Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction.

Increasing evidence indicates CD4+ T cells can recognize cancer-specific antigens and control tumor growth. However, it remains difficult to predict the antigens that will be presented by human leukocyte antigen class II molecules (HLA-II), hindering efforts to optimally target them therapeutically. Obstacles include inaccurate peptide-binding prediction and unsolved complexities of the HLA-II pathway. To address these challenges, we developed an improved technology for discovering HLA-II binding motifs and conducted a comprehensive analysis of tumor ligandomes to learn processing rules relevant in the tumor microenvironment. We profiled >40 HLA-II alleles and showed that binding motifs were highly sensitive to HLA-DM, a peptide-loading chaperone. We also revealed that intratumoral HLA-II presentation was dominated by professional antigen-presenting cells (APCs) rather than cancer cells. Integrating these observations, we developed algorithms that accurately predicted APC ligandomes, including peptides from phagocytosed cancer cells. These tools and biological insights will enable improved HLA-II-directed cancer therapies.

Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data.

Advances in library-based methods for peptide detection from data-independent acquisition (DIA) mass spectrometry have made it possible to detect and quantify tens of thousands of peptides in a single mass spectrometry run. However, many of these methods rely on a comprehensive, high-quality spectral library containing information about the expected retention time and fragmentation patterns of peptides in the sample. Empirical spectral libraries are often generated through data-dependent acquisition and may suffer from biases as a result. Spectral libraries can be generated in silico, but these models are not trained to handle all possible post-translational modifications. Here, we propose a false discovery rate-controlled spectrum-centric search workflow to generate spectral libraries directly from gas-phase fractionated DIA tandem mass spectrometry data. We demonstrate that this strategy is able to detect phosphorylated peptides and can be used to generate a spectral library for accurate peptide detection and quantitation in wide-window DIA data. We compare the results of this search workflow to other library-free approaches and demonstrate that our search is competitive in terms of accuracy and sensitivity. These results demonstrate that the proposed workflow has the capacity to generate spectral libraries while avoiding the limitations of other methods.

Effect of MRI-Guided Fibrosis Ablation vs Conventional Catheter Ablation on Atrial Arrhythmia Recurrence in Patients With Persistent Atrial Fibrillation: The DECAAF II Randomized Clinical Trial.

Importance: Ablation of persistent atrial fibrillation (AF) remains a challenge. Left atrial fibrosis plays an important role in the pathophysiology of AF and has been associated with poor procedural outcomes. Objective: To investigate the efficacy and adverse events of targeting atrial fibrosis detected on magnetic resonance imaging (MRI) in reducing atrial arrhythmia recurrence in persistent AF. Design, Setting, and Participants: The Efficacy of Delayed Enhancement-MRI-Guided Fibrosis Ablation vs Conventional Catheter Ablation of Atrial Fibrillation trial was an investigator-initiated, multicenter, randomized clinical trial involving 44 academic and nonacademic centers in 10 countries. A total of 843 patients with symptomatic or asymptomatic persistent AF and undergoing AF ablation were enrolled from July 2016 to January 2020, with follow-up through February 19, 2021. Interventions: Patients with persistent AF were randomly assigned to pulmonary vein isolation (PVI) plus MRI-guided atrial fibrosis ablation (421 patients) or PVI alone (422 patients). Delayed-enhancement MRI was performed in both groups before the ablation procedure to assess baseline atrial fibrosis and at 3 months postablation to assess for ablation scar. Main Outcomes and Measures: The primary end point was time to first atrial arrhythmia recurrence after a 90-day blanking period postablation. The primary safety composite outcome was defined by the occurrence of 1 or more of the following events within 30 days postablation: stroke, PV stenosis, bleeding, heart failure, or death. Results: Among 843 patients who were randomized (mean age 62.7 years; 178 [21.1%] women), 815 (96.9%) completed the 90-day blanking period and contributed to the efficacy analyses. There was no significant difference in atrial arrhythmia recurrence between groups (fibrosis-guided ablation plus PVI patients, 175 [43.0%] vs PVI-only patients, 188 [46.1%]; hazard ratio [HR], 0.95 [95% CI, 0.77-1.17]; P = .63). Patients in the fibrosis-guided ablation plus PVI group experienced a higher rate of safety outcomes (9 [2.2%] vs 0 in PVI group; P = .001). Six patients (1.5%) in the fibrosis-guided ablation plus PVI group had an ischemic stroke compared with none in PVI-only group. Two deaths occurred in the fibrosis-guided ablation plus PVI group, and the first one was possibly related to the procedure. Conclusions and Relevance: Among patients with persistent AF, MRI-guided fibrosis ablation plus PVI, compared with PVI catheter ablation only, resulted in no significant difference in atrial arrhythmia recurrence. Findings do not support the use of MRI-guided fibrosis ablation for the treatment of persistent AF. Trial Registration: ClinicalTrials.gov Identifier: NCT02529319.

