Computational image processing of CODEX data was performed to interrogate changes in number, size, morphology, and marker expression in tumor and immune cells. We have characterized BRCA1/2 tumors (n=47) on Tissue Microarrays (TMAs), and we have detected cytotoxic CD8+T and CD107a+NK cells in HRD low (&lt;42) and HRD high groups. Interestingly, their frequency and cytolytic function (measured by Granzyme A and perforin transcript level) appear to be associated with HRD scores. For instance, HRD low groups showed increased cytotoxic CD8+T and CD107a+NK cells whereas HRD high groups revealed decreased cell numbers as well as cytolytic function. We observed that HRD high, LOH positive was associated with increased DNA damage marker expression in tumor cells (H3pSer28, pATM, yH2AX) as well as NK cells (pATM) whereas immune checkpoint protein levels were decreased. We have planned quantitative analysis which allow us to determine the percentage of cell subtypes as well as the spatial compartmentalization of cells to interrogate the tumor microenvironment associated with BRCA1/2 mutations. In conclusion, BRCA1/2 mutated tumors with high HRD score revealed upregulated DNA damage expression in immune cells suggesting that BRCA1/2 mutations can impact HRR in CD8+T cells and CD107a+ NK cells and subsequently affect their ability to produce Granzyme A and Perforin. Our findings will decipher the role of DNA damage in BRCA1/2 mutated tumor cells and immune cell types. Outcomes can potentially predict treatment responses such as DNA damage, PARPi and checkpoint inhibitor therapies in TNBC BRCA1/2 breast cancer.

Citation Format: Dana Pueschl, Derek A. Oldrige, Jonathan Belman, Jake S. Shilan, Anupma Nayak, Bradley Wubbenhorst, John Pluta, Robert H. Vonderheide, Michael Feldman, Kara N. Maxwell, E. John Wherry, Susan M. Domchek, Katherine L. Nathanson. How BRCA1/2 mutations in TNBC affect TME and subsequently immune cell functions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2723.

Risk factors for the presence of residual disease in women after partial mastectomy for invasive breast cancer: A single institution experience

BACKGROUND

We hypothesize that in addition to specimen margin widths other clinical variables may help predict the presence of residual disease in the lumpectomy bed.

METHODS

Patients with Stage I-III invasive breast cancer (BC) who underwent partial mastectomy (PM) and re-excision from July 2010-June 2015 were retrospectively reviewed. Bivariate analyses were conducted using two-sample t-tests for continuous variables and Fisher's Exact tests for categorical variables. A multivariate logistic regression was then performed on significant bivariate analyses variables.

RESULTS

ne-hundred and eighty-four patients were included in our analysis; 47% had residual disease on re-excision, while 53% had no residual disease. Tumor and nodal stage, operation type, type of disease present at margin, and number of positive margins were significantly associated with residual disease. On multivariate logistic regression, DCIS alone at the margin (p = 0.02), operation type (PM with cavity margins) (p = 0.003), and number of positive margins (3 or more) (p < 0.001) remained predictive of residual disease at re-excision.

CONCLUSION

Based on a more comprehensive review of the initial pathology, there are additional factors that can help predict the likelihood of finding residual disease and help guide the surgeon in the decision for re-excision.

Computer extracted gland features from H&E predicts prostate cancer recurrence comparably to a genomic companion diagnostic test: a large multi-site study

