Phosphopeptide binding to the N-SH2 domain of tyrosine phosphatase SHP2 correlates with the unzipping of its central β-sheet

SHP2 is a tyrosine phosphatase that plays a regulatory role in multiple intracellular signaling cascades and is known to be oncogenic in certain contexts. In the absence of effectors, SHP2 adopts an autoinhibited conformation with its N-SH2 domain blocking the active site. Given the key role of N-SH2 in regulating SHP2, this domain has been extensively studied, often by X-ray crystallography. Using a combination of structural analyses and molecular dynamics (MD) simulations we show that the crystallographic environment can significantly influence the structure of the isolated N-SH2 domain, resulting in misleading interpretations. As an orthogonal method to X-ray crystallography, we use a combination of NMR spectroscopy and MD simulations to accurately determine the conformation of apo N-SH2 in solution. In contrast to earlier reports based on crystallographic data, our results indicate that apo N-SH2 in solution primarily adopts a conformation with a fully zipped central β-sheet, and that partial unzipping of this β-sheet is promoted by binding of either phosphopeptides or even phosphate/sulfate ions.

A multi-institutional meningioma MRI dataset for automated multi-sequence image segmentation

Meningiomas are the most common primary intracranial tumors and can be associated with significant morbidity and mortality. Radiologists, neurosurgeons, neuro-oncologists, and radiation oncologists rely on brain MRI for diagnosis, treatment planning, and longitudinal treatment monitoring. However, automated, objective, and quantitative tools for non-invasive assessment of meningiomas on multi-sequence MR images are not available. Here we present the BraTS Pre-operative Meningioma Dataset, as the largest multi-institutional expert annotated multilabel meningioma multi-sequence MR image dataset to date. This dataset includes 1,141 multi-sequence MR images from six sites, each with four structural MRI sequences (T2-, T2/FLAIR-, pre-contrast T1-, and post-contrast T1-weighted) accompanied by expert manually refined segmentations of three distinct meningioma sub-compartments: enhancing tumor, non-enhancing tumor, and surrounding non-enhancing T2/FLAIR hyperintensity. Basic demographic data are provided including age at time of initial imaging, sex, and CNS WHO grade. The goal of releasing this dataset is to facilitate the development of automated computational methods for meningioma segmentation and expedite their incorporation into clinical practice, ultimately targeting improvement in the care of meningioma patients.

Dose-Incorporated Deep Ensemble Learning for Improving Brain Metastasis Stereotactic Radiosurgery Outcome Prediction

PURPOSE

To develop a novel deep ensemble learning model for accurate prediction of brain metastasis (BM) local control outcomes after stereotactic radiosurgery (SRS).

METHODS AND MATERIALS

A total of 114 brain metastases (BMs) from 82 patients were evaluated, including 26 BMs that developed biopsy-confirmed local failure post-SRS. The SRS spatial dose distribution (Dmap) of each BM was registered to the planning contrast-enhanced T1 (T1-CE) magnetic resonance imaging (MRI). Axial slices of the Dmap, T1-CE, and planning target volume (PTV) segmentation (PTVseg) intersecting the BM center were extracted within a fixed field of view determined by the 60% isodose volume in Dmap. A spherical projection was implemented to transform planar image content onto a spherical surface using multiple projection centers, and the resultant T1-CE/Dmap/PTVseg projections were stacked as a 3-channel variable. Four Visual Geometry Group (VGG-19) deep encoders were used in an ensemble design, with each submodel using a different spherical projection formula as input for BM outcome prediction. In each submodel, clinical features after positional encoding were fused with VGG-19 deep features to generate logit results. The ensemble's outcome was synthesized from the 4 submodel results via logistic regression. In total, 10 model versions with random validation sample assignments were trained to study model robustness. Performance was compared with (1) a single VGG-19 encoder, (2) an ensemble with a T1-CE MRI as the sole image input after projections, and (3) an ensemble with the same image input design without clinical feature inclusion.

RESULTS

The ensemble model achieved an excellent area under the receiver operating characteristic curve (AUCROC: 0.89 ± 0.02) with high sensitivity (0.82 ± 0.05), specificity (0.84 ± 0.11), and accuracy (0.84 ± 0.08) results. This outperformed the MRI-only VGG-19 encoder (sensitivity: 0.35 ± 0.01, AUCROC: 0.64 ± 0.08), the MRI-only deep ensemble (sensitivity: 0.60 ± 0.09, AUCROC: 0.68 ± 0.06), and the 3-channel ensemble without clinical feature fusion (sensitivity: 0.78 ± 0.08, AUCROC: 0.84 ± 0.03).

CONCLUSIONS

Facilitated by the spherical image projection method, a deep ensemble model incorporating Dmap and clinical variables demonstrated excellent performance in predicting BM post-SRS local failure. Our novel approach could improve other radiation therapy outcome models and warrants further evaluation.

MRI order appropriateness for chronic neck pain: Comparison of ordering practices and treatment outcomes for primary care physicians and specialists

Chronic neck pain is a common reason for doctor visits in the United States. This diagnosis can be evaluated through patient history, physical examination, and judicious use of radiographs. However, possible inappropriate magnetic resonance imaging (MRI) ordering persists. We hypothesized that no difference in ordering practices, ordering appropriateness, and subsequent intervention would be appreciated regarding physician specialty, location, patient characteristics, and history and physical exam findings. A multisite retrospective review of cervical spine MRI between 2014 and 2018 was performed. A total of 332 patients were included. Statistical analysis was used to assess MRI order appropriateness, detail of history and physical exam findings, and intervention decision-making among different specialties. If significant differences were found, multiple linear regression was performed to evaluate the association of MRI order appropriateness regarding physician specialty, location, patient characteristics and history, and physical exam findings. The significance level for all tests was set at <0.05 Orthopedic surgeons ordered MRIs most appropriately with an average American College of Radiology (ACR) score of 8.4 (p < 0.005). Orthopedic surgeons had more comprehensive physical exams as compared to the remaining specialties. The decision for intervention did not vary by physician specialty or ACR score, except for patients of pain medicine physicians who received pain management (p = 0.000). Orthopedic surgeons utilize MRI most appropriately and have more comprehensive physical exams. These findings suggest a need for increased physician education on what indicates an appropriate MRI order to improve the use of resources and further protect patient risk-benefit profiles. Further research elucidating factors to minimize negative findings in "appropriate" MRIs is indicated. Clinical significance: More detailed physical exams may lead to more appropriately ordered MRIs, subsequently resulting in surgery or procedures being performed when appropriately indicated. This suggests the need for increased physician education on when MRI ordering is appropriate for chronic neck pain to improve the use of resources and further protect patient risk-benefit profiles.

Independent Monte Carlo dose calculation identifies single isocenter multi-target radiosurgery targets most likely to fail pre-treatment measurement

PURPOSE

For individual targets of single isocenter multi-target (SIMT) Stereotactic radiosurgery (SRS), we assess dose difference between the treatment planning system (TPS) and independent Monte Carlo (MC), and demonstrate persistence into the pre-treatment Quality Assurance (QA) measurement.

METHODS

Treatment plans from 31 SIMT SRS patients were recalculated in a series of scenarios designed to investigate sources of discrepancy between TPS and independent MC. Targets with > 5% discrepancy in DMean[Gy] after progressing through all scenarios were measured with SRS MapCHECK. A matched pair analysis was performed comparing SRS MapCHECK results for these targets with matched targets having similar characteristics (volume & distance from isocenter) but no such MC dose discrepancy.

RESULTS

Of 217 targets analyzed, individual target mean dose (DMean[Gy]) fell outside a 5% threshold for 28 and 24 targets before and after removing tissue heterogeneity effects, respectively, while only 5 exceeded the threshold after removing effect of patient geometry (via calculation on StereoPHAN geometry). Significant factors affecting agreement between the TPS and MC included target distance from isocenter (0.83% decrease in DMean[Gy] per 2 cm), volume (0.15% increase per cc), and degree of plan modulation (0.37% increase per 0.01 increase in modulation complexity score). SRS MapCHECK measurement had better agreement with MC than with TPS (2%/1 mm / 10% threshold gamma pass rate (GPR) = 99.4 ± 1.9% vs. 93.1 ± 13.9%, respectively). In the matched pair analysis, targets exceeding 5% for MC versus TPS also had larger discrepancies between TPS and measurement with no GPR (2%/1 mm / 10% threshold) exceeding 90% (71.5% ± 16.1%); whereas GPR was high for matched targets with no such MC versus TPS difference (96.5% ± 3.3%, p = 0.01).