Atrial fibrosis in non-atrial fibrillation individuals and prediction of atrial fibrillation by use of late gadolinium enhancement magnetic resonance imaging.

INTRODUCTION: Besides the traditional concept of atrial fibrillation (AF) perpetuating atrial structural remodeling, there is increasing evidence that atrial fibrosis might precede AF, highlighting the need for better characterization of the fibrotic substrate. We aimed to assess atrial fibrosis by use of late gadolinium enhancement magnetic resonance imaging (LGE-MRI) in non-AF individuals and to identify predisposing risk factors. A second aim was to establish a risk score for the prevalence of AF using atrial fibrosis in addition to established clinical variables. METHODS AND RESULTS: Non-AF individuals without structural heart disease (n = 91) and matched AF controls (n = 91) underwent MRI for assessment of LGE. According to the established UTAH classification, atrial LGE ≥20% was considered extensive. Mean left atrial (LA) fibrosis in non-AF and AF individuals were 8.8 ± 6.5% and 12.5 ± 5.8%, respectively. Body mass index (BMI) >30 kg/m 2 and LA volume were predictors of atrial fibrosis. Diastolic function was not significantly different with respect to atrial fibrosis. A novel scoring system for the prevalence of AF (2 points for arterial hypertension and/or left ventricular ejection fraction <55%; 3 points for atrial fibrosis >6%) was derived demonstrating that patients in the intermediate/high-risk group had a significantly increased risk of AF. CONCLUSION: This study reports unexpectedly high atrial fibrosis in non-AF patients without apparent heart disease, highlighting the concept that structural fibrotic alterations may precede AF onset in a significant proportion of individuals. BMI as a predictor of atrial fibrosis suggests that lifestyle and drug intervention, that is, weight reduction, could positively influence fibrosis development. The derived risk score for AF prevalence provides the basis for prospective studies on AF incidence.

Left atrial shape predicts recurrence after atrial fibrillation catheter ablation.

INTRODUCTION: Multiple markers left atrium (LA) remodeling, including LA shape, correlate with outcomes in atrial fibrillation (AF). Catheter ablation is an important treatment of AF, but better tools are needed to determine which patients will benefit. In this study, we use particle-based modeling to quantitatively assess LA shape, and determine to what degree it predicts AF recurrence after catheter ablation. METHODS AND RESULTS: There were 254 patients enrolled in the DECAAF study who underwent cardiac magnetic resonance imaging of the LA prior to AF ablation and were followed for recurrence for up to 475 days. We performed particle-based shape modeling on each patient's LA shape. We selected shape parameters using the LASSO method and factor analysis, and then added them to a Cox regression model, which included multiple clinical parameters and LA fibrosis. We computed Harrell's C-statistic with and without shape in the model. We used the model to stratify patients into recurrence risk classes by both shape and shape and fibrosis combined. Three shape parameters were selected for inclusion. The C-statistic increased from 0.68 to 0.72 when shape was added to the model (P < 0.05). Visualized shapes showed that a more round LA shape with a shorter, more laterally rotated appendage was predictive of recurrence. CONCLUSION: LA shape is an independent predictor of recurrence after AF ablation. When combined with LA fibrosis, shape analysis using PBM may improve patient selection for ablation.

