Undifferentiated small round cell sarcomas (USRS) of bone and soft tissue are a group of tumors with heterogenic genomic alterations sharing similar morphology. In the present study, we performed a comparative large-scale proteomic analysis of USRS (n = 42) with diverse genomic translocations including classic Ewing sarcomas with EWSR1::FLI1 fusions (n = 24) or EWSR1::ERG fusions (n = 4), sarcomas with an EWSR1 rearrangement (n = 2), CIC::DUX4 fusion (n = 8), as well as tumors classified as USRS with no genetic data available (n = 4). Proteins extracted from formalin-fixed, paraffin-embedded pretherapeutic biopsies were analyzed qualitatively and quantitatively using shotgun mass spectrometry (MS). More than 8000 protein groups could be quantified using data-independent acquisition. Unsupervised hierarchical cluster analysis based on proteomic data allowed stratification of the 42 cases into distinct groups reflecting the different molecular genotypes. Protein signatures that significantly correlated with the respective genomic translocations were identified and used to generate a heatmap of all 42 sarcomas with assignment of cases with unknown molecular genetic data to either the EWSR1- or CIC-rearranged groups. MS-based prediction of sarcoma subtypes was molecularly confirmed in 2 cases where next-generation sequencing was technically feasible. MS also detected proteins routinely used in the immunohistochemical approach for the differential diagnosis of USRS. BCL11B highly expressed in Ewing sarcomas, and BACH2 as well as ETS-1 highly expressed in CIC::DUX4-associated sarcomas, were among proteins identified by the present proteomic study, and were chosen for immunohistochemical confirmation of MS data in our study cohort. Differential expressions of these 3 markers in the 2 genetic groups were further validated in an independent cohort of n = 34 USRS. Finally, our proteomic results point toward diverging signaling pathways in the different USRS subgroups.

Supplementary Text from Genetic Alterations in the Tyrosine Kinase Transcriptome of Human Cancer Cell Lines

Supplementary Figure 1, Tables 1-7 from ADAM17 Regulates Epidermal Growth Factor Receptor Expression through the Activation of Notch1 in Non–Small Cell Lung Cancer

Supplementary Data from Protein Expression Profiling in Esophageal Adenocarcinoma Patients Indicates Association of Heat-Shock Protein 27 Expression and Chemotherapy Response

Supplementary Data - PDF file 158K, Supplementary Table S1. Target mutations and ligation probes for mutation specific and wild type CKIT or PDGFRA hybridisation. Patient numbers corresponding to Figure 2, their specific tumor/target mutations and the sequences of the hybridisation probes. Supplementary Table S2. Overview of test results in relation to clinical setting for patients with active disease. Allocation of test results corresponding to Table 2 and to patient numbers corresponding to Figure 2. Supplementary Figure S1. LINE1 levels of GIST patients in complete remission versus progression and relapse. Shown are the median LINE1 fragment numbers in 2 microl plasma DNA

Recurrent amplification and overexpression of FRS2 in STS.

Background: In Ewing sarcoma (EwS), long-term treatment effects and poor survival rates for relapsed or metastatic cases require individualization of therapy and the discovery of new treatment methods. Tumor glucose metabolic activity varies significantly between patients, and FDG-PET signals have been proposed as prognostic factors. However, the biological basis for the generally elevated but variable glucose metabolism in EwS is not well understood. Methods: We retrospectively included 19 EwS samples (17 patients). Affymetrix gene expression was correlated with maximal standardized uptake value (SUVmax) using machine learning, linear regression modelling, and gene set enrichment analyses for functional annotation. Results: Expression of five genes correlated (MYBL2, ELOVL2, NETO2) or anticorrelated (FAXDC2, PLSCR4) significantly with SUVmax (adjusted p-value ≤ 0.05). Additionally, we identified 23 genes with large SUVmax effect size, which were significantly enriched for “neuropeptide Y receptor activity (GO:0004983)” (adjusted p-value = 0.0007). The expression of the members of this signaling pathway (NPY, NPY1R, NPY5R) anticorrelated with SUVmax. In contrast, three transcription factors associated with maintaining stemness displayed enrichment of their target genes with higher SUVmax: RNF2, E2F family, and TCF3. Conclusion: Our large-scale analysis examined comprehensively the correlations between transcriptomics and tumor glucose utilization. Based on our findings, we hypothesize that stemness may be associated with increased glucose uptake, whereas neuroectodermal differentiation may anticorrelate with glucose uptake.