CONCLUSIONS

Independent MC complements pre-treatment QA measurement for SIMT SRS by identifying problematic individual targets prior to pre-treatment measurement, thus enabling plan modifications earlier in the planning process and guiding selection of targets for pre-treatment QA measurement.

Generation, validation, and benchmarking of a commercial independent Monte Carlo calculation beam model for multi-target SRS

BACKGROUND

Dosimetric validation of single isocenter multi-target radiosurgery plans is difficult due to conditions of electronic disequilibrium and the simultaneous irradiation of multiple off-axis lesions dispersed throughout the volume. Here we report the benchmarking of a customizable Monte Carlo secondary dose calculation algorithm specific for multi-target radiosurgery which future users may use to guide their commissioning and clinical implementation.

PURPOSE

To report the generation, validation, and clinical benchmarking of a volumetric Monte Carlo (MC) dose calculation beam model for single isocenter radiosurgery of intracranial multi-focal disease.

METHODS

The beam model was prepared within SciMoCa (ScientificRT, Munich Germany), a commercial independent dose calculation software, with the aim of broad availability via the commercial software for use with single isocenter radiosurgery. The process included (1) definition & acquisition of measurement data required for beam modeling, (2) tuning model parameters to match measurements, (3) validation of the beam model via independent measurements and end-to-end testing, and finally, (4) clinical benchmarking and validation of beam model utility in a patient specific QA setting. We utilized a 6X Flattening-Filter-Free photon beam from a TrueBeam STX linear accelerator (Siemens Healthineers, Munich Germany).

RESULTS

In addition to the measured data required for standard IMRT/VMAT (depth dose, central axis profiles & output factors, leaf gap), beam modeling and validation for single-isocenter SRS required central axis and off axis (5 cm & 9 cm) small field output factors and comparison between measurement and simulation of backscatter with aperture for jaw much greater than MLCs. Validation end-to-end measurements included SRS MapCHECK in StereoPHAN geometry (2%/1 mm Gamma = 99.2% ± 2.2%), and OSL & scintillator measurements in anthropomorphic STEEV phantom (6 targets, volume = 0.1-4.1cc, distance from isocenter = 1.2-7.9 cm) for which mean difference was -1.9% ± 2.2%. For 10 patient cases, MC for individual PTVs was -0.8% ± 1.5%, -1.3% ± 1.7%, and -0.5% ± 1.8% for mean dose, D95%, and D1%, respectively. This corresponded to custom passing rates action limits per AAPM TG-218 guidelines of ±5.2%, ±6.4%, and ±6.3%, respectively.

CONCLUSIONS

The beam modeling, validation, and clinical action criteria outlined here serves as a benchmark for future users of the customized beam model within SciMoCa for single isocenter radiosurgery of multi-focal disease.

Development of consensus-driven SPIRIT and CONSORT extensions for early phase dose-finding trials: the DEFINE study

BACKGROUND

Early phase dose-finding (EPDF) trials are crucial for the development of a new intervention and influence whether it should be investigated in further trials. Guidance exists for clinical trial protocols and completed trial reports in the SPIRIT and CONSORT guidelines, respectively. However, both guidelines and their extensions do not adequately address the characteristics of EPDF trials. Building on the SPIRIT and CONSORT checklists, the DEFINE study aims to develop international consensus-driven guidelines for EPDF trial protocols (SPIRIT-DEFINE) and reports (CONSORT-DEFINE).

METHODS

The initial generation of candidate items was informed by reviewing published EPDF trial reports. The early draft items were refined further through a review of the published and grey literature, analysis of real-world examples, citation and reference searches, and expert recommendations, followed by a two-round modified Delphi process. Patient and public involvement and engagement (PPIE) was pursued concurrently with the quantitative and thematic analysis of Delphi participants' feedback.

RESULTS

The Delphi survey included 79 new or modified SPIRIT-DEFINE (n = 36) and CONSORT-DEFINE (n = 43) extension candidate items. In Round One, 206 interdisciplinary stakeholders from 24 countries voted and 151 stakeholders voted in Round Two. Following Round One feedback, one item for CONSORT-DEFINE was added in Round Two. Of the 80 items, 60 met the threshold for inclusion (≥ 70% of respondents voted critical: 26 SPIRIT-DEFINE, 34 CONSORT-DEFINE), with the remaining 20 items to be further discussed at the consensus meeting. The parallel PPIE work resulted in the development of an EPDF lay summary toolkit consisting of a template with guidance notes and an exemplar.

CONCLUSIONS

By detailing the development journey of the DEFINE study and the decisions undertaken, we envision that this will enhance understanding and help researchers in the development of future guidelines. The SPIRIT-DEFINE and CONSORT-DEFINE guidelines will allow investigators to effectively address essential items that should be present in EPDF trial protocols and reports, thereby promoting transparency, comprehensiveness, and reproducibility.

TRIAL REGISTRATION

SPIRIT-DEFINE and CONSORT-DEFINE are registered with the EQUATOR Network ( https://www.equator-network.org/ ).

An NMR Study of a 300-kDa AAA+ Unfoldase

AAA+ ATPases are ubiquitous hexameric unfoldases acting in cellular protein quality control. In complex with proteases, they form protein degradation machinery (the proteasome) in both archaea and eukaryotes. Here, we use solution-state NMR spectroscopy to determine the symmetry properties of the archaeal PAN AAA+ unfoldase and gain insights into its functional mechanism. PAN consists of three folded domains: the coiled-coil (CC), OB and ATPase domains. We find that full-length PAN assembles into a hexamer with C2 symmetry, and that this symmetry extends over the CC, OB and ATPase domains. The NMR data, collected in the absence of substrate, are incompatible with the spiral staircase structure observed in electron-microscopy studies of archaeal PAN in the presence of substrate and in electron-microscopy studies of eukaryotic unfoldases both in the presence and in the absence of substrate. Based on the C2 symmetry revealed by NMR spectroscopy in solution, we propose that archaeal ATPases are flexible enzymes, which can adopt distinct conformations in different conditions. This study reaffirms the importance of studying dynamic systems in solution.

Experiment-guided molecular simulations define a heterogeneous structural ensemble for the PTPN11 tandem SH2 domains

SHP2 plays an important role in regulating cellular processes, and its pathogenic mutations cause developmental disorders and are linked to cancer. SHP2 is a multidomain protein, comprising two SH2 domains arranged in tandem, a catalytic PTP domain, and a disordered C-terminal tail. SHP2 is activated upon binding two linked phosphopeptides to its SH2 domains, and the peptide orientation and spacing between binding sites are critical for enzymatic activation. For decades, the tandem SH2 has been extensively studied to identify the relative orientation of the two SH2 domains that most effectively binds effectors. So far, neither crystallography nor experiments in solution have provided conclusive results. Using experiment-guided molecular simulations, we determine the heterogeneous structural ensemble of the tandem SH2 in solution in agreement with experimental data from small-angle X-ray scattering and NMR residual dipolar couplings. In the solution ensemble, N-SH2 adopts different orientations and positions relative to C-SH2. We suggest that the intrinsic structural plasticity of the tandem SH2 allows SHP2 to respond to external stimuli and is essential for its functional activity.

The ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge 2023: Intracranial Meningioma

Meningiomas are the most common primary intracranial tumor in adults and can be associated with significant morbidity and mortality. Radiologists, neurosurgeons, neuro-oncologists, and radiation oncologists rely on multiparametric MRI (mpMRI) for diagnosis, treatment planning, and longitudinal treatment monitoring; yet automated, objective, and quantitative tools for non-invasive assessment of meningiomas on mpMRI are lacking. The BraTS meningioma 2023 challenge will provide a community standard and benchmark for state-of-the-art automated intracranial meningioma segmentation models based on the largest expert annotated multilabel meningioma mpMRI dataset to date. Challenge competitors will develop automated segmentation models to predict three distinct meningioma sub-regions on MRI including enhancing tumor, non-enhancing tumor core, and surrounding nonenhancing T2/FLAIR hyperintensity. Models will be evaluated on separate validation and held-out test datasets using standardized metrics utilized across the BraTS 2023 series of challenges including the Dice similarity coefficient and Hausdorff distance. The models developed during the course of this challenge will aid in incorporation of automated meningioma MRI segmentation into clinical practice, which will ultimately improve care of patients with meningioma.