Existing tools for post-radical prostatectomy (RP) prostate cancer biochemical recurrence (BCR) prognosis rely on human pathologist-derived parameters such as tumor grade, with the resulting inter-reviewer variability. Genomic companion diagnostic tests such as Decipher tend to be tissue destructive, expensive, and not routinely available in most centers. We present a tissue non-destructive method for automated BCR prognosis, termed "Histotyping", that employs computational image analysis of morphologic patterns of prostate tissue from a single, routinely acquired hematoxylin and eosin slide. Patients from two institutions (n = 214) were used to train Histotyping for identifying high-risk patients based on six features of glandular morphology extracted from RP specimens. Histotyping was validated for post-RP BCR prognosis on a separate set of n = 675 patients from five institutions and compared against Decipher on n = 167 patients. Histotyping was prognostic of BCR in the validation set (p < 0.001, univariable hazard ratio [HR] = 2.83, 95% confidence interval [CI]: 2.03-3.93, concordance index [c-index] = 0.68, median years-to-BCR: 1.7). Histotyping was also prognostic in clinically stratified subsets, such as patients with Gleason grade group 3 (HR = 4.09) and negative surgical margins (HR = 3.26). Histotyping was prognostic independent of grade group, margin status, pathological stage, and preoperative prostate-specific antigen (PSA) (multivariable p < 0.001, HR = 2.09, 95% CI: 1.40-3.10, n = 648). The combination of Histotyping, grade group, and preoperative PSA outperformed Decipher (c-index = 0.75 vs. 0.70, n = 167). These results suggest that a prognostic classifier for prostate cancer based on digital images could serve as an alternative or complement to molecular-based companion diagnostic tests.

Computationally Derived Cribriform Area Index from Prostate Cancer Hematoxylin and Eosin Images Is Associated with Biochemical Recurrence Following Radical Prostatectomy and Is Most Prognostic in Gleason Grade Group 2

BACKGROUND

The presence of invasive cribriform adenocarcinoma (ICC), an expanse of cells containing punched-out lumina uninterrupted by stroma, in radical prostatectomy (RP) specimens has been associated with biochemical recurrence (BCR). However, ICC identification has only moderate inter-reviewer agreement.

OBJECTIVE

To investigate quantitative machine-based assessment of the extent and prognostic utility of ICC, especially within individual Gleason grade groups.

DESIGN, SETTING, AND PARTICIPANTS

A machine learning approach was developed for ICC segmentation using 70 RP patients and validated in a cohort of 749 patients from four sites whose median year of surgery was 2007 and with median follow-up of 28 mo. ICC was segmented on one representative hematoxylin and eosin RP slide per patient and the fraction of tumor area composed of ICC, the cribriform area index (CAI), was measured.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

The association between CAI and BCR was measured in terms of the concordance index (c index) and hazard ratio (HR).

RESULTS AND LIMITATIONS

CAI was correlated with BCR (c index 0.62) in the validation set of 411 patients with ICC morphology, especially those with Gleason grade group 2 cancer (n = 192; c index 0.66), and was less prognostic when patients without ICC were included (c index 0.54). A doubling of CAI in the group with ICC morphology was prognostic after controlling for Gleason grade, surgical margin positivity, preoperative prostate-specific antigen level, pathological T stage, and age (HR 1.19, 95% confidence interval 1.03-1.38; p = 0.018).

CONCLUSIONS

Automated image analysis and machine learning could provide an objective, quantitative, reproducible, and high-throughput method of quantifying ICC area. The performance of CAI for grade group 2 cancer suggests that for patients with little Gleason 4 pattern, the ICC fraction has a strong prognostic role.

PATIENT SUMMARY

Machine-based measurement of a specific cell pattern (cribriform; sieve-like, with lots of spaces) in images of prostate specimens could improve risk stratification for patients with prostate cancer. In the future, this could help in expanding the criteria for active surveillance.

Arthroscopic Repair of a PASTA of the Shoulder Using a Bursal Split

PASTA (partial articular supraspinatus tendon avulsion) lesions are a subset of partial rotator cuff tears that are commonly treated by surgeons. Multiple surgical techniques exist for managing these lesions, including debridement, transtendinous repair, and completion of the tear and repair. Each of these techniques provides its own set of advantages and disadvantages, and currently there is no consensus on which method provides the best clinical outcomes or ease of procedure. Here, we present our repair technique for PASTA lesions, which involves a bursal split that takes the advantages of previous techniques by allowing improved visualization of the footprint and suture passing while avoiding the takedown any of Sharpey's fibers.