In this study, we sought to determine the prognostic value of both the European Organization for Research and Treatment of Cancer-Soft Tissue and Bone Sarcoma Group (EORTC-STBSG) score and the histologic parameters viable tumor, coagulative necrosis, hyalinization/fibrosis, and infarction in patients (n=64) with localized, nonmetastatic high-grade soft-tissue sarcomas after preoperative radiomonotherapy. A standardized macroscopic workup for pretreated surgical specimen including evaluation of a whole section of high-grade soft tissue sarcomas in the largest diameter, was used. Association with overall survival and disease-free survival was assessed. Limb salvage could be accomplished in 98.4% of patients. Overall, 90.6% tumors had negative resection margins. The median postoperative tumor diameter was 9 cm. Undifferentiated pleomorphic sarcoma (42.2%) and myxofibrosarcoma (17.2%) were the most common diagnoses. In all, 9.4% of patients had local recurrence despite clear resection margins, and 50% had distant metastases. Morphologic mapping suggests an overall heterogenous intratumoral response to radiotherapy, with significant differences among histologic subtypes. Complete regression (0% vital tumor cells) was not seen. Categorizing the results according to the proposed EORTC-STBSG 5-tier response score, <1% viable tumor cells were seen in 3.1%, ≥1% to <10% viable tumor cells in 20.4%, ≥10% to <50% viable tumor cells in 35.9% and ≥50% viable tumor cells in 40.6% of cases. Mean values for viable tumor cells were 40% (range: 1% to 100%), coagulative necrosis 5% (0% to 60%), hyalinization/fibrosis 25% (0% to 90%) and infarction 15% (0% to 79%). Hyalinization/fibrosis was a significant independent prognostic factor for overall survival (hazard ratio=4.4; P =0.047), while the other histologic parameters including the EORTC-STBSG score were not prognostic.

Objectives To evaluate the performance and reproducibility of MR imaging features in the diagnosis of joint invasion (JI) by malignant bone tumors. Methods MR images of patients with and without JI ( n = 24 each), who underwent surgical resection at our institution, were read by three radiologists. Direct (intrasynovial tumor tissue (ITT), intraarticular destruction of cartilage/bone, invasion of capsular/ligamentous insertions) and indirect (tumor size, signal alterations of epiphyseal/transarticular bone (bone marrow replacement/edema-like), synovial contrast enhancement, joint effusion) signs of JI were assessed. Odds ratios, sensitivity, specificity, PPV, NPV, and reproducibilities (Cohen’s and Fleiss’ κ ) were calculated for each feature. Moreover, the diagnostic performance of combinations of direct features was assessed. Results Forty-eight patients (28.7 ± 21.4 years, 26 men) were evaluated. All readers reliably assessed the presence of JI (sensitivity = 92–100 %; specificity = 88–100%, respectively). Best predictors for JI were direct visualization of ITT (OR = 186–229, p < 0.001) and destruction of intraarticular bone (69–324, p < 0.001). Direct visualization of ITT was also highly reliable in assessing JI (sensitivity, specificity, PPV, NPV = 92–100 %), with excellent reproducibility ( κ = 0.83). Epiphyseal bone marrow replacement and synovial contrast enhancement were the most sensitive indirect signs, but lacked specificity (29–54%). By combining direct signs with high specificity, sensitivity was increased (96 %) and specificity (100 %) was maintained. Conclusion JI by malignant bone tumors can reliably be assessed on preoperative MR images with high sensitivity, specificity, and reproducibility. Particularly direct visualization of ITT, destruction of intraarticular bone, and a combination of highly specific direct signs were valuable, while indirect signs were less predictive and specific. Key Points • Direct visualization of intrasynovial tumor was the single most sensitive and specific (92–100%) MR imaging sign of joint invasion. • Indirect signs of joint invasion, such as joint effusion or synovial enhancement, were less sensitive and specific compared to direct signs. • A combination of the most specific direct signs of joint invasion showed best results with perfect specificity and PPV (both 100%) and excellent sensitivity and NPV (both 96 %).