A real-time analysis of GFP unfolding by the AAA+ unfoldase PAN

Protein quality control systems are essential to maintain a healthy proteome. They often consist of an unfoldase unit, typically an AAA+ ATPase, coupled with a protease unit. In all kingdoms of life, they function to eliminate misfolded proteins, and thus prevent that their aggregates do harm to the cell, and to rapidly regulate protein levels in the presence of environmental changes. Despite the huge progress made in the past two decades in understanding the mechanism of function of protein degradation systems, the fate of the substrate during the unfolding and proteolytic processes remains poorly understood. Here we exploit an NMR-based approach to monitor GFP processing by the archaeal PAN unfoldase and the PAN-20S degradation system in real time. We find that PAN-dependent unfolding of GFP does not involve the release of partially-folded GFP molecules resulting from futile unfolding attempts. In contrast, once stably engaged with PAN, GFP molecules are efficiently transferred to the proteolytic chamber of the 20S subunit, despite the only weak affinity of PAN for the 20S subunit in the absence of substrate. This is essential to guarantee that unfolded but not proteolyzed proteins are not released into solution, where they would form toxic aggregates. The results of our studies are in good agreement with previous results derived from real-time small-angle-neutron-scattering experiments and have the advantage of allowing the investigation of substrates and products at amino-acid resolution.

The EJC disassembly factor PYM is an intrinsically disordered protein and forms a fuzzy complex with RNA

The discovery of several functional interactions where one or even both partners remain disordered has demonstrated that specific interactions do not necessarily require well-defined intermolecular interfaces. Here we describe a fuzzy protein–RNA complex formed by the intrinsically unfolded protein PYM and RNA. PYM is a cytosolic protein, which has been reported to bind the exon junction complex (EJC). In the process of oskar mRNA localization in Drosophila melanogaster, removal of the first intron and deposition of the EJC are essential, while PYM is required to recycle the EJC components after localization has been accomplished. Here we demonstrate that the first 160 amino acids of PYM (PYM1–160) are intrinsically disordered. PYM1–160 binds RNA independently of its nucleotide sequence, forming a fuzzy protein–RNA complex that is incompatible with PYM’s function as an EJC recycling factor. We propose that the role of RNA binding consists in down-regulating PYM activity by blocking the EJC interaction surface of PYM until localization has been accomplished. We suggest that the largely unstructured character of PYM may act to enable binding to a variety of diverse interaction partners, such as multiple RNA sequences and the EJC proteins Y14 and Mago.

Efficacy of Laser Interstitial Thermal Therapy (LITT) for Biopsy-Proven Radiation Necrosis in Radiographically Recurrent Brain Metastases

Background

LITT (laser interstitial thermal therapy) in the setting of post-SRS radiation necrosis (RN) for patients with brain metastases has growing evidence for efficacy. However, questions remain regarding hospitalization, local control, symptom control, and concurrent use of therapies.

Methods

Demographics, intraprocedural data, safety, Karnofsky performance status (KPS) and survival data were prospectively collected then analyzed on patients consented between 2016-2020 and who were undergoing LITT for biopsy-proven RN at one of 14 U.S. centers. Data was monitored for accuracy. Statistical analysis included individual variable summaries, multivariable Fine and Gray analysis, and Kaplan Meier estimated survival.

Results

Ninety patients met the inclusion criteria. Four patients underwent two ablations on the same day. Median hospitalization time was 32.5hrs. The median time to corticosteroid cessation after LITT was 13.0 days (0.0, 1229.0) and cumulative incidence of lesional progression was 19% at 1-year. Median post-procedure overall survival was 2.55 years [1.66, infinity] and 77.1% at one year as estimated by Kaplan Meier. Median KPS remained at 80 through 2-year follow-up. Seizure prevalence was 12% within 1-month post-LITT and 7.9% at three months; down from 34.4% within 60-days prior to procedure.

Conclusions

LITT for RN was not only again found to be safe with low patient morbidity but was also a highly effective treatment for RN for both local control and symptom management (including seizures). In addition to averting expected neurological death, LITT facilitates ongoing systemic therapy (in particular immunotherapy) by enabling the rapid cessation of steroids, thereby facilitating maximal possible survival for these patients.

Doxycycline for the prevention of progression of COVID-19 to severe disease requiring intensive care unit (ICU) admission: A randomized, controlled, open-label, parallel group trial (DOXPREVENT.ICU)

BACKGROUND

After admission to hospital, COVID-19 progresses in a substantial proportion of patients to critical disease that requires intensive care unit (ICU) admission.

METHODS

In a pragmatic, non-blinded trial, 387 patients aged 40-90 years were randomised to receive treatment with SoC plus doxycycline (n = 192) or SoC only (n = 195). The primary outcome was the need for ICU admission as judged by the attending physicians. Three types of analyses were carried out for the primary outcome: "Intention to treat" (ITT) based on randomisation; "Per protocol" (PP), excluding patients not treated according to randomisation; and "As treated" (AT), based on actual treatment received. The trial was undertaken in six hospitals in India with high-quality ICU facilities. An online application serving as the electronic case report form was developed to enable screening, randomisation and collection of outcomes data.

RESULTS

Adherence to treatment per protocol was 95.1%. Among all 387 participants, 77 (19.9%) developed critical disease needing ICU admission. In all three primary outcome analyses, doxycycline was associated with a relative risk reduction (RRR) and absolute risk reduction (ARR): ITT 31.6% RRR, 7.4% ARR (P = 0.063); PP 40.7% RRR, 9.6% ARR (P = 0.017); AT 43.2% RRR, 10.8% ARR (P = 0.007), with numbers needed to treat (NTT) of 13.4 (ITT), 10.4 (PP), and 9.3 (AT), respectively. Doxycycline was well tolerated with not a single patient stopping treatment due to adverse events.

CONCLUSIONS

In hospitalized COVID-19 patients, doxycycline, a safe, inexpensive, and widely available antibiotic with anti-inflammatory properties, reduces the need for ICU admission when added to SoC.

1272 A PILOT ROUTINE ELECTRONIC HEALTH RECORD FUNCTIONAL TRACKING SCORE FOR OLDER PATIENTS IN HOSPITAL

Introduction

Approximately one-third of older patients leave hospital with a new functional impairment. Tracking rehabilitation progress following acute illness could improve recognition and understanding of hospital-acquired disability. However, traditional mobility and functional scores include measures that are not part of routine rehabilitation therapy, adding a time burden for staff to report. Capturing data already recorded in routine electronic records could provide an efficient patient tracking measure of rehabilitation success.

Methods

A scoping literature review appraised existing scores of mobility and functional status. Analysis of 15 admissions through the Royal Infirmary of Edinburgh identified mobility and functional domains which were reliably recorded in free text electronic health records. A pilot score was drafted, comprising admission and discharge scores (0-30 points), medical progress (0-10), physiotherapy and occupational therapy tracking (0-30). Higher scores indicate greater functional independence. Expert feedback was obtained through focus group discussion with physiotherapists and occupational therapists. The approach was tested in a fresh set of six case studies. Two independent scorers applied the scoring schema and agreement was assessed using Cohen’s weighted-kappa coefficient.

Results

The selected electronic health records contained 438 medical, 352 nursing and 183 therapist entries. Existing measures such as the Barthel Index were not recorded for any patient. Focus group discussion identified value in the overall approach and informed item-weighting. The pilot functional score allowed visualisation of rehabilitation trajectories over the course of each admission. Excellent inter-rater reliability was demonstrated for the medical (Cohen’s Kappa 0.99, 95% confidence interval [CI] 0.96–1.00) and physiotherapy (Kappa 0.96, 95% CI 0.93–0.99) components.

Conclusions

A functional tracking score generated from routine health records proved feasible and reproducible in this pilot. Future development should assess validity, reliability and prognostic power in larger populations, exploring automation using natural language processing. Development of graphic visualisations may aid communication within multidisciplinary teams.

RADT-02. IMPACT OF SINGLE AND DUAL IMMUNE CHECKPOINT BLOCKADE ON RISK OF RADIATION NECROSIS AND LOCAL CONTROL AMONG PATIENTS WITH BRAIN METASTASES TREATED WITH STEREOTACTIC RADIOSURGERY

PURPOSE

Single and dual immune checkpoint inhibition (ICPI) are common treatment options for patients, particularly with melanoma and non-small cell lung cancer (NSCLC). While data suggest a cancer control benefit of combining stereotactic radiosurgery (SRS) and ICPI, we hypothesized that concurrent dual ICPI and SRS increases risk for radiation necrosis (RN).