Air Activated Self-Decontaminating Polydicyclopentadiene PolyHIPE Foams for Rapid Decontamination of Chemical Warfare Agents.

The threat of chemical warfare agents (CWA) compels research into novel self-decontaminating materials (SDM) for the continued safety of first-responders, civilians, and active service personnel. The capacity to actively detoxify, as opposed to merely sequester, offending agents under typical environmental conditions defines the added value of SDMs in comparison to traditional adsorptive materials. Porous polymers, synthesized via the high internal phase emulsion (HIPE) templating, provide a facile fabrication method for materials with permeable open cellular structures that may serve in air filtration applications. PolyHIPEs comprising polydicyclopentadiene (polyDCPD) networks form stable hydroperoxide species following activation in air under ambient conditions. The hydroperoxide-containing polyDCPD materials react quickly with CWA simulants, Demeton-S and 2-chloroethyl ethyl sulfide, forming oxidation products as confirmed via gas chromatography mass spectrometry. The simplicity of the detoxification chemistry paired with the porous foam form factor presents an exciting opportunity for the development of self-decontaminating filter media.

Resilin-PEG Hybrid Hydrogels Yield Degradable Elastomeric Scaffolds with Heterogeneous Microstructure.

Hydrogels derived from resilin-like polypeptides (RLPs) have shown outstanding mechanical resilience and cytocompatibility; expanding the versatility of RLP-based materials via conjugation with other polypeptides and polymers would offer great promise in the design of a range of materials. Here, we present an investigation of the biochemical and mechanical properties of hybrid hydrogels composed of a recombinant RLP and a multiarm PEG macromer. These hybrid hydrogels can be rapidly cross-linked through a Michael-type addition reaction between the thiols of cysteine residues on the RLP and vinyl sulfone groups on the multiarm PEG. Oscillatory rheology and tensile testing confirmed the formation of elastomeric hydrogels with mechanical resilience comparable to aortic elastin; hydrogel stiffness was easily modulated through the cross-linking ratio. Macromolecular phase separation of the RLP-PEG hydrogels offers the unique advantage of imparting a heterogeneous microstructure, which can be used to localize cells, through simple mixing and cross-linking. Assessment of degradation of the RLP by matrix metalloproteinases (MMPs) illustrated the specific proteolysis of the polypeptide in both its soluble form and when cross-linked into hydrogels. Finally, the successful encapsulation and viable three-dimensional culture of human mesenchymal stem cells (hMSCs) demonstrated the cytocompatibility of the RLP-PEG gels. Overall, the cytocompatibility, elastomeric mechanical properties, microheterogeneity, and degradability of the RLP-PEG hybrid hydrogels offer a suite of promising properties for the development of cell-instructive, structured tissue engineering scaffolds.

Wideband late gadolinium enhanced magnetic resonance imaging for imaging myocardial scar without image artefacts induced by implantable cardioverter-defibrillator: a feasibility study at 3 T.