Background Small soft tissue masses are often falsely assumed to be benign and resected with failure to achieve tumor-free margins. Therefore, this study retrospectively investigated the distribution of histopathologic diagnosis to be encountered in small soft tissue tumors (≤ 5 cm) in a large series of a tertiary referral center. Methods Patients with a soft tissue mass (STM) with a maximum diameter of 5 cm presenting at our institution over a period of 10 years, who had undergone preoperative Magnetic resonance imaging and consequent biopsy or/and surgical resection, were included in this study. A final histopathological diagnosis was available in all cases. The maximum tumor diameter was determined on MR images by one radiologist. Moreover, tumor localization (head/neck, trunk, upper extremity, lower extremity, hand, foot) and depth (superficial / deep to fascia) were assessed. Results In total, histopathologic results and MR images of 1753 patients were reviewed. Eight hundred seventy patients (49.63%) showed a STM ≤ 5 cm and were therefore included in this study (46.79 +/− 18.08 years, 464 women). Mean maximum diameter of the assessed STMs was 2.88 cm. Of 870 analyzed lesions ≤ 5 cm, 170 (19.54%) were classified as superficial and 700 (80.46%) as deep. The malignancy rate of all lesions ≤ 5 cm was at 22.41% (superficial: 23.53% / deep: 22.14%). The malignancy rate dropped to 16.49% (20.79% / 15.32%) when assessing lesions ≤ 3 cm ( p = 0.007) and to 15.0% (18.18% / 13.79%) when assessing lesions ≤ 2 cm ( p = 0.006). Overall, lipoma was the most common benign lesion of superficial STMs (29.41%) and tenosynovial giant cell tumor was the most common benign lesion of deep STMs (23.29%). Undifferentiated pleomorphic sarcoma was the most common malignant diagnosis among both, superficial (5.29%) and deep (3.57%) STMs. Conclusions The rate of malignancy decreased significantly with tumor size in both, superficial and deep STMs. The distribution of entities was different between superficial and deep STMs, yet there was no significant difference found in the malignancy rate.

Zielsetzung Da kleine Weichteiltumore häufig fälschlicherweise als benigne angesehen werden erfolgt hier nicht selten eine Resektion ohne aussreichenden Sicherheitsabstand. Daher war es Ziel dieser retrospektiven Studie, in einem großen Patientenkollektiv die Verteilung von histopathologischen Entitäten, welche in kleinen Weichteiltumoren (≤ 5 cm) zu erwarten sind, zu untersuchen.

Purpose: To compare the glycosaminoglycan (GAG) content of intervertebral discs (IVDs) of lumbar spines of patients with ankylosing spondylitis (AS) and healthy volunteers, and to assess the relationship between GAG loss and disease-related features.Materials and Methods: 50 AS patients (mean age 50 ± 10.5 years) and 30 age-matched volunteers underwent 3-T magnetic resonance imaging (MRI) and conventional radiography (CR).The MRI protocol included high-resolution morphological and GAG-Chemical-Exchange-Saturation-Transfer (gagCEST) sequences of lumbar spines.Morphological images were evaluated for disk degeneration, inflammation, fatty deposits, and structural changes.Clinical and serological markers included and Bath AS Function (BASFI) and Bath AS Disease Activity (BASDAI) indices, and C-reactive protein (CRP) levels.GagCEST values were compared using a linear mixed model.Results: GagCEST values were significantly lower in patients with AS (2.0 ± 1.7%) than in healthy subjects (2.4 ± 1.8%), p = 0.001.Small, but significant correlations were found between gagCEST values and CRP values (τ = -0.14, p = 0.007), BASFI (τ = -0.18,p <0.001) and the presence of syndesmophytes (τ = -0.17,p = 0.001).No significant correlations were found with inflammation, fat deposition MRI scores, and BASDAI.Conclusion: Lumbar IVDs of patients with AS suffer from significant GAG depletion, which is associated with syndesmophyte formation, functional disability and elevated serum CRP-levels.In addition to elucidating the pathophysiological role of cartilage in AS, these results suggest that gagCEST imaging could play an additional confirmatory role in the assessment of disease-related pathological MRI findings in AS.