METHODS

We retrospectively reviewed patients with metastatic melanoma or NSCLC treated with SRS for intact brain metastases from 2014-2020. Patients were stratified by receipt of dual ICPI, single ICPI, and SRS alone. Concurrent ICPI was defined as treatment within 30 days of SRS. RN and local control (LC) were biopsy confirmed or determined radiographically and longitudinally, in combination with clinical assessment and steroid use. Kaplan-Meier estimates were used to compare rates of RN and LC between cohorts.

RESULTS

673 brain lesions from 93 patients met inclusion criteria [median (Q1, Q3): 5.0 (2.0-10.0) lesions per patient]. Median follow-up was 8.1 months (95% CI: 7.3-8.7). Histologies included melanoma (53.5%), adenocarcinoma NSCLC (27.3%), squamous cell NSCLC (6.1%), and NSCLC NOS (6.1%). 88 lesions from 25 patients (27%) developed RN and 11 (13%) were biopsy-proven. ICPI use was enriched among lesions that developed RN (85.2%) versus those that did not (19.8%). RN was associated with concurrent ICPI (p&lt; 0.001). Freedom from RN at 6 months was 80% for dual ICPI, 82% for single ICPI, and 97% for SRS alone; 12-month rates were 78% in each ICPI cohort and 95% with SRS alone (p=0.0002). LC differed among dual (97.5%), single (88.7%), and no ICPI (79.7%, p &lt; 0.001). There was a trend toward improved LC with RN (96.6% vs 91.8%; p=0.087).

CONCLUSIONS

In a large cohort of brain metastases, we observed increased risk of RN and improved LC with SRS plus concurrent dual or single ICPI. Awareness of these associations is critical for patient management.

Graded Prognostic Assessment (GPA) for Patients With Lung Cancer and Brain Metastases: Initial Report of the Small Cell Lung Cancer GPA and Update of the Non-Small Cell Lung Cancer GPA Including the Effect of Programmed Death Ligand 1 and Other Prognostic Factors

PURPOSE

Patients with lung cancer and brain metastases represent a markedly heterogeneous population. Accurate prognosis is essential to optimally individualize care. In prior publications, we described the graded prognostic assessment (GPA), but a GPA for patients with small cell lung cancer (SCLC) has never been reported, and in non-small cell lung cancer (NSCLC), the effect of programmed death ligand 1 (PD-L1) was unknown. The 3-fold purpose of this work is to provide the initial report of an SCLC GPA, to evaluate the effect of PD-L1 on survival in patients with NSCLC, and to update the Lung GPA accordingly.

METHODS AND MATERIALS

A multivariable analysis of prognostic factors and treatments associated with survival was performed on 4183 patients with lung cancer (3002 adenocarcinoma, 611 nonadenocarcinoma, 570 SCLC) with newly diagnosed brain metastases between January 1, 2015, and December 31, 2020, using a multi-institutional retrospective database. Significant variables were used to update the Lung GPA.

RESULTS

Overall median survival for lung adenocarcinoma, SCLC, and nonadenocarcinoma was 17, 10, and 8 months, respectively, but varied widely by GPA from 2 to 52 months. In SCLC, the significant prognostic factors were age, performance status, extracranial metastases, and number of brain metastases. In NSCLC, the distribution of molecular markers among patients with lung adenocarcinoma and known primary tumor molecular status revealed alterations/expression in PD-L1 50% to 100%, PD-L1 1% to 49%, epidermal growth factor receptor, and anaplastic lymphoma kinase in 32%, 31%, 30%, and 7%, respectively. Median survival of patients with lung adenocarcinoma and brain metastases with 0, 1% to 49%, and ≥50% PD-L1 expression was 17, 19, and 24 months, respectively (P < .01), confirming PD-L1 is a prognostic factor. Previously identified prognostic factors for NSCLC (epidermal growth factor receptor and anaplastic lymphoma kinase status, performance status, age, number of brain metastases, and extracranial metastases) were reaffirmed. These factors were incorporated into the updated Lung GPA with robust separation between subgroups for all histologies.

CONCLUSIONS

Survival for patients with lung cancer and brain metastases has improved but varies widely. The initial report of a GPA for SCLC is presented. For patients with NSCLC-adenocarcinoma and brain metastases, PD-L1 is a newly identified significant prognostic factor, and the previously identified factors were reaffirmed. The updated indices establish unique criteria for SCLC, NSCLC-nonadenocarcinoma, and NSCLC-adenocarcinoma (incorporating PD-L1). The updated Lung GPA, available for free at brainmetgpa.com, provides an accurate tool to estimate survival, individualize treatment, and stratify clinical trials.

MMAP-07 IMPACT OF SINGLE AND DUAL IMMUNE CHECKPOINT BLOCKADE ON RISK OF RADIATION NECROSIS AMONG PATIENTS WITH BRAIN METASTASES TREATED WITH STEREOTACTIC RADIOSURGERY

PURPOSE

While stereotactic radiosurgery (SRS) is often an efficacious treatment for brain metastases, it carries a significant risk of radionecrosis (RN). Single and dual immune checkpoint inhibition (ICPI) have emerged as common treatment options for many patients, particularly those with melanoma and non-small cell lung cancer (NSCLC). While data suggest a cancer control benefit of combining SRS and ICPI, we hypothesized that concurrent receipt of dual ICPI with SRS increases the risk for RN.

METHODS

We performed a retrospective review of serial patients with metastatic melanoma or NSCLC treated with SRS for intact brain metastases from 2014-2020 at our single institution. Patients were stratified by receipt of dual vs. single ICPI vs. SRS alone. RN was biopsy confirmed or determined radiographically, in combination with clinical assessment and steroid use. Kaplan-Meier estimates were used to compare rates of RN between cohorts.

RESULTS

673 brain lesions from 93 patients met inclusion criteria [median (Q1, Q3): 5.0 (2.0-10.0) lesions per patient]. Median follow-up of lesions was 8.1 months (95% CI: 7.3, 8.7). Most (82.8%) lesions were supratentorial and histologies included melanoma (53.5%), adenocarcinoma NSCLC (27.3%), squamous cell NSCLC (6.1%), and NSCLC NOS (6.1%). In the entire cohort, 88 lesions from 25 patients (27%) developed RN. 77 (87%) lesions were diagnosed clinico-radiographically and 11 (13%) were biopsy-proven. ICPI use was highly enriched among lesions that developed RN (85.2%) versus those that did not (19.8%). Freedom from RN at 6 months was 80% for dual ICPI, 82% for single ICPI, and 97% for SRS alone; 12 month rates were 78% in each of the ICPI cohorts and 95% with SRS alone (P=0.0002).

CONCLUSIONS

In a large cohort of SRS-treated brain metastases, we observed an increased risk of RN among patients who received either dual or single ICPI concurrently with SRS.

SPCR-03 NEUROCOGNITIVE OUTCOMES FROM PHASE 1 TRIAL OF BMX-001 IN COMBINATION WITH CONCURRENT RADIATION THERAPY AND TEMOZOLOMIDE IN NEWLY DIAGNOSED HIGH-GRADE GLIOMA PATIENTS

INTRODUCTION

Neurocognitive dysfunction can result from radiation therapy which is the mainstay of treatment for high-grade glioma, particularly glioblastoma. Preclinical observations found that BMX-001, a novel metalloporphyrin, acts as a radioprotectant for normal CNS cells yet as a radiosensitizer to cancer cells in human GBM xenograft experiments. In a phase 1 study evaluating the safety of BMX-001 in combination with concurrent radiation therapy and temozolomide, we further studied neurocognitive function before and after concurrent radiation therapy and temozolomide in newly diagnosed high-grade glioma patients.

METHODS

We performed a phase 1 study of BMX-001 combined with radiation therapy (6-week total of 59.4-60 Gy) and temozolomide (75 mg/m2/day for 42 days). We administered BMX-001 as a subcutaneous injection at a loading dose before radiation therapy and temozolomide and then subsequent doses twice weekly for eight weeks. A key secondary endpoint was the evaluation of neurocognition. We performed neurocognitive testing with the computerized program CNS Vital Signsâ. This battery consists of seven tests: verbal memory, visual memory, finger tapping, symbol digit coding, the Stroop Test, a test of shifting attention, and a continuous performance test. We defined neurocognitive impairment at baseline as a z-score ≥ 1.5 SDs below the normative mean. We described improvements or declines in neurocognition at 2 and 6 months from baseline.