AIM: Late gadolinium enhanced (LGE) magnetic resonance imaging (MRI) is a useful tool for facilitating ventricular tachycardia (VT) ablation. Unfortunately, most VT ablation candidates often have prophylactic implantable cardioverter-defibrillator (ICD) and do not undergo cardiac MRI largely due to image artefacts generated by ICD. A prior study has reported success of 'wideband' LGE MRI for imaging myocardial scar without image artefacts induced by ICD at 1.5T. The purpose of this study was to widen the availability of wideband LGE MRI to 3T, since it has the potential to achieve higher spatial resolution than 1.5T. METHODS AND RESULTS: We compared the performance of standard and wideband LGE MRI pulse sequences in phantoms and canines with myocardial lesions created by radiofrequency ablation. Standard LGE MRI produced image artefacts induced by ICD and 49% accuracy in detecting 97 myocardial scars examined in this study, whereas wideband LGE MRI produced artefact-free images and 94% accuracy in detecting scars. The mean image quality score (1 = nondiagnostic, 2 = poor, 3 = adequate, 4 = good, 5 = excellent) was significantly (P < 0.001) higher for wideband (3.7 ± 0.8) than for standard LGE MRI (2.1 ± 0.7). The mean artefact level score (1 = minimal, 2 = mild, 3 = moderate, 4 = severe, 5 = nondiagnostic) was significantly (P < 0.001) lower for wideband (2.1 ± 0.8) than for standard LGE MRI (4.0 ± 0.6). Wideband LGE MRI agreed better with gross pathology than standard LGE MRI. CONCLUSION: This study demonstrates the feasibility of wideband LGE MRI for suppression of image artefacts induced by ICD at 3T.

Evaluation of highly accelerated real-time cardiac cine MRI in tachycardia.

Electrocardiogram (ECG)-gated breath-hold cine MRI is considered to be the gold standard test for the assessment of cardiac function. However, it may fail in patients with arrhythmia, impaired breath-hold capacity and poor ECG gating. Although ungated real-time cine MRI may mitigate these problems, commercially available real-time cine MRI pulse sequences using parallel imaging typically yield relatively poor spatiotemporal resolution because of their low image acquisition efficiency. As an extension of our previous work, the purpose of this study was to evaluate the diagnostic quality and accuracy of eight-fold-accelerated real-time cine MRI with compressed sensing (CS) for the quantification of cardiac function in tachycardia, where it is challenging for real-time cine MRI to provide sufficient spatiotemporal resolution. We evaluated the performances of eight-fold-accelerated cine MRI with CS, three-fold-accelerated real-time cine MRI with temporal generalized autocalibrating partially parallel acquisitions (TGRAPPA) and ECG-gated breath-hold cine MRI in 21 large animals with tachycardia (mean heart rate, 104 beats per minute) at 3T. For each cine MRI method, two expert readers evaluated the diagnostic quality in four categories (image quality, temporal fidelity of wall motion, artifacts and apparent noise) using a Likert scale (1-5, worst to best). One reader evaluated the left ventricular functional parameters. The diagnostic quality scores were significantly different between the three cine pulse sequences, except for the artifact level between CS and TGRAPPA real-time cine MRI. Both ECG-gated breath-hold cine MRI and eight-fold accelerated real-time cine MRI yielded all four scores of ≥ 3.0 (acceptable), whereas three-fold-accelerated real-time cine MRI yielded all scores below 3.0, except for artifact (3.0). The left ventricular ejection fraction (LVEF) measurements agreed better between ECG-gated cine MRI and eight-fold-accelerated real-time cine MRI (mean difference, -1.6%) than between ECG-gated cine MRI and three-fold-accelerated real-time cine MRI (mean difference, -5.7%). Eight-fold-accelerated real-time cine MRI with CS yields acceptable diagnostic quality and relatively accurate LVEF measurements in the challenging setting of tachycardia.

Lineage-specific proteome remodeling of diverse lung cancer cells by targeted epigenetic inhibitors.

Epigenetic inhibitors exhibit powerful antiproliferative and anticancer activities. However, cellular responses to small-molecule epigenetic inhibition are heterogenous and dependent on factors such as the genetic background, metabolic state, and on-/off-target engagement of individual small-molecule drugs. To determine the mechanisms that drive these heterogeneous cellular responses, we quantified chromatin, proteome, and transcriptome remodeling due to histone deacetylase inhibitor (HDACi) -treated cells derived from diverse genetic backgrounds. We utilized high-throughput sample multiplexed proteomics and integrated intelligent data acquisition methods to map proteomes of cancer cell lines in response to HDACi. We determined cell type-specific and ubiquitous cellular responses based on the quantification of 10,621 total proteins. We then established how coordinated remodeling of the proteome, transcriptome and chromatin state of HDACi treated cancer cells revealed convergent (JUN, MAP2K3, CDKN1A) and divergent (CCND3, ASF1B, BRD7) molecular phenotypes. HDACi-regulated proteins differ greatly across cell lines owing to heterogeneous molecular states of these cell lines. Finally, we demonstrated that HDACi treatment drove a highly cell-type specific response that may in part be explained by cell line-specific off-target drug engagement.

DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci.

The accuracy of crucial nuclear processes such as transcription, replication, and repair, depends on the local composition of chromatin and the regulatory proteins that reside there. Understanding these DNA-protein interactions at the level of specific genomic loci has remained challenging due to technical limitations. Here, we introduce a method termed "DNA O-MAP", which uses programmable peroxidase-conjugated oligonucleotide probes to biotinylate nearby proteins. We show that DNA O-MAP can be coupled with sample multiplexed quantitative proteomics and next-generation sequencing to quantify DNA-protein and DNA-DNA interactions at specific genomic loci.

Association of atrial fibrosis quantified using LGE-MRI with atrial appendage thrombus and spontaneous contrast on transesophageal echocardiography in patients with atrial fibrillation.

INTRODUCTION: Transesophageal echocardiography (TEE) is used to evaluate for left atrial appendage (LAA) thrombi prior to restoration of sinus rhythm in atrial fibrillation (AF). We examined the relationship of atrial fibrosis quantified using late gadolinium enhancement MRI (LGE-MRI) with TEE findings. METHODS AND RESULTS: We included 178 patients with AF, undergoing TEE and LGE-MRI prior to ablation or cardioversion. LGE-MRI and subsequent image processing was used to quantify atrial fibrosis based on signal intensity analysis. The mean CHADS2 score was 1.24 ± 1.08 and CHA2 DS2 -VASc was 2.08 ± 1.33. The LAA was classified as normal, spontaneous echocardiographic contrast (SEC) present or thrombus present. LAA thrombus was found in 12 patients (6.7%) while SEC was identified in 19 patients (10.7%). Patients with thrombus had higher atrial fibrosis compared to patients without thrombus (26.9 ± 17.4% vs 16.7 ± 10.5%; P < 0.01). Atrial fibrosis was also higher in patients with SEC (23.3 ± 13.7%) compared to those without SEC (16.7 ± 10.8%; P = 0.01). Patients with high atrial fibrosis (>20%) were more likely to have a LAA thrombus (odds ratio 4.6; P = 0.02) and SEC (odds ratio 2.6; P = 0.06). Multivariate logistic regression showed high fibrosis (odds ratio 3.6; P < 0.01) and CHADS2 ≥2 (odds ratio 3.5; P < 0.01) were significant predictors of TEE abnormalities (LAA thrombus or SEC). The area under the curve for the model including high fibrosis, AF type and CHADS2 ≥2 or CHA2 DS2 -VASc ≥2 was 0.73 compared to 0.63 and 0.65 for CHADS2 and CHA2 DS2 -VASc alone. CONCLUSIONS: Atrial fibrosis is independently associated with appendage thrombus and spontaneous contrast. It provides additional risk stratification not captured by clinical parameters.

Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ.

Throughout biology, RNA molecules form complex networks of molecular interactions that are central to their function, but remain challenging to investigate. Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP), a straightforward method for elucidating the biomolecules near an RNA of interest, within its native cellular context. O-MAP uses programmable oligonucleotide probes to deliver proximity-biotinylating enzymes to a target RNA, enabling nearby molecules to be enriched by streptavidin pulldown. O-MAP induces exceptionally precise RNA-localized in situ biotinylation, and unlike alternative methods it enables straightforward optimization of its targeting accuracy. Using the 47S pre-ribosomal RNA and long noncoding RNA Xist as models, we develop O-MAP workflows for unbiased discovery of RNA-proximal proteins, transcripts, and genomic loci. This revealed unexpected co-compartmentalization of Xist and other chromatin-regulatory RNAs and enabled systematic characterization of nucleolar-chromatin interactions across multiple cell lines. O-MAP is portable to cultured cells, organoids, and tissues, and to RNAs of various lengths, abundances, and sequence composition. And, O-MAP requires no genetic manipulation and uses exclusively off-the-shelf parts. We therefore anticipate its application to a broad array of RNA phenomena.