Purpose: In high-grade soft-tissue sarcomas (STS) the standard of care encompasses multimodal therapy regimens. While there is a growing body of evidence for prognostic pretreatment radiomic models, we hypothesized that temporal changes in radiomic features following neoadjuvant treatment ("delta-radio mics") may be able to predict the pathological complete response (pCR). Methods: MRI scans (T1-weighted with fat-saturation and contrast-enhancement (T1FSGd) and T2 weighted with fat-saturation (T2FS)) of patients with STS of the extremities and trunk treated with neoadjuvant therapy were gathered from two independent institutions (training: 103, external testing: 53 patients). pCR was defined as <5% viable cells. After segmentation and preprocessing, 105 radiomic features were extracted. Delta-radiomic features were calculated by subtraction of features derived from MRI scans obtained before and after neoadjuvant therapy. After feature reduction, machine learning modeling was performed in 100 iterations of 3-fold nested cross-validation. Delta-radiomic models were compared with single timepoint models in the testing cohort. Results: The combined delta-radiomic models achieved the best area under the receiver operating characteristic curve (AUC) of 0.75. Pre-therapeutic tumor volume was the best conventional predictor (AUC 0.70). The T2FS-based delta-radiomic model had the most balanced classification performance with a balanced accuracy of 0.69. Delta-radiomic models achieved better reproducibility than single timepoint radiomic models, RECIST or the peri-therapeutic volume change. Delta-radiomic models were significantly associated with survival in multivariate Cox regression. Conclusion: This exploratory analysis demonstrated that MRI-based delta-radiomics improves prediction of pCR over tumor volume and RECIST. Delta-radiomics may one day function as a biomarker for personalized treatment adaptations. (c) 2021 Elsevier B.V. All rights reserved. Radiotherapy and Oncology 164 (2021) 73-82

BACKGROUND:In patients with soft-tissue sarcomas, tumor grading constitutes a decisive factor to determine the best treatment decision. Tumor grading is obtained by pathological work-up after focal biopsies. Deep learning (DL)-based imaging analysis may pose an alternative way to characterize STS tissue. In this work, we sought to non-invasively differentiate tumor grading into low-grade (G1) and high-grade (G2/G3) STS using DL techniques based on MR-imaging. METHODS:Contrast-enhanced T1-weighted fat-saturated (T1FSGd) MRI sequences and fat-saturated T2-weighted (T2FS) sequences were collected from two independent retrospective cohorts (training: 148 patients, testing: 158 patients). Tumor grading was determined following the French Federation of Cancer Centers Sarcoma Group in pre-therapeutic biopsies. DL models were developed using transfer learning based on the DenseNet 161 architecture. RESULTS:The T1FSGd and T2FS-based DL models achieved area under the receiver operator characteristic curve (AUC) values of 0.75 and 0.76 on the test cohort, respectively. T1FSGd achieved the best F1-score of all models (0.90). The T2FS-based DL model was able to significantly risk-stratify for overall survival. Attention maps revealed relevant features within the tumor volume and in border regions. CONCLUSIONS:MRI-based DL models are capable of predicting tumor grading with good reproducibility in external validation.