RESULTS

Fifteen patients (age 19-80 years) enrolled and underwent neurocognitive testing before and after RT. All patients had WHO grade 4 glioblastoma. Most subjects had neurocognitive impairment ranging from 46.7-to 80% on specific neurocognitive tests. At two months (N=15) and six months (N=9), most testing demonstrated improved neurocognitive performance.

CONCLUSIONS

Neurocognitive function is maintained and can improve after concurrent radiation therapy and temozolomide in this high-grade glioma cohort treated with BMX-001 during concurrent radiation therapy and temozolomide.

CTIM-10. REPRODUCIBILITY OF CLINICAL TRIALS USING CMV-TARGETED DENDRITIC CELL VACCINES IN PATIENTS WITH GLIOBLASTOMA

INTRODUCTION

Vaccination with dendritic cells (DCs) fares poorly in primary and recurrent glioblastoma (GBM). Moreover, GBM vaccine trials are often underpowered due to limited sample size.

METHODS

To address these limitations, we conducted three sequential clinical trials utilizing Cytomegalovirus (CMV)-specific DC vaccines in patients with primary GBM. Autologous DCs were generated and electroporated with mRNA encoding for the CMV protein pp65. Serial vaccination was given throughout adjuvant temozolomide cycles, and 111Indium radiolabeling was implemented to assess migration efficiency of DC vaccines. Patients were followed for median overall survival (mOS) and OS.

RESULTS

Our initial study was the phase II ATTAC study (NCT00639639; total n=12) with 6 patients randomized to vaccine site preconditioning with tetanus-diphtheria (Td) toxoid. This led to an expanded cohort trial (ATTAC-GM; NCT00639639) of 11 patients receiving CMV DC vaccines containing granulocyte-macrophage colony-stimulating factor (GM-CSF). Follow-up data from ATTAC and ATTAC-GM revealed 5-year OS rates of 33.3% (mOS 38.3 months; CI95 17.5-undefined) and 36.4% (mOS 37.7 months; CI95 18.2-109.1), respectively. ATTAC additionally revealed a significant increase in DC migration to draining lymph nodes following Td preconditioning (P=0.049). Increased DC migration was associated with OS (Cox proportional hazards model, HR=0.820, P=0.023). Td-mediated increased migration has been recapitulated in our larger confirmatory trial ELEVATE (NCT02366728) of 43 patients randomized to preconditioning (Wilcoxon rank sum, Td n=24, unpulsed DC n=19; 24h, P=0.031 and 48h, P=0.0195). In ELEVATE, median follow-up of 42.2 months revealed significantly longer OS in patients randomized to Td (P=0.026). The 3-year OS for Td-treated patients in ELEVATE was 34% (CI95 19-63%) compared to 6% given unpulsed DCs (CI95 1-42%).

CONCLUSION

We report reproducibility of our findings across three sequential clinical trials using CMV pp65 DCs. Despite their small numbers, these successive trials demonstrate consistent survival outcomes, thus supporting the efficacy of CMV DC vaccine therapy in GBM.

1H, 13C, and 15N backbone chemical-shift assignments of SARS-CoV-2 non-structural protein 1 (leader protein)

The current COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has become a worldwide health crisis, necessitating coordinated scientific research and urgent identification of new drug targets for treatment of COVID-19 lung disease. The covid19-nmr consortium seeks to support drug development by providing publicly accessible NMR data on the viral RNA elements and proteins. The SARS-CoV-2 genome comprises a single RNA of about 30 kb in length, in which 14 open reading frames (ORFs) have been annotated, and encodes approximately 30 proteins. The first two-thirds of the SARS-CoV-2 genome is made up of two large overlapping open-reading-frames (ORF1a and ORF1b) encoding a replicase polyprotein, which is subsequently cleaved to yield 16 so-called non-structural proteins. The non-structural protein 1 (Nsp1), which is considered to be a major virulence factor, suppresses host immune functions by associating with host ribosomal complexes at the very end of its C-terminus. Furthermore, Nsp1 facilitates initiation of viral RNA translation via an interaction of its N-terminal domain with the 5' untranslated region (UTR) of the viral RNA. Here, we report the near-complete backbone chemical-shift assignments of full-length SARS-CoV-2 Nsp1 (19.8 kDa), which reveal the domain organization, secondary structure and backbone dynamics of Nsp1, and which will be of value to further NMR-based investigations of both the biochemical and physiological functions of Nsp1.

Identification of RNA base pairs and complete assignment of nucleobase resonances by 1H-detected solid-state NMR spectroscopy at 100 kHz MAS

Knowledge of RNA structure, either in isolation or in complex, is fundamental to understand the mechanism of cellular processes. Solid‐state NMR (ssNMR) is applicable to high molecular‐weight complexes and does not require crystallization; thus, it is well‐suited to study RNA as part of large multicomponent assemblies. Recently, we solved the first structures of both RNA and an RNA‐protein complex by ssNMR using conventional ¹³C‐ and ¹⁵N‐detection. This approach is limited by the severe overlap of the RNA peaks together with the low sensitivity of multidimensional experiments. Here, we overcome the limitations in sensitivity and resolution by using ¹H‐detection at fast MAS rates. We develop experiments that allow the identification of complete nucleobase spin‐systems together with their site‐specific base pair pattern using sub‐milligram quantities of one uniformly labelled RNA sample. These experiments provide rapid access to RNA secondary structure by ssNMR in protein‐RNA complexes of any size.

RADI-09. Clinical factors associated with death after radiotherapy for brain metastases

Introduction

It can be challenging to accurately identify patients with brain metastases who have very poor prognosis and are unlikely to benefit from radiation (RT). We characterized factors of patients who died within 30 days of receiving RT for brain metastases.

Methods

Patients who received whole brain RT (WBRT) or stereotactic radiosurgery (SRS) for brain metastases between 1/1/2017–9/30/2020 at a single institution were identified. Patient, tumor, treatment, and death variables were collected. Characteristics between those who did and did not die within 30 days were compared using the Wilcoxon Rank-Sum or Chi-Square test. Survival was estimated with Kaplan-Meier method.

Results

636 patients received WBRT (n=117) or SRS (n=519). Median age was 61. Median survival was 6 months (95% CI 5–7 months). 75 (12%) died within 30 days of RT. Patients who died within 30 days had worse median KPS (50 vs 80, p<0.001). A higher proportion who died within 30 days had innumerable intracranial metastases (45% vs 11%, p<0.001), leptomeningeal disease (16% vs 5%, p<0.001), and higher burden of neurologic symptoms at presentation (seizures (12% vs 4%, p=0.003); cranial neuropathies (32% vs 9%, p<0.001); motor/sensory deficits (51% vs 29%, p<0.001); altered mentation (60% vs 26%, p<0.001); headaches (48% vs 30%, p<0.001); steroid use (68% vs 48%, p<0.001)). Patients who died within 30 days had progressive extracranial disease (intrathoracic: 87% vs 50%; spinal: 57% vs 18%; liver/adrenal: 60% vs 24%), p<0.001. More patients who died within 30 days received inpatient RT (39% vs 4%, <0.001) and did not complete RT (24% vs 1%, p<0.001).

Discussion

Patients who died within 30 days of RT had worse KPS, intracranial/extracranial disease burden, and neurologic symptoms. Future analyses will assess whether these factors can inform a prognostic model to identify patients with poor prognosis who may be appropriate for supportive care alone.

Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium's collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.

Phosphotyrosine couples peptide binding and SHP2 activation via a dynamic allosteric network

SHP2 is a ubiquitous protein tyrosine phosphatase, whose activity is regulated by phosphotyrosine (pY)-containing peptides generated in response to extracellular stimuli. Its crystal structure reveals a closed, auto-inhibited conformation in which the N-terminal Src homology 2 (N-SH2) domain occludes the catalytic site of the phosphatase (PTP) domain. High-affinity mono-phosphorylated peptides promote catalytic activity by binding to N-SH2 and disrupting the interaction with the PTP. The mechanism behind this process is not entirely clear, especially because N-SH2 is incapable of accommodating complete peptide binding when SHP2 is in the auto-inhibited state. Here, we show that pY performs an essential role in this process; in addition to its contribution to overall peptide-binding energy, pY-recognition leads to enhanced dynamics of the N-SH2 EF and BG loops via an allosteric communication network, which destabilizes the N-SH2-PTP interaction surface and simultaneously generates a fully accessible binding pocket for the C-terminal half of the phosphopeptide. Subsequently, full binding of the phosphopeptide is associated with the stabilization of activated SHP2. We demonstrate that this allosteric network exists only in N-SH2, which is directly involved in the regulation of SHP2 activity, while the C-terminal SH2 domain (C-SH2) functions primarily to recruit high-affinity bidentate phosphopeptides.