Prognostication of patients with COVID-19 using artificial intelligence based on chest x-rays and clinical data: a retrospective study

BACKGROUND

Chest x-ray is a relatively accessible, inexpensive, fast imaging modality that might be valuable in the prognostication of patients with COVID-19. We aimed to develop and evaluate an artificial intelligence system using chest x-rays and clinical data to predict disease severity and progression in patients with COVID-19.

METHODS

We did a retrospective study in multiple hospitals in the University of Pennsylvania Health System in Philadelphia, PA, USA, and Brown University affiliated hospitals in Providence, RI, USA. Patients who presented to a hospital in the University of Pennsylvania Health System via the emergency department, with a diagnosis of COVID-19 confirmed by RT-PCR and with an available chest x-ray from their initial presentation or admission, were retrospectively identified and randomly divided into training, validation, and test sets (7:1:2). Using the chest x-rays as input to an EfficientNet deep neural network and clinical data, models were trained to predict the binary outcome of disease severity (ie, critical or non-critical). The deep-learning features extracted from the model and clinical data were used to build time-to-event models to predict the risk of disease progression. The models were externally tested on patients who presented to an independent multicentre institution, Brown University affiliated hospitals, and compared with severity scores provided by radiologists.

FINDINGS

1834 patients who presented via the University of Pennsylvania Health System between March 9 and July 20, 2020, were identified and assigned to the model training (n=1285), validation (n=183), or testing (n=366) sets. 475 patients who presented via the Brown University affiliated hospitals between March 1 and July 18, 2020, were identified for external testing of the models. When chest x-rays were added to clinical data for severity prediction, area under the receiver operating characteristic curve (ROC-AUC) increased from 0·821 (95% CI 0·796-0·828) to 0·846 (0·815-0·852; p<0·0001) on internal testing and 0·731 (0·712-0·738) to 0·792 (0·780-0 ·803; p<0·0001) on external testing. When deep-learning features were added to clinical data for progression prediction, the concordance index (C-index) increased from 0·769 (0·755-0·786) to 0·805 (0·800-0·820; p<0·0001) on internal testing and 0·707 (0·695-0·729) to 0·752 (0·739-0·764; p<0·0001) on external testing. The image and clinical data combined model had significantly better prognostic performance than combined severity scores and clinical data on internal testing (C-index 0·805 vs 0·781; p=0·0002) and external testing (C-index 0·752 vs 0·715; p<0·0001).

INTERPRETATION

In patients with COVID-19, artificial intelligence based on chest x-rays had better prognostic performance than clinical data or radiologist-derived severity scores. Using artificial intelligence, chest x-rays can augment clinical data in predicting the risk of progression to critical illness in patients with COVID-19.

FUNDING

Brown University, Amazon Web Services Diagnostic Development Initiative, Radiological Society of North America, National Cancer Institute and National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health.

Vascular Inflammation in Lungs of Patients with Fatal Coronavirus Disease 2019 (COVID-19) Infection: Possible role for the NLRP3 inflammasome

Hyperinflammation is a key event that occurs with SARS-CoV-2 infection. In the lung, hyperinflammation leads to structural damage to tissue. To date, numerous lung histological studies have shown extensive alveolar damage, but there is scarce documentation of vascular inflammation in postmortem lung tissue. Here we document histopathological features and monitor the NLRP3 inflammasome in fatal cases of disease caused by SARS Cov2 (COVID-19). We posit that inflammasome formation along the vessel wall is a characteristic of lung inflammation that accompanies COVID-19 and that it is a probable candidate that drives amplification of inflammation post infection.

Machine Learning-Based Prediction of COVID-19 Severity and Progression to Critical Illness Using CT Imaging and Clinical Data

Objective

To develop a machine learning (ML) pipeline based on radiomics to predict Coronavirus Disease 2019 (COVID-19) severity and the future deterioration to critical illness using CT and clinical variables.