Atrial fibrosis quantified using late gadolinium enhancement MRI is associated with sinus node dysfunction requiring pacemaker implant.

INTRODUCTION: Sinus node dysfunction (SND) commonly manifests with atrial arrhythmias alternating with sinus pauses and sinus bradycardia. The underlying process is thought to be because of atrial fibrosis. We assessed the value of atrial fibrosis, quantified using late gadolinium enhanced-MRI (LGE-MRI), in predicting significant SND requiring pacemaker implant. METHODS: Three hundred forty-four patients with atrial fibrillation (AF) presenting for catheter ablation underwent LGE-MRI. Left atrial (LA) fibrosis was quantified in all patients and right atrial (RA) fibrosis in 134 patients. All patients underwent catheter ablation with pulmonary vein isolation with posterior wall and septal debulking. Patients were followed prospectively for 329 ± 245 days. Ambulatory monitoring was instituted every 3 months. Symptomatic pauses and bradycardia were treated with pacemaker implantation per published guidelines. RESULTS: The average patient age was 65 ± 12 years. The average wall fibrosis was 16.7 ± 11.1% in the LA, and 5.3 ± 6.4% in the RA. RA fibrosis was correlated with LA fibrosis (R(2) = 0.26; P < 0.01). Patients were divided into 4 stages of LA fibrosis (Utah I: <5%, Utah II: 5-20%, Utah III: 20-35%, Utah IV: >35%). Twenty-two patients (mean atrial fibrosis, 23.9%) required pacemaker implantation during follow-up. Univariate and multivariate analysis identified LA fibrosis stage (OR, 2.2) as a significant predictor for pacemaker implantation with an area under the curve of 0.704. CONCLUSIONS: In patients with AF presenting for catheter ablation, LGE-MRI quantification of atrial fibrosis demonstrates preferential LA involvement. Significant atrial fibrosis is associated with clinically significant SND requiring pacemaker implantation.

Elastomeric polypeptides.

Elastomeric polypeptides are very interesting biopolymers and are characterized by rubber-like elasticity, large extensibility before rupture, reversible deformation without loss of energy, and high resilience upon stretching. Their useful properties have motivated their use in a wide variety of materials and biological applications. This chapter focuses on elastin and resilin - two elastomeric biopolymers - and the recombinant polypeptides derived from them (elastin-like polypeptides and resilin-like polypeptides). This chapter also discusses the applications of these recombinant polypeptides in the fields of purification, drug delivery, and tissue engineering.

Saturation recovery-prepared magnetic resonance angiography for assessment of left atrial and esophageal anatomy.