Machine learning enables completely automatic tuning of a quantum device faster than human experts

Variability is a problem for the scalability of semiconductor quantum devices. The parameter space is large, and the operating range is small. Our statistical tuning algorithm searches for specific electron transport features in gate-defined quantum dot devices with a gate voltage space of up to eight dimensions. Starting from the full range of each gate voltage, our machine learning algorithm can tune each device to optimal performance in a median time of under 70 minutes. This performance surpassed our best human benchmark (although both human and machine performance can be improved). The algorithm is approximately 180 times faster than an automated random search of the parameter space, and is suitable for different material systems and device architectures. Our results yield a quantitative measurement of device variability, from one device to another and after thermal cycling. Our machine learning algorithm can be extended to higher dimensions and other technologies.

A distal regulatory region of a class I human histone deacetylase

Histone deacetylases (HDACs) are key enzymes in epigenetics and important drug targets in cancer biology. Whilst it has been established that HDACs regulate many cellular processes, far less is known about the regulation of these enzymes themselves. Here, we show that HDAC8 is allosterically regulated by shifts in populations between exchanging states. An inactive state is identified, which is stabilised by a range of mutations and resembles a sparsely-populated state in equilibrium with active HDAC8. Computational models show that the inactive and active states differ by small changes in a regulatory region that extends up to 28 Å from the active site. The regulatory allosteric region identified here in HDAC8 corresponds to regions in other class I HDACs known to bind regulators, thus suggesting a general mechanism. The presented results pave the way for the development of allosteric HDAC inhibitors and regulators to improve the therapy for several disease states.

The guide sRNA sequence determines the activity level of box C/D RNPs

2'-O-rRNA methylation, which is essential in eukaryotes and archaea, is catalysed by the Box C/D RNP complex in an RNA-guided manner. Despite the conservation of the methylation sites, the abundance of site-specific modifications shows variability across species and tissues, suggesting that rRNA methylation may provide a means of controlling gene expression. As all Box C/D RNPs are thought to adopt a similar structure, it remains unclear how the methylation efficiency is regulated. Here, we provide the first structural evidence that, in the context of the Box C/D RNP, the affinity of the catalytic module fibrillarin for the substrate-guide helix is dependent on the RNA sequence outside the methylation site, thus providing a mechanism by which both the substrate and guide RNA sequences determine the degree of methylation. To reach this result, we develop an iterative structure-calculation protocol that exploits the power of integrative structural biology to characterize conformational ensembles.

Molecular mechanism of SHP2 activation by PD-1 stimulation

In cancer, the programmed death-1 (PD-1) pathway suppresses T cell stimulation and mediates immune escape. Upon stimulation, PD-1 becomes phosphorylated at its immune receptor tyrosine-based inhibitory motif (ITIM) and immune receptor tyrosine-based switch motif (ITSM), which then bind the Src homology 2 (SH2) domains of SH2-containing phosphatase 2 (SHP2), initiating T cell inactivation. The SHP2-PD-1 complex structure and the exact functions of the two SH2 domains and phosphorylated motifs remain unknown. Here, we explain the structural basis and provide functional evidence for the mechanism of PD-1-mediated SHP2 activation. We demonstrate that full activation is obtained only upon phosphorylation of both ITIM and ITSM: ITSM binds C-SH2 with strong affinity, recruiting SHP2 to PD-1, while ITIM binds N-SH2, displacing it from the catalytic pocket and activating SHP2. This binding event requires the formation of a new inter-domain interface, offering opportunities for the development of novel immunotherapeutic approaches.

HOUT-21. CHARACTERISTICS OF SHORT-TERM SURVIVAL IN PATIENTS WITH GLIOBLASTOMA: A RETROSPECTIVE ANALYSIS

We sought to identify characteristics of glioblastoma (GBM) patients with short survival (< 10 months) in order to identify prognostic factors useful for guiding treatment management. This is an IRB-approved retrospective analysis of adult newly diagnosed GBM patients from 2008–2016 who survived < 10 months from diagnosis. We extracted demographics, tumor characteristics, and treatment details. We calculated survival from surgical diagnosis to date of death. The cohort includes 197 subjects (61% male) with a median age of 68 years (range 19–94). The majority (93%) are non-Hispanic white. The cohort has a median survival of 144 days (95% CI: 130–160). We focused on traditional prognostic indicators, including extent of surgical resection and KPS. A majority had biopsy only (n=92, 46.7%) rather than gross total (n=59, 29.9%) or subtotal (n=46, 23.4%) resection. Moreover, 160 out of 197 patients had a documented KPS with a majority being below 90 (KPS=70–80 (n=96); KPS < 70 (n=31)). Of 179 patients with data on RT course, 18% (n=32) received no RT or opted for hospice after diagnosis, 3% (n=6) received only RT, 54% (n=97) received RT+temozolomide (TMZ), and 24% (n=43) received RT+TMZ+bevacizumab. Of the 147 subjects receiving RT, 79% completed their RT course as prescribed. Most commonly, RT was prescribed as a 6- to 6-1/2-week course (85%), typically 59.4 Gy (45Gy primary, 14.4Gy boost) over 33 fractions or 60 Gy over 30 fractions. In contrast, 15% received a 3-week RT course, typically scheduled as 15 fractions of 2.667 Gy. We concluded that GBM patients with survival < 10 months were more likely to have biopsy only and a KPS < 90, notably associated with poorer prognosis. We continue to explore this dataset for further prognostic factors, particularly inability to complete planned RT course, and are comparing these traits to a larger cohort.

TRLS-10. MITIGATING NEUROCOGNITIVE DEFICITS FROM WHOLE-BRAIN RADIOTHERAPY IN PATIENTS WITH NUMEROUS BRAIN METASTASES VIA A NOVEL SUPEROXIDE DISMUTASE MIMETIC: RATIONALE & DESIGN OF A CLINICAL TRIAL

BACKGROUND: Patients with a large number of brain metastases (BM) and/or micrometastatic disease in the brain present a clinical challenge. While technical innovations in stereotactic radiosurgery (SRS) have extended the number of BM that can be effectively treated, SRS does not treat occult disease and distant brain failure (DBF) post-SRS remains high. Immuno- and targeted therapies show promise in treating metastatic disease to the brain, though response rates are variable. In contrast, whole-brain radiotherapy (WBRT) provides high rates of local control and, compared to SRS, reduces the risk of distant brain failure. Unfortunately, WBRT is also associated with substantial neurocognitive deficits and neither altered fractionation nor the use of available neuroprotectants has adequately addressed this issue. An agent that safely minimizes the adverse effects of WBRT while preserving or enhancing tumor control would provide meaningful clinical benefit. TRIAL DESIGN: BMX-001, a novel Mn-porphyrin superoxide dismutase mimetic, has been shown to protect normal tissues from ionizing radiation in preclinical trials, reducing neurocognitive adverse effects as well as enhancing tumor response. Based on the first-in-human trial of this agent in patients with high-grade gliomas, we have instituted a clinical trial of WBRT +/- BMX-001 in adult patients with more than 10 BM from melanoma, non-small-cell lung, breast and renal cancer. Following a safety lead-in of 5 patients, all of whom will receive WBRT and BMX-001, 69 patients will be randomized to WBRT (3Gy/fraction x 10 fractions) with or without BMX-001 administered subcutaneously before, twice weekly during and once after WBRT (6 injections total.) The primary endpoint is cognition, as measured by the Hopkins Verbal Learning, Trailmaking A/B and Controlled Oral Word Association tests. Secondary endpoints include health-related quality-of-life, overall and progression-free survival, rates of radiation necrosis, DBF and neurologic death. Enrollment began January 2019. (ClinicalTrials.gov Identifier: NCT03608020.)