Materials and Methods

Clinical data were collected from 981 patients from a multi-institutional international cohort with real-time polymerase chain reaction-confirmed COVID-19. Radiomics features were extracted from chest CT of the patients. The data of the cohort were randomly divided into training, validation, and test sets using a 7:1:2 ratio. A ML pipeline consisting of a model to predict severity and time-to-event model to predict progression to critical illness were trained on radiomics features and clinical variables. The receiver operating characteristic area under the curve (ROC-AUC), concordance index (C-index), and time-dependent ROC-AUC were calculated to determine model performance, which was compared with consensus CT severity scores obtained by visual interpretation by radiologists.

Results

Among 981 patients with confirmed COVID-19, 274 patients developed critical illness. Radiomics features and clinical variables resulted in the best performance for the prediction of disease severity with a highest test ROC-AUC of 0.76 compared with 0.70 (0.76 vs. 0.70, p = 0.023) for visual CT severity score and clinical variables. The progression prediction model achieved a test C-index of 0.868 when it was based on the combination of CT radiomics and clinical variables compared with 0.767 when based on CT radiomics features alone (p < 0.001), 0.847 when based on clinical variables alone (p = 0.110), and 0.860 when based on the combination of visual CT severity scores and clinical variables (p = 0.549). Furthermore, the model based on the combination of CT radiomics and clinical variables achieved time-dependent ROC-AUCs of 0.897, 0.933, and 0.927 for the prediction of progression risks at 3, 5 and 7 days, respectively.

Conclusion

CT radiomics features combined with clinical variables were predictive of COVID-19 severity and progression to critical illness with fairly high accuracy.

Multi-centre implementation of an Educational program to improve the Cardiac Arrest diagnostic accuracy of ambulance Telecommunicators and survival outcomes for sudden cardiac arrest victims: the EduCATe study design and methodology

Background

Sudden cardiac death remains a leading cause of mortality in Canada, resulting in more than 35,000 deaths annually. Most cardiac arrest victims collapse in their own home (85% of the time) and 50% are witnessed by a family member or bystander. Survivors have a quality of life similar to the general population, but the overall survival rate for out-of-hospital cardiac arrest (OHCA) rarely exceeds 8%. Victims are almost four times more likely to survive when receiving bystander CPR, but bystander CPR rates have remained low in Canada over the past decade, not exceeding 15–25% until recently. Telecommunication-assisted CPR instructions have been shown to significantly increase bystander CPR rates, but agonal breathing may be misinterpreted as a sign of life by 9–1-1 callers and telecommunicators, and is responsible for as much as 50% of missed OHCA diagnoses.

We sought to improve the ability and speed with which ambulance telecommunicators can recognize OHCA over the phone, initiate timely CPR instructions, and improve survival.

Methods

In this multi-center national study, we will implement and evaluate an educational program developed for ambulance telecommunicators using a multiple baseline interrupted time-series design. We will compare outcomes 12 months before and after the implementation of a 20-min theory-based educational video addressing barriers to recognition of OHCA while in the presence of agonal breathing. Participating Canadian sites demonstrated prior ability to collect standardized data on OHCA. Data will be collected from eligible 9–1-1 recordings, paramedic documentation and hospital medical records. Eligible cases will include suspected or confirmed OHCA of presumed cardiac origin in patients of any age with attempted resuscitation.

Discussion

The ability of telecommunication-assisted CPR instructions to improve bystander CPR and survival rates for OHCA victims is undeniable. The ability of telecommunicators to recognize OHCA over the phone is unequivocally impeded by relative lack of training on agonal breathing, and reluctance to initiate CPR instructions when in doubt. Our pilot data suggests the potential impact of this project will be to increase absolute OHCA recognition and bystander CPR rates by at least 10%, and absolute out-of-hospital cardiac arrest survival by 5% or more.

Trial registration

Prospectively registered on March 28, 2019 at ClinicalTrials.gov identifier: NCT03894059.

Evaluation of COVID-19 Testing Strategies for Repopulating College and University Campuses: A Decision Tree Analysis

PURPOSE

The optimal approach to identify SARS-CoV-2 infection among college students returning to campus is unknown. Recommendations vary from no testing to two tests per student. This research determined the strategy that optimizes the number of true positives and negatives detected and reverse transcription polymerase chain reaction (RT-PCR) tests needed.

