Characterizing the human leukocyte antigen (HLA) bound ligandome by mass spectrometry (MS) holds great promise for developing vaccines and drugs for immune-oncology. Still, the identification of ...non-tryptic peptides presents substantial computational challenges. To address these, we synthesized and analyzed >300,000 peptides by multi-modal LC-MS/MS within the ProteomeTools project representing HLA class I & II ligands and products of the proteases AspN and LysN. The resulting data enabled training of a single model using the deep learning framework Prosit, allowing the accurate prediction of fragment ion spectra for tryptic and non-tryptic peptides. Applying Prosit demonstrates that the identification of HLA peptides can be improved up to 7-fold, that 87% of the proposed proteasomally spliced HLA peptides may be incorrect and that dozens of additional immunogenic neo-epitopes can be identified from patient tumors in published data. Together, the provided peptides, spectra and computational tools substantially expand the analytical depth of immunopeptidomics workflows.
Purpose
To investigate the interobserver agreement (IA) and the impact of consensus reading using four risk stratification systems for thyroid nodules (TN).
Methods
Four experienced specialists ...independently rated US images of 80 TN according to the Kwak-TIRADS, EU-TIRADS, ACR TI-RADS, and ATA Guidelines. The cases were randomly extracted from a prospectively acquired database (
n
> 1500 TN). The observers were blinded to clinical data. This study was divided into two sessions (S1 and S2) with 40 image sets each. After every session, a consensus reading was carried out (C1, C2). Subsequently, the effect of C1 was tested in S2 with 40 new cases followed by C2. Fleiss’ kappa (κ) was calculated for S1 and S2 to estimate the IA and learning curves. The results of C1 and C2 were used as reference for diagnostic accuracy calculations.
Results
IA significantly increased (
p
< 0.01) after C1 with κ values of 0.375 (0.615), 0.411 (0.596), 0.321 (0.569), and 0.410 (0.583) for the Kwak-TIRADS, EU-TIRADS, ACR TI-RADS, and ATA Guidelines in S1 (S2), respectively. ROC analysis (C1 + C2) revealed similar areas under the curve (AUC) for the Kwak-TIRADS, EU-TIRADS, ACR TI-RADS, and ATA Guidelines (0.635, 0.675, 0.694, and 0.654, respectively, n.s.). AUC did not increase from C1 (0.677 ± 0.010) to C2 (0.632 ± 0.052, n.s.). ATA Guidelines were not applicable in five cases.
Conclusions
IA and diagnostic accuracy were very similar for the four investigated risk stratification systems. Consensus reading sessions significantly improved the IA but did not affect the diagnostic accuracy.
Systemic pan-tumor analyses may reveal the significance of common features implicated in cancer immunogenicity and patient survival. Here, we provide a comprehensive multi-omics data set for 32 ...patients across 25 tumor types for proteogenomic-based discovery of neoantigens. By using an optimized computational approach, we discover a large number of tumor-specific and tumor-associated antigens. To create a pipeline for the identification of neoantigens in our cohort, we combine DNA and RNA sequencing with MS-based immunopeptidomics of tumor specimens, followed by the assessment of their immunogenicity and an in-depth validation process. We detect a broad variety of non-canonical HLA-binding peptides in the majority of patients demonstrating partially immunogenicity. Our validation process allows for the selection of 32 potential neoantigen candidates. The majority of neoantigen candidates originates from variants identified in the RNA data set, illustrating the relevance of RNA as a still understudied source of cancer antigens. This study underlines the importance of RNA-centered variant detection for the identification of shared biomarkers and potentially relevant neoantigen candidates.
In conventional thyroid diagnostics, the topographical correlation between thyroid nodules (TN) depicted on ultrasound (US) in axial or sagittal orientation and coronally displayed scintigraphy ...images can be challenging. Sensor-navigated I-124-PET/US fusion imaging has been introduced as a problem-solving tool for ambiguous cases. The purpose of this study was to investigate the results of multiple unexperienced medical students (MS) versus multiple nuclear medicine physicians (MD) regarding the overvalue of I-124-PET/US in comparison to conventional diagnostics (CD) for the functional assessment of TN.
Out of clinical routine, cases with ambiguous findings on CD were selected for I-124-PET/US fusion imaging. Sixty-eight digital patient case files (PCF) of 34 patients (CDonly and CD+PET/US PCF) comprising 66 TN were provided to be retrospectively evaluated by 70 MD and 70 MS, respectively. A total of 2174 ratings (32.9 per TN) were carried out: 555 ratings (8.4 per TN) for CDonly and 532 ratings (8.1 per TN) for CD+PET/US by each MD and MS.
Functional assessment revealed 8.5%/11.7% (n.s.) (16.4%/25.8% (
= 0.0002)), 41.8%/28.5% (
< 0.0001) (23.9%/17.9% (
= 0.0193)), 36.0%/30.5% (n.s.) (57.3%/53.9% (n.s.)), and 13.7%/29.4% (
< 0.0001) (2.4%/2.4% (n.s.)) hyperfunctioning, indifferent, hypofunctioning, and not rateable TNs for CDonly (CD+PET/US) and MD/MS, respectively. The respective rating confidence was indicated as absolute certain, quite certain, equivocal, uncertain, and not rateable in 11.7/3.4% (
< 0.0001) (44.9%/38.9% (
= 0.0541), 51.9%/26.7% (
< 0.0001) (46.2%/41.5% (n.s.)), 21.6%/29.0% (
= 0.0051) (6.2%/14.8% (
< 0.0001)), 1.1%/11.5% (
< 0.0001) (0.2%/2.3% (
= 0.0032)), and 13.7%/29.4% (
< 0.0001) (2.4%/2.4% (n.s.)) by MD/MS, respectively. There was a significant difference in the diversity of the observers' functional assessment of TN (MD 0.84 vs. MS 1.02,
= 0.0006) and the respective confidence in functional assessment (MD 0.93 vs. MS 1.16,
< 0.0001) between MD and MS on CDonly, whereas CD+PET/US revealed weaker differences for both groups (MD 0.48 vs. MS 0.47,
= 0.57; and MD 0.66 vs. MS 0.83,
= 0.0437). With the additional application of I-124-PET/US, the rating diversity of both MD and MS markedly tends towards more consistency (
< 0.0001 in each case).
The additional application of sensor-navigated I-124-PET/US fusion imaging significantly influenced the functional assessment of TN positively, especially for unexperienced observers.
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