RADI-06. SINGLE- VERSUS MULTI-FRACTION STEREOTACTIC RADIOSURGERY FOR BRAINSTEM METASTASES

BACKGROUND: For intracranial metastases with planning target volume (PTV) overlap of the brainstem (BSmet), the radiosurgical dose-fractionation that optimizes the therapeutic window is unknown. MATERIALS/METHODS: A retrospective review of brain metastases (BM) with/without BSmets treated with single-fraction stereotactic radiosurgery (SRS) or hypofractionated (2–5 fractions) radiosurgery (HF-SRS) between 2012–2016 was performed. Brainstem biologically effective doses (BED) and single-fraction equivalents of brainstem V10/V12 were calculated using α/β=3. Characteristics were compared between patients with/without BSmet and between SRS/HF-SRS cohorts using Wilcoxon rank sum, chi-square, or Fisher’s exact tests. Radiographic progression (RP) was assessed in patients with post-treatment contrasted MRI and defined as BSmet enlargement regardless of etiology (progression, radionecrosis, indeterminate). Kaplan-Meier estimates were compared between cohorts using log-rank test. RESULTS: 634 SRS/HF-SRS courses were identified, of which 59 (9.3%) treated ≥1 BSmet in 55 patients. BSmets occurred more commonly in patients with &gt;4 BM (31% vs 10%, p&lt; 0.001) and intracranial recurrence (39% vs 20%, p=0.003). BSmets were treated in 1 (22/59; 37%), 2 (1/59; 2%), or 5 (36/59; 61%) fractions. Age, KPS, and primary tumor site were balanced between SRS/HF-SRS cohorts. The HF-SRS cohort had significantly larger BSmet PTV (median 1.39cc vs 0.39cc, p=0.021), marginal dose (median 25Gy vs 15Gy, p&lt; 0.001), brainstem V10 (median 1.60cc vs 0.47cc, p&lt; 0.001), brainstem V12 (median 0.78cc vs 0.06cc, p&lt; 0.001), and mean brainstem BED (median 9.27Gy3 vs 6.55Gy3, p=0.019). The SRS cohort was more likely to have prior whole brain radiotherapy (50% vs 14%, p=0.005) and restart steroids post-treatment (78% vs 41%, p=0.019). RP occurred in 6/17 vs 2/25 patients in the SRS vs HF-SRS cohorts, respectively (p=0.045). HF-SRS trended to higher freedom from RP (93% vs 74% @12mo; p=0.072). There was no overall survival difference (p=0.36). CONCLUSIONS: HF-SRS was associated with decreased RP and decreased likelihood of restarting steroids despite treating larger BSmets.

Histone chaperone exploits intrinsic disorder to switch acetylation specificity

Histones, the principal protein components of chromatin, contain long disordered sequences, which are extensively post-translationally modified. Although histone chaperones are known to control both the activity and specificity of histone-modifying enzymes, the mechanisms promoting modification of highly disordered substrates, such as lysine-acetylation within the N-terminal tail of histone H3, are not understood. Here, to understand how histone chaperones Asf1 and Vps75 together promote H3 K9-acetylation, we establish the solution structural model of the acetyltransferase Rtt109 in complex with Asf1 and Vps75 and the histone dimer H3:H4. We show that Vps75 promotes K9-acetylation by engaging the H3 N-terminal tail in fuzzy electrostatic interactions with its disordered C-terminal domain, thereby confining the H3 tail to a wide central cavity faced by the Rtt109 active site. These fuzzy interactions between disordered domains achieve localization of lysine residues in the H3 tail to the catalytic site with minimal loss of entropy, and may represent a common mechanism of enzymatic reactions involving highly disordered substrates.

Structural characterization of the Asf1-Rtt109 interaction and its role in histone acetylation

Acetylation of histone H3 at lysine-56 by the histone acetyltransferase Rtt109 in lower eukaryotes is important for maintaining genomic integrity and is required for C. albicans pathogenicity. Rtt109 is activated by association with two different histone chaperones, Vps75 and Asf1, through an unknown mechanism. Here, we reveal that the Rtt109 C-terminus interacts directly with Asf1 and elucidate the structural basis of this interaction. In addition, we find that the H3 N-terminus can interact via the same interface on Asf1, leading to a competition between the two interaction partners. This, together with the recruitment and position of the substrate, provides an explanation of the role of the Rtt109 C-terminus in Asf1-dependent Rtt109 activation.

Perspectives on Inflammatory Breast Cancer (IBC) Research, Clinical Management and Community Engagement from the Duke IBC Consortium

Inflammatory breast cancer (IBC) is an understudied and aggressive form of breast cancer with a poor prognosis, accounting for 2-6% of new breast cancer diagnoses but 10% of all breast cancer-related deaths in the United States. Currently there are no therapeutic regimens developed specifically for IBC, and it is critical to recognize that all aspects of treating IBC - including staging, diagnosis, and therapy - are vastly different than other breast cancers. In December 2014, under the umbrella of an interdisciplinary initiative supported by the Duke School of Medicine, researchers, clinicians, research administrators, and patient advocates formed the Duke Consortium for IBC to address the needs of patients in North Carolina (an ethnically and economically diverse state with 100 counties) and across the Southeastern United States. The primary goal of this group is to translate research into action and improve both awareness and patient care through collaborations with local, national and international IBC programs. The consortium held its inaugural meeting on Feb 28, 2018, which also marked Rare Disease Day and convened national research experts, clinicians, patients, advocates, government representatives, foundation leaders, staff, and trainees. The meeting focused on new developments and challenges in the clinical management of IBC, research challenges and opportunities, and an interactive session to garner input from patients, advocates, and community partners that would inform a strategic plan toward continuing improvements in IBC patient care, research, and education.

Assessment of concurrent stereotactic radiosurgery and bevacizumab treatment of recurrent malignant gliomas using multi-modality MRI imaging and radiomics analysis

PURPOSE

To assess the response and predict the overall survival (OS) of recurrent malignant gliomas (MG) patients treated with concurrent BVZ/SRS using multi-modality MRI imaging and radiomics analysis.Methods and materials: SRS was delivered in a single fraction (18/24Gy) or 25Gy in 5 fractions. BVZ was administered immediately before SRS and 2 weeks after. MRI scans were performed before SRS, 1 week and 2 months after SRS. The MR protocol included 2 anatomical (T1w and T2w) and 2 functional (dynamic contrast-enhanced DCE-MRI and diffusion weighted DW-MRI) modalities. Functional biomarkers including apparent diffusion coefficient (ADC), micro-vascular transfer constant Ktrans, brain blood flow F_B, and blood volume V_B were analyzed. Radiomics analysis was performed to extract imaging features from anatomical MRI images and functional biomarker maps. Wicoxon signed rank tests were performed to evaluate treatment-induced changes, and Mann-Whitney U tests were performed to compare the differences of treatment-induced changes between different patient groups. Selected biomarkers and radiomics features were used to predict the OS after treatment using Support Vector Regression (SVR) with leave-one-out cross validation (LOOCV).

RESULTS

Twelve patients with recurrent MG were studied. The median OS was 13.8 months post SRS. DCE results showed that Ktrans (p=0.035) and V_B (p=0.035) showed significant decrease 2 months after SRS, and F_B showed significant decrease as early as 1 week (p=0.017) after SRS. No functional parameters reflected statistically significant treatment response 1 week after SRS. A total of 888 radiomics features were extracted. 31/126 features demonstrated significant changes 1 week/2 months after SRS, respectively. 9 features' changes were significantly different between WHO Grade III vs IV patient groups, and 6 features' changes were found to be linearly correlated with OS. Using 5 selected features, 9 patients' survival time could be accurately predicted (Mean absolute error = 1.47 months, RMSE = 2.10 months).

CONCLUSION

The results of this work demonstrate the potential of combined radiomics analysis and functional MR imaging in quantitatively identifying early treatment response of concurrent SRS/BVZ.