METHODS

A decision tree analysis evaluated five strategies: (1) classifying students with symptoms as having COVID-19, (2) RT-PCR testing for symptomatic students, (3) RT-PCR testing for all students, (4) RT-PCR testing for all students and retesting symptomatic students with a negative first test, and (5) RT-PCR testing for all students and retesting all students with a negative first test. The number of true positives, true negatives, RT-PCR tests, and RT-PCR tests per true positive (TTP) was calculated.

RESULTS

Strategy 5 detected the most true positives but also required the most tests. The percentage of correctly identified infections was 40.6%, 29.0%, 53.7%, 72.5%, and 86.9% for Strategies 1-5, respectively. All RT-PCR strategies detected more true negatives than the symptom-only strategy. Analysis of TTP demonstrated that the repeat RT-PCR strategies weakly dominated the single RT-PCR strategy and that the thresholds for more intensive RT-PCR testing decreased as the prevalence of infection increased.

CONCLUSION

Based on TTP, the single RT-PCR strategy is never preferred. If the cost of RT-PCR testing is of concern, a staged approach involving initial testing of all returning students followed by a repeat testing decision based on the measured prevalence of infection might be considered.

EPID-20. NOVEL GLIOBLASTOMA POPULATION-BASED HISTOLOGIC STAIN NORMALIZATION

Histopathologic evaluation has been an integral part of clinical diagnosis for central nervous system tumors, providing information essential for classification, management, and treatment of the disease. Hematoxylin and eosin (H&E) staining is routinely used in histology, providing detail of tissue morphology, structure, and cellular composition. MOTIVATION: Slide staining is rife with color intensity variations, mainly due to differences in materials and staining protocols among others. These variations introduce inaccuracies in downstream computational analysis and quantification of disease, disabling the generalization of computational models. To overcome these variations, current approaches arbitrarily select a slide within the cohort to normalize all slides of the cohort, leading to non-reproducible results in other cohorts. We develop a population-based whole slide image (WSI) normalization method based on overall region driven stain vectors and color histogram, weighted by corresponding percent contribution to overall slide (PCOS). METHODS: We identified a cohort of 509 H&E stained WSIs with corresponding anatomical annotations from the Ivy Glioblastoma Atlas Project. These WSIs and annotations were reviewed by two neuropathologists for correctly annotated regions. Each region was weighted according to PCOS, WSIs with PCOS &lt; 0.05% were discarded. Then, the optical densities and histograms calculated. Resulting color histogram and optical density was applied to the WSI cohort. Finally, stain intensity variability pre- and post- normalization was compared. RESULTS: Normalizing WSIs based on our approach, results in a significant (p &lt; 0.01, Wilcoxon) improvement in color intensity variation for eight of nine regions tested, with the exception of “Pseudopalisading Cells with no visible Necrosis” (p = 0.8). DISCUSSION: This novel transformative technique is insensitive to artificially staining background density and straightforward to apply. Furthermore, the approach shows promise towards a viable and robust tool for stain normalization in large WSIs cohorts, with the potential towards a stain normalization standard generalizable to other diseases.

Genomic landscape of metastatic breast cancer identifies preferentially dysregulated pathways and targets