OBJECTIVES: Magnetic resonance angiography (MRA) has been established as an important imaging method in cardiac ablation procedures. In pulmonary vein (PV) isolation procedures, MRA has the potential to minimize the risk of severe complications, such as atrio-esophageal fistula, by providing detailed information on esophageal position relatively to cardiac structures. However, traditional non-gated, first-pass (FP) MRA approaches have several limitations, such as long breath-holds, non-uniform signal intensity throughout the left atrium (LA), and poor esophageal visualization. The aim of this observational study was to validate a respiratory-navigated, ECG-gated (EC), saturation recovery-prepared MRA technique for simultaneous imaging of LA, LA appendage, PVs, esophagus, and adjacent anatomical structures. METHODS: Before PVI, 106 consecutive patients with a history of AF underwent either conventional FP-MRA (n = 53 patients) or our new EC-MRA (n = 53 patients). Five quality scores (QS) of LA and esophagus visibility were assessed by two experienced readers. The non-parametric Mann-Whitney U-test was used to compare QS between FP-MRA and EC-MRA groups, and linear regression was applied to assess clinical contributors to image quality. RESULTS: EC-MRA demonstrated significantly better image quality than FP-MRA in every quality category. Esophageal visibility using the new MRA technique was markedly better than with the conventional FP-MRA technique (median 3.5 [IQR 1] vs median 1.0, p < 0.001). In contrast to FP-MRA, overall image quality of EC-MRA was not influenced by heart rate. CONCLUSION: Our ECG-gated, respiratory-navigated, saturation recovery-prepared MRA technique provides significantly better image quality and esophageal visibility than the established non-gated, breath-holding FP-MRA. Image quality of EC-MRA technique has the additional advantage of being unaffected by heart rate. ADVANCES IN KNOWLEDGE: Detailed information of cardiac anatomy has the potential to minimize the risk of severe complications and improve success rates in invasive electrophysiological studies. Our novel ECG-gated, respiratory-navigated, saturation recovery-prepared MRA technique provides significantly better image quality of LA and esophageal structures than the traditional first-pass algorithm. This new MRA technique is robust to arrhythmia (tachycardic, irregular heart rates) frequently observed in AF patients.

Systematic discovery and validation of T cell targets directed against oncogenic KRAS mutations.

Oncogenic mutations in KRAS can be recognized by T cells on specific class I human leukocyte antigen (HLA-I) molecules, leading to tumor control. To date, the discovery of T cell targets from KRAS mutations has relied on occasional T cell responses in patient samples or the use of transgenic mice. To overcome these limitations, we have developed a systematic target discovery and validation pipeline. We evaluate the presentation of mutant KRAS peptides on individual HLA-I molecules using targeted mass spectrometry and identify 13 unpublished KRASG12C/D/R/V mutation/HLA-I pairs and nine previously described pairs. We assess immunogenicity, generating T cell responses to nearly all targets. Using cytotoxicity assays, we demonstrate that KRAS-specific T cells and T cell receptors specifically recognize endogenous KRAS mutations. The discovery and validation of T cell targets from KRAS mutations demonstrate the potential for this pipeline to aid the development of immunotherapies for important cancer targets.

Detection and quantification of left atrial structural remodeling with delayed-enhancement magnetic resonance imaging in patients with atrial fibrillation.

BACKGROUND: Atrial fibrillation (AF) is associated with diffuse left atrial fibrosis and a reduction in endocardial voltage. These changes are indicators of AF severity and appear to be predictors of treatment outcome. In this study, we report the utility of delayed-enhancement magnetic resonance imaging (DE-MRI) in detecting abnormal atrial tissue before radiofrequency ablation and in predicting procedural outcome. METHODS AND RESULTS: Eighty-one patients presenting for pulmonary vein antrum isolation for treatment of AF underwent 3-dimensional DE-MRI of the left atrium before the ablation. Six healthy volunteers also were scanned. DE-MRI images were manually segmented to isolate the left atrium, and custom software was implemented to quantify the spatial extent of delayed enhancement, which was then compared with the regions of low voltage from electroanatomic maps from the pulmonary vein antrum isolation procedure. Patients were assessed for AF recurrence at least 6 months after pulmonary vein antrum isolation, with an average follow-up of 9.6+/-3.7 months (range, 6 to 19 months). On the basis of the extent of preablation enhancement, 43 patients were classified as having minimal enhancement (average enhancement, 8.0+/-4.2%), 30 as having moderate enhancement (21.3+/-5.8%), and 8 as having extensive enhancement (50.1+/-15.4%). The rate of AF recurrence was 6 patients (14.0%) with minimal enhancement, 13 (43.3%) with moderate enhancement, and 6 (75%) with extensive enhancement (P<0.001). CONCLUSIONS: DE-MRI provides a noninvasive means of assessing left atrial myocardial tissue in patients suffering from AF and might provide insight into the progress of the disease. Preablation DE-MRI holds promise for predicting responders to AF ablation and may provide a metric of overall disease progression.