Characterization of Water-Clear Polymeric Gels for Use as Radiotherapy Bolus

Our purpose was to investigate polymeric gels for use as a highly transparent radiotherapy bolus and determine the relevant physical and dosimetric properties. We first quantified tensile properties (maximum stress, strain, and Young modulus) for various polymeric gels, along with a commercial bolus product in order to illustrate the wide variety of potential materials. For a select polymeric gel with tensile properties similar to currently used radiotherapy bolus, we also evaluated mass and electron density, effective atomic number, optical transparency, and percent depth dose in clinical megavoltage photon and electron beams. For this polymeric gel, mass density was 872 ± 12 and 896 ± 13 g/cm³ when measured via weight/volume and computed tomography Hounsfield units, respectively. Electron density was 2.95 ± 0.04 ×10²³ electrons/cm³. Adding fused silica (9% by weight) increases density to that of water. The ratio of the effective atomic number to that of water without and with added silica was 0.780 and 0.835 at 1 MeV, 0.767 and 0.826 at 6 MeV, and 0.746 and 0.809 at 20 MeV. Percent depth dose for 6 MV photons was within 2% of water within the first 2.5 cm and after scaling by the density coincided within 1% out to >7 cm. For 6 and 20 MeV electrons, after scaling for density D_80% was within 1.3 and 1.5 mm of water, respectively. The high transparency and mechanical flexibility of polymeric gels indicate potential for use as a radiotherapy bolus; differences in density from water may be managed via either using “water equivalent thickness” or by incorporating fused silica into the material.

Re-examining TG-142 recommendations in light of modern techniques for linear accelerator based radiosurgery

PURPOSE

The recent development of multifocal stereotactic radiosurgery (SRS) using a single isocenter volumetric modulated arc theory (VMAT) technique warrants a re-examination of the quality assurance (QA) tolerances for routine mechanical QA recommended by the American Association of Physicists in Medicine Task Group Report Number 142. Multifocal SRS can result in targets with small volumes being at a large off-axis distance from the treatment isocenter. Consequently, angular errors in the collimator, patient support assembly (PSA), or gantry could have an increased impact on target coverage.

METHODS

The authors performed a retrospective analysis of dose deviations caused by systematic errors in PSA, collimator, and gantry angle at the tolerance level for routine linear accelerator QA as recommended by TG-142. Dosimetric deviations from multifocal SRS plans (N = 10) were compared to traditional single target SRS using dynamic conformal arcs (N = 10). The chief dosimetric quantities used in determining clinical impact were V_100% and D_99% of the individual planning target volumes and V_12Gy of the healthy brain.

RESULTS

Induced errors at tolerance levels showed the greatest change in multifocal SRS target coverage for collimator rotations (±1.0°) with the average changes to V_100% and D_99% being 5% and 6%, respectively, with maximum changes of 33% and 20%. A reduction in the induced error to half the TG-142 tolerance (±0.5°) demonstrated similar changes in coverage loss to traditional single target SRS assessed at the recommended tolerance level. The observed change in coverage for multifocal SRS was reduced for gantry errors (±1.0°) at 2% and 4.5% for V_100% and D_99%, respectively, with maximum changes of 18% and 12%. Minimal change in coverage was noted for errors in PSA rotation.

CONCLUSIONS

This study indicates that institutions utilizing a single isocenter VMAT technique for multifocal disease should pay careful attention to the angular mechanical tolerances in designing a robust and complete QA program.

Abstract P5-08-12: HER2 status remains the primary predictor of improved survival in patients with BCBM over the past 2 decades (1996-2015)

BACKGROUND: Brain metastasis is a complication in advanced breast cancer (ABC) and is associated with poor prognosis. Incidence of breast cancer brain metastasis (BCBM) is increasing with advances in therapy, allowing patients to survive long enough to develop CNS metastasis. Improved outcomes have been documented in ABC over the past decades, largely related to the use of trastuzumab in HER2+ ABC. However, it remains unclear whether survival has improved in HER2- ABC in patients with BCBM. This study asks: has the improvement in systemic and radiotherapies for HER2- breast cancer impacted survival in patients with breast cancer brain metastasis.

OBJECTIVES: 1) To estimate whether date of BCBM diagnosis is associated with overall survival (OS) in patients diagnosed between 1996-2015. 2) To estimate whether OS of this patient population depends upon other demographic and clinical factors.

METHODS: This is a retrospective chart review of patients with diagnosis of BCBM between 1996-2015. Data collection includes: age at BCBM diagnosis, ethnicity, ER/PR/HER2 status, date of BCBM diagnosis, date of primary breast cancer diagnosis, date of death/last clinical follow-up, and treatment. Kaplan-Meier analysis and the log-rank test compared OS (time from diagnosis of BCBM until death or last clinical FU) between groups diagnosed in 5-year cohorts (1996-2000, 2001-2005, 2006-2010, 2011-2015). A univariate proportional hazards model was used to regress OS on date of diagnosis. A multivariate proportional hazards model was used which included the subset of patients diagnosed with BCBM in 2001 and later. This model adjusted for additional factors: race, time to development of BCBM diagnosis, age at the time of BCBM diagnosis, year of diagnosis as a continuous factor, ER, PR, while testing the significance of HER2 status. A p-value &lt; 0.05 was significant.

RESULTS: A total of 165 patients with BCBM were included in this analysis, with a median age of 53.8 (SD 13.0) at time of BCBM diagnosis. Most patients were Caucasian (66%; 109/165) or African-American (29%; 48/165). Although statistical significance was not attained, greater median overall survival was seen for patients diagnosed with BCBM in more recent 5-year cohorts (2011-2016, 9.5 months; 2006-2010, 8 months) than patients in older cohorts (2001-2006, 3.6 months; 1996-2000, 5.3 months), p=0.3. Date of diagnosis of BCBM as a continuous variable is predictive of overall survival (HR 0.83 [95% CI: 0.71-0.97] comparing 5-year intervals, p=0.016). After adjusting for the covariates listed above, HER2 positive status is predictive of overall survival (HR 0.34 [95% CI: 0.34-0.56]; p&lt;0.0001).

CONCLUSIONS: While survival has improved by 5.9 months over the past two decades, it remains highly dependent on HER2 status. Novel therapies for BCBM are greatly needed for ER+ and triple negative subtypes. Final results will include an expanded analysis to incorporate additional cases and three other categorical covariates measured during follow-up: whether the patient received radiotherapy, surgery, and/or medical therapy after diagnosis of brain metastases.

GRANT FUNDING: TL-1 CTSA Pre-Doctoral Training Grant (5TL1TR001116-03).

Citation Format: Narloch JL, Harnden K, Broadwater G, Peterson B, Hyslop T, Kirkpatrick J, Fecci P, Kim G, Blackwell KL. HER2 status remains the primary predictor of improved survival in patients with BCBM over the past 2 decades (1996-2015) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P5-08-12.

The horseshoe kidney: Surgical anatomy and embryology

Horseshoe kidneys are a common, yet enigmatic, renal malformation. This review critically appraised the literature surrounding the embryology, etiology and clinical anatomy of horseshoe kidneys. The systematic literature search produced 104 articles, and 56 primary and further secondary references. There were several etiological theories regarding horseshoe kidneys. The established view was that during ascent, the kidneys come into close apposition as they pass through an arterial fork. Another possible mechanism related to lateral flexion of the trunk or rotation of the caudal embryo; the association of asymmetrical horseshoe kidneys with a number of vertebral conditions supported this hypothesis. More recent animal models implicated the notochord and sonic hedgehog signaling. Furthermore, it has been suggested that the isthmus may be the result of ectopic mesenchymal tissue. Surgical anatomy of the horseshoe kidney is complex, due to variability in location, orientation and blood supply. Both arterial and venous anatomy is highly variable. This raised the question of whether anomalous blood supply is the cause or result of abnormal renal position. In the majority of cases, the isthmus contained functional renal parenchyma. In over 90% of cases, fusion between the kidneys occurred at the lower pole. Despite commonly being quoted as 'held back by the inferior mesenteric artery' at L3, in reality the isthmus was only found immediately inferior to this in 40% of cases.

Outcomes and toxicity of stereotactic radiosurgery for melanoma brain metastases in patients receiving ipilimumab

Purpose

Patients with melanoma treated with ipilimumab and radiosurgery (stereotactic radiosurgery [SRS]) were reviewed for efficacy/safety.

Methods

Patients who received ipilimumab and SRS for brain metastases were analyzed for control of SRS-treated metastasis and overall survival.

Results

We identified 27 patients, 26 were assessable for outcomes. Median time-to-treated metastasis progression was 6.3 months (95% CI: 3.1-12.2). Overall survival was 23.4 months (95% CI: 5.7-not estimable) for SRS prior to/during ipilimumab (n = 14), and 10.4 months (95% CI: 1.9-not estimable) for SRS after ipilimumab (n = 12). Overall, no unexpected toxicities were seen: 11% of patients experienced grade 3 CNS toxicity and 7% developed radionecrosis.

Conclusion

SRS for melanoma brain metastases with ipilimumab was well-tolerated. There may be improved survival for patients receiving SRS prior to/during ipilimumab.