Nearly all breast cancer deaths result from metastatic disease. Despite this, the genomic events that drive metastatic recurrence are poorly understood. We performed whole-exome and shallow whole-genome sequencing to identify genes and pathways preferentially mutated or copy-number altered in metastases compared with the paired primary tumors from which they arose. Seven genes were preferentially mutated in metastases - MYLK, PEAK1, SLC2A4RG, EVC2, XIRP2, PALB2, and ESR1 - 5 of which are not significantly mutated in any type of human primary cancer. Four regions were preferentially copy-number altered: loss of STK11 and CDKN2A/B, as well as gain of PTK6 and the membrane-bound progesterone receptor, PAQR8. PAQR8 gain was mutually exclusive with mutations in the nuclear estrogen and progesterone receptors, suggesting a role in treatment resistance. Several pathways were preferentially mutated or altered in metastases, including mTOR, CDK/RB, cAMP/PKA, WNT, HKMT, and focal adhesion. Immunohistochemical analyses revealed that metastases preferentially inactivate pRB, upregulate the mTORC1 and WNT signaling pathways, and exhibit nuclear localization of activated PKA. Our findings identify multiple therapeutic targets in metastatic recurrence that are not significantly mutated in primary cancers, implicate membrane progesterone signaling and nuclear PKA in metastatic recurrence, and provide genomic bases for the efficacy of mTORC1, CDK4/6, and PARP inhibitors in metastatic breast cancer.

Perioperative intravenous contrast administration and the incidence of acute kidney injury after major gastrointestinal surgery: prospective, multicentre cohort study

BACKGROUND

This study aimed to determine the impact of preoperative exposure to intravenous contrast for CT and the risk of developing postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery.

METHODS

This prospective, multicentre cohort study included adults undergoing gastrointestinal resection, stoma reversal or liver resection. Both elective and emergency procedures were included. Preoperative exposure to intravenous contrast was defined as exposure to contrast administered for the purposes of CT up to 7 days before surgery. The primary endpoint was the rate of AKI within 7 days. Propensity score-matched models were adjusted for patient, disease and operative variables. In a sensitivity analysis, a propensity score-matched model explored the association between preoperative exposure to contrast and AKI in the first 48 h after surgery.

RESULTS

A total of 5378 patients were included across 173 centres. Overall, 1249 patients (23·2 per cent) received intravenous contrast. The overall rate of AKI within 7 days of surgery was 13·4 per cent (718 of 5378). In the propensity score-matched model, preoperative exposure to contrast was not associated with AKI within 7 days (odds ratio (OR) 0·95, 95 per cent c.i. 0·73 to 1·21; P = 0·669). The sensitivity analysis showed no association between preoperative contrast administration and AKI within 48 h after operation (OR 1·09, 0·84 to 1·41; P = 0·498).

CONCLUSION

There was no association between preoperative intravenous contrast administered for CT up to 7 days before surgery and postoperative AKI. Risk of contrast-induced nephropathy should not be used as a reason to avoid contrast-enhanced CT.

HistoQC: An Open-Source Quality Control Tool for Digital Pathology Slides

PURPOSE

Digital pathology (DP), referring to the digitization of tissue slides, is beginning to change the landscape of clinical diagnostic workflows and has engendered active research within the area of computational pathology. One of the challenges in DP is the presence of artefacts and batch effects, unintentionally introduced during both routine slide preparation (eg, staining, tissue folding) and digitization (eg, blurriness, variations in contrast and hue). Manual review of glass and digital slides is laborious, qualitative, and subject to intra- and inter-reader variability. Therefore, there is a critical need for a reproducible automated approach of precisely localizing artefacts to identify slides that need to be reproduced or regions that should be avoided during computational analysis.

METHODS

Here we present HistoQC, a tool for rapidly performing quality control to not only identify and delineate artefacts but also discover cohort-level outliers (eg, slides stained darker or lighter than others in the cohort). This open-source tool employs a combination of image metrics (eg, color histograms, brightness, contrast), features (eg, edge detectors), and supervised classifiers (eg, pen detection) to identify artefact-free regions on digitized slides. These regions and metrics are presented to the user via an interactive graphical user interface, facilitating artefact detection through real-time visualization and filtering. These same metrics afford users the opportunity to explicitly define acceptable tolerances for their workflows.

RESULTS

The output of HistoQC on 450 slides from The Cancer Genome Atlas was reviewed by two pathologists and found to be suitable for computational analysis more than 95% of the time.

CONCLUSION

These results suggest that HistoQC could provide an automated, quantifiable, quality control process for identifying artefacts and measuring slide quality, in turn helping to improve both the repeatability and robustness of DP workflows.