A 49-year-old woman consulted her general practitioner (GP) regarding epigastric pain that she had experienced for 2 months. Physical examination and laboratory results were unremarkable. An abdominal ultrasound indicated a solid pancreatic tumor, which was confirmed on subsequent CT and MRI. Endoscopic ultrasound (EUS) showed a well-defined heterogeneous, predominantly hypoechoic mass in the pancreatic body, so a neuroendocrine tumor (NET) was suspected. However, EUS-guided fine-needle aspiration (EUS-FNA) was performed and based on (immuno-)histochemical findings, the extremely rare diagnosis of a perivascular epithelioid cell tumor (PEComa) of the pancreas was made. Due to the malignant potential of pancreatic PEComas, laparoscopic left-sided pancreatectomy was performed. We present a case diagnosed by preoperative EUS-FNA highlighting the clinical and endosonographic features which help to distinguish it from its most important differential diagnosis, neuroendocrine tumors (NETs) of the pancreas.

PURPOSE:The objective of this study was to investigate potential correlations between pathologic fractures (PFs) and prognosis of patients with primary central high-grade osteosarcoma of the extremities.METHODS:We retrospectively analyzed 2,847 patients registered in the Consecutive Cooperative Osteosarcoma Study Group database with primary central high-grade osteosarcoma of the extremities, treated between 1980 and 2010. Intended treatment included pre- and postoperative chemotherapy and surgery. Univariable and multivariable survival analyses were performed for all patients and then differentiated for adult and pediatric (≤ 18 years at time of diagnosis) patients.RESULTS:A total of 2,193 patients were ≤ 18 years of age; 11.3% of all patients had PFs. In the overall cohort, presence of PF correlated significantly with tumor site, histologic subtype, relative tumor size, and primary metastases, but not with body mass index or local surgical remission. In univariable analysis, 5-year overall survival (OAS) of patients with and without PF was 63% versus 71%, respectively (P = .007), and 5-year event-free survival (EFS) was 51% versus 58% (P = .026). In pediatric patients, OAS and EFS did not differ significantly between patients with and without PF. In adults, 5-year OAS in patients with and without PF was 46% versus 69% (P < .001), and 5-year EFS was 36% versus 56% (P < .001). In multivariable analysis, PF was not a statistically significant factor for OAS or EFS in the total cohort or in pediatric patients. In adult patients, PF remained an independent prognostic factor for OAS (P = .013; hazard ratio [HR], 1.893). It was not a significant prognostic factor for EFS (P = .263; HR, 1.312).CONCLUSION:In this largest study to date with extremity osteosarcomas, we observed the occurrence of PF to correlate with inferior OAS expectancies in adult but not in pediatric patients.

Objectives: Adjuvant chemotherapy decision in patients with hormone receptor positive, HER2 negative breast cancer (BC) is challenging. Ki-67 is widely used for adjuvant therapy decision in BC. The multigene assay EndoPredict (EP) has shown to provide valid and additional information about the risk of recurrence compared to traditional pathological factors. In this study, we compared Ki-67 with EP assay generated risk groups. Methods: We analyzed the results from prospective EP testing (n = 373) and tumor proliferation assessed by Ki-67 staining in luminal breast cancer. We statistically investigated the association of both parameters and probed for equivalence in risk stratification. Results: Evaluation of Ki-67 was feasible in 307 (82%) BC specimens with known EP test results. The EPscore (now called 12-gene molecular score) delineated 140 low and 167 high scores. After combining the EPscore with pathological tumor stage and nodal status, we received 203 EPclin low-risk and 104 EPclin high-risk classifications. EPscore and EPclin were significantly associated with Ki-67 indices and tumor grade (p < 0.001). Overall, we observed a moderate correlation between Ki-67 and the EPscore (r = 0.63) as well as the EPclin score (r = 0.59). Conclusion: Ki-67 values above 25% partly overlap with EP test results and therefore indicate a high-risk profile. In these cases, the additional prognostic information from EP testing might be rather low. However, low and intermediate Ki-67 values (less than 25%) alone were not reliable in predicting a low risk EP profile, indicating that EP testing is useful in this subgroup.

This case study deals with the case of a 16-year-old male patient with a low-grade parosteal osteosarcoma of the distal femur with focal differentiation. Case history, disease course, and surgery as well as the pathological workup with final diagnosis are presented. Relevant radiologic and pathologic differential diagnoses und diagnostic pitfalls are explained in detail and discussed. Additionally, postoperative treatment options are illustrated.